diff --git a/docker/sim/Dockerfile b/docker/sim/Dockerfile
new file mode 100644
index 0000000..442e565
--- /dev/null
+++ b/docker/sim/Dockerfile
@@ -0,0 +1,15 @@
+# Text2WetLab simulator image: runs third-party lab-automation protocols with no hardware and no network.
+#   Opentrons OT-2 / Flex : opentrons_simulate (Opentrons 7.5.0, the benchmark's grader version)
+#   Hamilton STAR / STARlet, Tecan EVO and others : PyLabRobot simulated backends
+# Run untrusted protocol code with:  docker run --rm --network none -v <repo>:/work:ro -v <out>:/out t2w-sim ...
+FROM python:3.10-slim
+ENV PIP_NO_CACHE_DIR=1 PYTHONDONTWRITEBYTECODE=1 OT_SMOOTHIE_ID=AMA
+RUN pip install "opentrons==7.5.0" "pylabrobot" numpy pandas
+# Opentrons fetches nothing at simulate time once its shared data is installed; warm it so --network none works.
+RUN python -c "from opentrons import simulate; print('opentrons ok')" && python -c "import pylabrobot; print('pylabrobot ok')"
+COPY runlog.py mylog.py /t2w/
+COPY simulate_all.py hamilton_ape.py /t2w/
+RUN useradd -m sim
+USER sim
+WORKDIR /tmp
+ENTRYPOINT ["python", "/t2w/simulate_all.py"]
diff --git a/docker/sim/hamilton_ape.py b/docker/sim/hamilton_ape.py
new file mode 100644
index 0000000..38f3c15
--- /dev/null
+++ b/docker/sim/hamilton_ape.py
@@ -0,0 +1,126 @@
+"""Run the har1eyk STARlet "Automated Protein Extraction" protocol on PyLabRobot's simulated backend and log it.
+
+usage (in the container): python /t2w/hamilton_ape.py <protocol_dir> <out.json>
+The deck is rebuilt from the authors' APE_96w notebook (rails 25 tips, 13 and 19 MFX carriers). Every
+liquid-handler call is recorded with resource names so the host can replay it on a 3D STARlet; waits,
+manual pauses and prints become comment events instead of real delays.
+"""
+import asyncio, builtins, json, sys, time
+
+from pylabrobot.liquid_handling import LiquidHandler
+from pylabrobot.liquid_handling.backends import LiquidHandlerChatterboxBackend
+from pylabrobot.resources.hamilton import STARLetDeck, MFX_CAR_L5_base, TIP_CAR_480_A00
+from pylabrobot.resources.hamilton.mfx_modules import Hamilton_MFX_plateholder_DWP_metal_tapped
+from pylabrobot.resources.diy.grindbio.modules import Hamilton_MFX_plateholder_DWP_metal_tapped_10mm_3dprint
+from pylabrobot.resources.alpaqua import Alpaqua_96_magnum_flx
+from pylabrobot.resources.bioer.plates import BioER_96_wellplate_Vb_2200uL
+from pylabrobot.resources.agenbio.plates import AGenBio_1_troughplate_100000uL_Fl
+from pylabrobot.resources import hamilton_96_tiprack_1000uL, set_tip_tracking, set_volume_tracking
+
+EVENTS = []
+
+
+class SimulatedSTAR(LiquidHandlerChatterboxBackend):
+  """The generic simulated backend, answering any STAR-only firmware command (CoRe gripper tools, sensors) as a no-op."""
+
+  def __getattr__(self, name):
+    if name.startswith("_"):
+      raise AttributeError(name)
+
+    async def no_op(*a, **k):
+      return True
+    return no_op
+
+
+def names(xs):
+  return [getattr(x, "name", str(x)) for x in xs]
+
+
+def build(lh):
+  tip_car = TIP_CAR_480_A00("tip_car")
+  lh.deck.assign_child_resource(tip_car, rails=25)
+  racks = [hamilton_96_tiprack_1000uL(f"tips_0{i}") for i in range(3)]
+  for i, r in enumerate(racks):
+    tip_car[i] = r
+  m13 = {i: Hamilton_MFX_plateholder_DWP_metal_tapped_10mm_3dprint(n) for i, n in enumerate(
+    ["rail13_mag_module", "rail13_waste_module", "rail13_elution_plate_module", "rail13_wash1_module", "rail13_wash2_module"])}
+  lh.deck.assign_child_resource(MFX_CAR_L5_base("car_13", modules=m13), rails=13)
+  r13 = [Alpaqua_96_magnum_flx("mag_plate"), AGenBio_1_troughplate_100000uL_Fl("waste_trough"),
+         BioER_96_wellplate_Vb_2200uL("elution_plate"), AGenBio_1_troughplate_100000uL_Fl("wash1_trough"),
+         AGenBio_1_troughplate_100000uL_Fl("wash2_trough")]
+  for i, r in enumerate(r13):
+    m13[i].assign_child_resource(r)
+  m19 = {i: Hamilton_MFX_plateholder_DWP_metal_tapped(n) for i, n in enumerate(
+    ["rail19_binding_module", "rail19_source_module", "rail19_flowthrough_module", "rail19_binding_trough_module", "rail19_elution_trough_module"])}
+  lh.deck.assign_child_resource(MFX_CAR_L5_base("car_19", modules=m19), rails=19)
+  r19 = [BioER_96_wellplate_Vb_2200uL("binding_plate"), BioER_96_wellplate_Vb_2200uL("source_plate"),
+         BioER_96_wellplate_Vb_2200uL("flowthrough_plate"), AGenBio_1_troughplate_100000uL_Fl("binding_trough"),
+         AGenBio_1_troughplate_100000uL_Fl("elution_trough")]
+  for i, r in enumerate(r19):
+    m19[i].assign_child_resource(r)
+  res = {r.name: r for r in r13 + r19}
+  return res, racks
+
+
+def record(lh):
+  def wrap(method, kind, fn):
+    orig = getattr(lh, method)
+
+    async def inner(*a, **k):
+      EVENTS.append(fn(*a, **k) | {"kind": kind})
+      try:
+        return await orig(*a, **k)
+      except ValueError as e:  # PLR 0.2.2 cannot spread 8 channels in one trough; newer PLR can. Logged, not simulated.
+        if "space channels" not in str(e):
+          raise
+    setattr(lh, method, inner)
+
+  arg = lambda a, k, i, *keys: a[i] if len(a) > i else next((k[x] for x in keys if x in k), None)
+  wrap("pick_up_tips", "pick", lambda *a, **k: {"spots": names(arg(a, k, 0, "tip_spots") or [])})
+  wrap("drop_tips", "drop", lambda *a, **k: {"spots": names(arg(a, k, 0, "tip_spots") or [])})
+  wrap("return_tips", "drop", lambda *a, **k: {"spots": []})
+  wrap("aspirate", "aspirate", lambda *a, **k: {"wells": names(arg(a, k, 0, "resources") or []), "vols": list(arg(a, k, 1, "vols") or [])})
+  wrap("dispense", "dispense", lambda *a, **k: {"wells": names(arg(a, k, 0, "resources") or []), "vols": list(arg(a, k, 1, "vols") or [])})
+  wrap("move_plate", "move", lambda *a, **k: {"plate": getattr(arg(a, k, 0, "plate"), "name", "?"), "to": getattr(arg(a, k, 1, "to"), "name", "?")})
+  wrap("move_resource", "move", lambda *a, **k: {"plate": getattr(arg(a, k, 0, "resource"), "name", "?"), "to": getattr(arg(a, k, 1, "to"), "name", "?")})
+
+
+async def main(proto_dir, out):
+  sys.path.insert(0, proto_dir)
+  set_tip_tracking(False)
+  set_volume_tracking(False)
+  _print = builtins.print
+  builtins.input = lambda *a, **k: EVENTS.append({"kind": "comment", "text": "Operator pause: " + " ".join(map(str, a))[:140]}) or ""
+  _sleep = asyncio.sleep
+
+  async def no_wait(s, *a, **k):
+    if s >= 1:
+      EVENTS.append({"kind": "delay", "seconds": float(s)})
+    await _sleep(0)
+  asyncio.sleep = no_wait
+  time.sleep = lambda s: EVENTS.append({"kind": "delay", "seconds": float(s)})
+
+  backend = SimulatedSTAR(num_channels=8)
+  lh = LiquidHandler(backend=backend, deck=STARLetDeck(core_grippers="1000uL-at-waste"))
+  await lh.setup()
+  res, racks = build(lh)
+  record(lh)
+  import ape_96w_protocol as ape
+  ape.print = lambda *a, **k: EVENTS.append({"kind": "comment", "text": " ".join(map(str, a))[:160]})  # protocol's own messages only
+  ok, err = True, None
+  try:
+    await ape.run_ape_96w(lh, binding_plate=res["binding_plate"], source_plate=res["source_plate"],
+      flowthrough_plate=res["flowthrough_plate"], elution_plate=res["elution_plate"], mag_plate=res["mag_plate"],
+      binding_trough=res["binding_trough"], wash1_trough=res["wash1_trough"], wash2_trough=res["wash2_trough"],
+      waste_trough=res["waste_trough"], elution_trough=res["elution_trough"], tip_racks=racks,
+      lysate_volume=300, binding_buffer_volume=1500, bead_volume_note=50, wash_volume=900, elution_volume=120,
+      binding_mix_rounds=6, binding_incubation_seconds=30, wash_mix_rounds=1, wash1_cycles=1, magnet_settle_seconds=20,
+      wash_incubation_seconds=2, elution_incubation_seconds=120)
+  except Exception as e:
+    ok, err = False, f"{type(e).__name__}: {e}"[:400]
+  json.dump({"ok": ok, "error": err, "events": EVENTS}, open(out, "w"))
+  print("ok" if ok else "FAIL " + err, len(EVENTS), "events")
+
+
+if __name__ == "__main__":
+  asyncio.run(main(sys.argv[1], sys.argv[2]))
diff --git a/docker/sim/mylog.py b/docker/sim/mylog.py
new file mode 100644
index 0000000..3f6f6db
--- /dev/null
+++ b/docker/sim/mylog.py
@@ -0,0 +1,13 @@
+"""eval/runlog.py, but keeping protocol comments as caption events."""
+import json, sys
+sys.path.insert(0, sys.argv[4])
+import runlog
+_parse = runlog.parse
+def parse(text, payload):
+    if text.startswith("COMMENT: "):
+        return {"kind": "comment", "text": text[9:], "instrument": "", "channels": 1}
+    return _parse(text, payload)
+runlog.parse = parse
+out = runlog.main(sys.argv[1], sys.argv[2])
+open(sys.argv[3], "w").write(json.dumps(out))
+print(sys.argv[1].split("results/")[-1], "ok" if out["ok"] else out["error"][:200], len(out.get("events", [])))
diff --git a/docker/sim/runlog.py b/docker/sim/runlog.py
new file mode 100644
index 0000000..5ac1a83
--- /dev/null
+++ b/docker/sim/runlog.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+"""Simulate an OT-2 protocol and print its robot actions as JSON events."""
+import json
+import re
+import sys
+import traceback
+
+from opentrons import protocol_api, simulate
+
+WELL = r"([A-P]\d{1,2}) (?:of|in) (.+?)(?: at [\d.]+ uL/sec)?$"
+PATTERNS = [
+    ("aspirate", re.compile(r"^Aspirating ([\d.]+) uL from " + WELL)),
+    ("dispense", re.compile(r"^Dispensing ([\d.]+) uL into " + WELL)),
+    ("pick", re.compile(r"^Picking up tip")),
+    ("drop", re.compile(r"^(?:Dropping|Returning) tip")),
+    ("delay", re.compile(r"^Delaying for (\d+) minutes and ([\d.]+) seconds")),
+    ("engage", re.compile(r"^Engaging Magnetic Module")),
+    ("disengage", re.compile(r"^Disengaging Magnetic Module")),
+    ("temp", re.compile(r"^Setting Temperature Module temperature to ([\d.]+)")),
+    # Thermocycler module actions (lid, block temperature and hold times, profiles); kept as the simulator words them.
+    ("thermocycler", re.compile(r"^((?:Opening|Closing|Setting|Deactivating|Executing|Thermocycler).*[Tt]hermocycler.*)$")),
+]
+INSTRUMENT_KINDS = {"aspirate", "dispense", "pick", "drop"}
+
+_comment = protocol_api.ProtocolContext.comment
+LOADNAMES: dict[str, str] = {}   # str(labware) as it appears in the run log -> the load name it was created from
+
+
+def _key(labware):
+    """'<label or display name> on <slot>', whatever the API level: str(labware) drops the slot from 2.14 on, and the
+    run log says 'on slot 2' there and 'on 2' before."""
+    slot = re.sub(r"^slot ", "", str(labware.parent))
+    name = labware.name if labware.name != labware.load_name else re.sub(r" on .*$", "", str(labware))
+    return f"{name} on {slot}"
+
+
+def _recording(original):
+    def load_labware(self, load_name, *args, **kwargs):
+        labware = original(self, load_name, *args, **kwargs)
+        LOADNAMES[_key(labware)] = labware.load_name
+        return labware
+    return load_labware
+
+
+for _cls in (protocol_api.ProtocolContext, protocol_api.ModuleContext):
+    _cls.load_labware = _recording(_cls.load_labware)
+
+
+def tagged_comment(self, msg):
+    return _comment(self, f"COMMENT: {msg}")
+
+
+def parse(text: str, payload: dict) -> dict | None:
+    if text.startswith("COMMENT: "):
+        return None
+    for kind, pattern in PATTERNS:
+        match = pattern.search(text)
+        if not match:
+            continue
+        instrument = str(payload.get("instrument", ""))
+        if kind in INSTRUMENT_KINDS and not instrument:
+            return None
+        event = {"kind": kind, "instrument": instrument}
+        event["channels"] = 8 if "8-Channel" in instrument else 1
+        if kind in {"aspirate", "dispense"}:
+            event.update(volume=float(match[1]), well=match[2], labware=re.sub(r" on slot ", " on ", match[3]))
+        elif kind == "delay":
+            event["seconds"] = int(match[1]) * 60 + float(match[2])
+        elif kind == "temp":
+            event["celsius"] = float(match[1])
+        elif kind == "thermocycler":
+            event["text"] = match[1].strip()
+        return event
+    return None
+
+
+def main(protocol: str, labware_dir: str) -> dict:
+    protocol_api.ProtocolContext.comment = tagged_comment
+    try:
+        with open(protocol) as handle:
+            runlog, _ = simulate.simulate(
+                handle, protocol, custom_labware_paths=[labware_dir]
+            )
+    except Exception as exc:
+        return {"ok": False, "error": f"{type(exc).__name__}: {exc}"[-3000:],
+                "traceback": traceback.format_exc()[-3000:]}
+    events: list[dict] = []
+    pending_air = False
+
+    def walk(entries):
+        nonlocal pending_air
+        for entry in entries:
+            payload = entry.get("payload", {})
+            text = str(payload.get("text", ""))
+            if text.startswith("Air gap"):
+                pending_air = True
+            event = parse(text, payload)
+            if event:
+                if pending_air and event["kind"] == "aspirate":
+                    event["kind"] = "air"
+                    pending_air = False
+                events.append(event)
+            walk(entry.get("subcommands", []))
+
+    walk(runlog)
+    return {"ok": True, "events": events, "n_commands": len(runlog), "labware": dict(LOADNAMES)}
+
+
+if __name__ == "__main__":
+    result = json.dumps(main(sys.argv[1], sys.argv[2]))
+    if len(sys.argv) > 3:       # the grader names a file for the result; stdout is not trusted (a protocol can print)
+        with open(sys.argv[3], "w") as handle:
+            handle.write(result)
+    print(result)
diff --git a/docker/sim/simulate_all.py b/docker/sim/simulate_all.py
new file mode 100644
index 0000000..6a32e5b
--- /dev/null
+++ b/docker/sim/simulate_all.py
@@ -0,0 +1,68 @@
+"""Inside the container: simulate every Opentrons protocol in /work/<candidate>/... and write run logs to /out.
+
+usage (entrypoint): simulate_all.py <candidate>[,<candidate>...] | all
+Each candidate folder is a cloned repo mounted read-only. For every .py with `def run` and an Opentrons
+marker, writes /out/<candidate>/<file-slug>.json (events + labware, or the error), using eval/runlog.py
+plus comment events (mylog.py). Custom labware JSON anywhere in the repo is passed to the simulator.
+"""
+import json, os, re, subprocess, sys
+
+WORK, OUT = "/work", "/out"
+MARK = re.compile(r"apiLevel|from opentrons|import opentrons")
+
+
+def labware_dirs(repo):
+    dirs = set()
+    for root, _, files in os.walk(repo):
+        if ".git" in root:
+            continue
+        for f in files:
+            if f.endswith(".json"):
+                try:
+                    if '"wellOrdering"' in open(os.path.join(root, f), errors="replace").read(200000):
+                        dirs.add(root)
+                except OSError:
+                    pass
+    return sorted(dirs)
+
+
+def main(sel):
+    names = sorted(os.listdir(WORK)) if sel == "all" else sel.split(",")
+    for name in names:
+        repo = os.path.join(WORK, name)
+        lw = labware_dirs(repo)
+        lwdir = "/tmp/lw_" + name
+        os.makedirs(lwdir, exist_ok=True)
+        for d in lw:  # runlog.py takes one labware dir: merge them
+            for f in os.listdir(d):
+                if f.endswith(".json"):
+                    src = os.path.join(d, f)
+                    try:
+                        open(os.path.join(lwdir, f), "w").write(open(src).read())
+                    except OSError:
+                        pass
+        for root, dirs, files in os.walk(repo):
+            dirs[:] = [d for d in dirs if d not in (".git", "node_modules", ".venv", "venv")]
+            for f in sorted(files):
+                if not f.endswith(".py"):
+                    continue
+                path = os.path.join(root, f)
+                text = open(path, errors="replace").read()
+                if "def run" not in text or not MARK.search(text):
+                    continue
+                rel = os.path.relpath(path, repo)
+                slug = re.sub(r"[^A-Za-z0-9]+", "_", rel)[:120]
+                os.makedirs(os.path.join(OUT, name), exist_ok=True)
+                out = os.path.join(OUT, name, slug + ".json")
+                try:
+                    p = subprocess.run([sys.executable, "/t2w/mylog.py", path, lwdir, out, "/t2w"],
+                                       capture_output=True, text=True, timeout=180, cwd="/tmp")
+                    ok = os.path.exists(out) and json.load(open(out)).get("ok")
+                except subprocess.TimeoutExpired:
+                    json.dump({"ok": False, "error": "timed out after 180 s"}, open(out, "w"))
+                    ok = False
+                print(f"{name}/{rel}: {'ok' if ok else 'FAIL'}", flush=True)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1] if len(sys.argv) > 1 else "all")
diff --git a/research/expansion/ANALYSIS.md b/research/expansion/ANALYSIS.md
new file mode 100644
index 0000000..fc0f95d
--- /dev/null
+++ b/research/expansion/ANALYSIS.md
@@ -0,0 +1,122 @@
+# Text2WetLab: benchmark analysis and expansion plan
+
+## How tasks are classified
+
+Every task gets three discrete labels instead of a numeric score.
+
+- **Structure** is what the robot has to coordinate, read from the protocol:
+  **S1** single transfer (one source to some wells) · **S2** plate set-up (several reagents added to the same wells) ·
+  **S3** wash cycles (liquid added then removed again) · **S4** module-coordinated (pipetting interleaved with magnet,
+  temperature or thermocycler steps and timed waits) · **S5** multi-reaction workflow (one reaction's product is the next reaction's input).
+- **Specification** is what the model has to work out: **E** explicit (every step and volume given) ·
+  **P** paper-assisted (steps given, paper fills gaps) · **D** paper-derived (the protocol must be extracted from the paper).
+- **Observed** is how models did in Harbor (pass@1, 2026-10-04): solved by all · split · unsolved · not run.
+
+A fourth, expert-labelled tag records why failures happen: **bench-ready**, **needs training** (bead handling, magnet timing),
+or **needs domain judgement** (rules a paper does not state, such as not pipette-mixing competent cells).
+
+Non-liquid-handling candidates have no pipetting structure, so they get a **family** instead: **PL** protocol program
+(XDL, LabOP, Autoprotocol) · **IM** microscope acquisition · **BR** closed-loop culture control · **OR** workcell
+orchestration and scheduling · **SD** self-driving lab campaign · **OT** other.
+
+## 1. The 11 current tasks
+
+| Task | Structure | Spec | Observed | Opus / Sonnet / Fable | Tag | Description |
+|---|---|---|---|---|---|---|
+| `split-200ul-two-wells` | S1 | E | Solved by all | 1 / 1 / 1 | Bench-ready | Calibration task: split one reservoir volume equally into two wells. Checks labware loading, pipette choice and a single transfer. |
+| `a1-a12-100ul` | S1 | E | Solved by all | 1 / 1 / 1 | Bench-ready | Calibration task: dispense the same volume into every well of one plate row. Checks well addressing and repeated dispensing. |
+| `ecoli-heat-shock-transformation` | S2 | E | Split | 0.8 / 1 / 1 | Domain judgement | Introduce a plasmid into competent E. coli in one tube and add recovery medium; the heat shock and incubation are operator steps. The pipetting is trivial; the catch is handling fragile cells gently. |
+| `ecoli-heat-shock-transformation-hard` | S4 | D | Not run | – | Domain judgement | The same transformation for eight plasmids on the thermocycler module, with volumes and the temperature program taken from the APEX paper. |
+| `colony-pcr-screening` | S2 | P | Solved by all | 1 / 1 / 1 | Bench-ready | Set up 96 colony PCR reactions to find which colonies carry the right plasmid: master mix, one colony and its primers per well, a fresh tip for every colony. |
+| `colony-pcr-screening-hard` | S2 | D | Not run | – | Training | The same 96-well colony PCR with quantities and order worked out from the Slowpoke paper and adapted to the deck's reagents. |
+| `ampure-bead-cleanup` | S3 | E | Solved by all | 1 / 1 / 1 | Training | Clean 96 PCR products with magnetic beads: bind, remove supernatant, two ethanol washes, dry, elute into a fresh plate. The largest task by robot actions. |
+| `golden-gate-assembly` | S5 | P | Solved by all | 1 / 1 / 1 | Training | AssemblyTron's DNA assembly: PCR seven fragments, remove template, join fragments into four plasmids by Golden Gate, then transform. Each stage's product feeds the next. |
+| `golden-gate-assembly-hard` | S5 | D | Not run | – | Training | The same AssemblyTron workflow with reaction quantities and fragment ratios derived from the paper. |
+| `opentrons-rna-extraction` | S4 | P | Split | 0.6 / 0.4 / 0.8 | Domain judgement | Extract viral RNA from 48 samples with magnetic beads, washes and a chilled elution plate, using two pipettes and two modules. All models recovered more eluate than the method specifies; Sonnet also added samples before the beads. |
+| `opentrons-rna-extraction-hard` | S4 | D | Not run | – | Domain judgement | The same extraction with volumes, order and timings taken from the paper. |
+
+### Current tasks on the grid
+
+| | E Explicit | P Paper-assisted | D Paper-derived |
+|---|---|---|---|
+| **S1** Single transfer | split ✅, a1-a12 ✅ | – | – |
+| **S2** Plate set-up | heat shock ⚠️ | colony PCR ✅ | colony PCR hard ◻ |
+| **S3** Wash cycles | AMPure ✅ | – | – |
+| **S4** Module-coordinated | – | RNA extraction ⚠️ | RNA hard ◻, heat shock hard ◻ |
+| **S5** Multi-reaction workflow | – | Golden Gate ✅ | Golden Gate hard ◻ |
+
+✅ solved by all · ⚠️ split · ◻ not run. Every paper-derived task is unrun, and nothing at S1–S3 is paper-derived.
+Failures come from domain judgement, not size: all models pass Golden Gate (S5) and AMPure (over 5,000 liquid moves).
+
+## 2. The new candidates
+
+All 210 new candidates are listed with a plain-English description in [`CANDIDATES.md`](CANDIDATES.md)
+(also posted below as follow-up comments). Structure and family are assigned by the same keyword rules for every candidate,
+so they are estimates until each task is built.
+
+### New liquid-handling candidates by structure and readiness
+
+| Structure | Ready | Partial | No usable code | Total |
+|---|---|---|---|---|
+| **S1** Single transfer | 1 | 3 | 2 | 6 |
+| **S2** Plate set-up | 13 | 32 | 18 | 63 |
+| **S3** Wash cycles | 4 | 9 | 1 | 14 |
+| **S4** Module-coordinated | 1 | 2 | 4 | 7 |
+| **S5** Multi-reaction workflow | 6 | 12 | 0 | 18 |
+
+### New non-liquid-handling candidates by family and readiness
+
+| Family | Ready | Partial | No usable code | Total |
+|---|---|---|---|---|
+| **PL** Protocol program (XDL, LabOP, Autoprotocol) | 5 | 5 | 0 | 10 |
+| **IM** Microscope acquisition | 7 | 8 | 0 | 15 |
+| **BR** Closed-loop culture control | 1 | 5 | 2 | 8 |
+| **OR** Workcell orchestration / scheduling | 3 | 6 | 2 | 11 |
+| **SD** Self-driving lab campaign | 3 | 14 | 4 | 21 |
+| **OT** Other automation | 0 | 12 | 25 | 37 |
+
+### Which specification levels the new candidates can support
+
+| Specification | Candidates |
+|---|---|
+| P + D | 138 |
+| D (needs a written oracle) | 51 |
+| E only (no paper) | 21 |
+
+Every candidate with both a paper and code (138) can become a paper-assisted **and** a paper-derived task, which fills the
+empty D column above. The largest gains are in S2 plate set-ups (13 ready) and S5 multi-reaction workflows (6 ready);
+S4 module-coordinated work stays thin (1 ready), so it needs hand-built tasks.
+
+## 3. Where the models go wrong
+
+A deterministic diff of each model's run log against the oracle's (`tools/fault_detect.py`, `fault_report.md`) agrees with the judge on every task:
+
+| Task | Opus 5.5 | Sonnet 5.5 | Fable 5.1 |
+|---|---|---|---|
+| Heat shock | mixes the competent cells | clean | mixes the competent cells |
+| RNA extraction | recovers 100 µL eluate (oracle 80) | samples before beads; 100 µL eluate; 5% extra waste removed | 100 µL eluate |
+
+- **Judge inconsistency:** Opus and Fable do the same thing on heat shock but score 0.8 and 1.0. Make this a deterministic check.
+- **The RNA oracle is the authors' script, not the task spec:** it waits longer and uses the magnet more than the task asks, and scores 0.6 itself.
+- **The simulator does not track liquid**, so over-aspiration and harm to fragile cells pass simulation.
+
+## 4. Size of the expanded benchmark
+
+| Scenario | Tasks |
+|---|---|
+| Today | 11 |
+| + 12 corpus papers that already have IR but no task | ~61 |
+| + new ready candidates (2 tasks each) | ~149 |
+| + all new paper + code candidates | ~340–410 |
+| Theoretical ceiling (incl. partial, ACRA, AEGIS) | ~500–600 |
+
+Simulator check (`VERIFIED.md`): of 128 protocol files in the 25 ready liquid-handling repos, 30 pass `opentrons_simulate` unchanged (10 repos).
+The 98 failures are setup issues: labware files on the author's disk (43), newer API (24), extra packages (15), missing inputs (5), other (11).
+
+## 5. Recommendations
+
+1. Run the four `-hard` variants in Harbor; they fill the D column and are the most demanding tasks.
+2. Turn domain-rule judge items (gentle cell handling, elution volume) into deterministic checks; add a spec oracle for RNA extraction.
+3. Build next from the 12 corpus papers with IR and the 10 repos that already simulate, prioritising D variants at S1–S3.
+4. Re-run verification with labware vendored and a newer Opentrons release.
+5. Add new grader families only where hardware-free execution exists: PL (Cronin ACRA, 100+ executed literature→XDL pairs), IM, OR.
diff --git a/research/expansion/CANDIDATES.md b/research/expansion/CANDIDATES.md
new file mode 100644
index 0000000..a6f7938
--- /dev/null
+++ b/research/expansion/CANDIDATES.md
@@ -0,0 +1,234 @@
+# All new expansion candidates (plain-English descriptions)
+
+210 new candidates found by the four searches, after removing papers already in the corpus.
+Structure (S1–S5, liquid handling) or family (non-liquid-handling) is assigned by fixed keyword rules over each
+candidate's recorded robot work, so it is an estimate until the task is built. Specification: P = paper-assisted,
+D = paper-derived, E = explicit steps. Simulator status is from `VERIFIED.md` (ready liquid-handling candidates only).
+
+Structure levels: S1 single transfer · S2 plate set-up · S3 wash cycles · S4 module-coordinated · S5 multi-reaction workflow.
+Families: PL protocol program · IM microscope acquisition · BR closed-loop culture control · OR workcell orchestration · SD self-driving lab campaign · OT other.
+
+## Ready (44)
+
+| Candidate | Level | Spec | Simulator | Licence | Description |
+|---|---|---|---|---|---|
+| [`evolver-2018`](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035058/) | BR | P + D | not run | MIT | Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Robot work: Closed-loop culture control. Reported result: Turbidostat/chemostat growth curves and selection experiments across 16 vials reported with fitness measurements. |
+| [`eda-event-driven`](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613693/) | IM | P + D | not run | BSD-3-Clause | Event-driven acquisition for content-enriched microscopy. Robot work: Microscope acquisition. Reported result: Adaptive frame-rate imaging of mitochondrial and bacterial division events with reported photobleaching reduction. |
+| [`etsted`](https://www.nature.com/articles/s41592-022-01588-y) | IM | P + D | not run | GPL-3.0 | Event-triggered STED imaging. Robot work: Microscope acquisition. Reported result: Event-triggered STED of vesicle/synaptic events with reported detection rates. |
+| [`mantis-shrimpy`](https://academic.oup.com/pnasnexus/article/3/9/pgae323/7742297) | IM | P + D | not run | BSD-3-Clause | Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells. Robot work: Microscope acquisition. Reported result: Multi-well 4D imaging of cell lines acquired and analysed with reported throughput. |
+| [`navigate-2024`](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540721/) | IM | P + D | not run | BSD-style (LICENSE.md) | Navigate: an open-source platform for smart light-sheet microscopy. Robot work: Microscope acquisition. Reported result: Smart acquisition (autofocus, tiling, decision-based imaging) demonstrated on multiple microscopes with images. |
+| [`openflexure-autofocus`](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13064) | IM | P + D | not run | GPL-3.0 | Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope. Robot work: Microscope acquisition. Reported result: Automated malaria blood-smear tiling scans with autofocus success rates reported. |
+| [`pycromanager-2021`](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532176/) | IM | P + D | not run | BSD-3-Clause | Pycro-Manager: open-source software for customized and reproducible microscope control. Robot work: Microscope acquisition. Reported result: Applications in paper (adaptive illumination, light-sheet, high-throughput imaging) with acquired data. |
+| [`pymmcore-plus-mda`](https://pymmcore-plus.github.io/pymmcore-plus/) | IM | P + D | not run | BSD-3-Clause | pymmcore-plus + useq-schema (multi-dimensional acquisition engine). Robot work: Microscope acquisition. Reported result: Software; validated through downstream papers (e.g., Mantis PNAS Nexus 2024). |
+| [`alabos-alab`](https://pubs.rsc.org/en/content/articlehtml/2024/dd/d4dd00129j) | OR | P + D | not run | MIT | AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories (A-Lab). Robot work: Workcell orchestration / scheduling. Reported result: AlabOS ran A-Lab for months (>3500 samples) of solid-state synthesis; A-Lab Nature 2023 reported 41 synthesized targets (later disputed). |
+| [`openworkstation`](https://www.sciencedirect.com/science/article/pii/S2468067220300468) | OR | P + D | not run | CC BY-SA (repo) | OpenWorkstation: A modular open-source technology for automated in vitro workflows. Robot work: Workcell orchestration / scheduling. Reported result: Automated microphysiometry/cell-culture workflow demonstrated with measurements. |
+| [`slab-scheduling`](https://journals.sagepub.com/doi/10.1177/24726303211021790) | OR | P + D | not run | MIT | Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints. Robot work: Workcell orchestration / scheduling. Reported result: Schedules for cell-culture protocols computed and compared to baseline; executed on Maholo. |
+| [`autoprotocol-dnada`](https://pubs.acs.org/doi/10.1021/acssynbio.3c00292) | PL | P + D | not run | Apache-2.0 | Automated Platform for the Plasmid Construction Process (DNAda -> Autoprotocol). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Hundreds of plasmid constructions executed with reported success rates. |
+| [`chemputer-acra`](https://www.nature.com/articles/s42004-026-01993-w) | PL | P + D | not run | (LICENSE present,… | Verification and execution of the scientific literature via chemputation augmented by large language models. Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: LLM-generated XDL from literature procedures executed on the Chemputer with yields reported; >100 reference XDLs released. |
+| [`chemputer-blueprints`](https://www.nature.com/articles/s41467-024-54238-6) | PL | P + D | not run | see GitLab (unverified) | Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer. Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Parallel chiral syntheses executed with reported yields/ee using XDL blueprints. |
+| [`clairify-xdl`](https://link.springer.com/article/10.1007/s10514-023-10136-2) | PL | P + D | not run | MIT | Large language models for chemistry robotics (CLAIRify: NL -> XDL). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Generated XDL executed on a Franka robot for solubility/recrystallisation; expert-evaluated XDL validity on 108 protocols. |
+| [`labop`](https://bioprotocols.github.io/labop/) | PL | P + D | not run | MIT | LabOP (Laboratory Open Protocol language, formerly PAML) - iGEM interlab growth-curve/calibration protocols. Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Protocols used in the iGEM Interlab study (results published separately); executable via converters. |
+| [`roche-pipetting-performance-ot2`](https://doi.org/10.1016/j.slast.2024.100180) | S1 | P + D | fails (setup) | GPL-3.0 | Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment. Robot work: liquid-handler QC: photometric pipetting accuracy/precision (dye dilution). Reported result: SLAS Technology 2024 (Roche pRED) reports OT-2 integration into AutoLab and pipetting accuracy/precision benchmarks (CV, systematic error) per volume. |
+| [`blots-ot2`](https://doi.org/10.1002/cpz1.70454) | S2 | P + D | fails (setup) | none | Bacterial Lysis Observation Over Time Assay (BLOTS) for High-Throughput Isolation and Screening. Robot work: 384-well assay plate assembly / lysis kinetics screening. Reported result: Assay plates assembled by the robot yielded time-resolved lysis curves used to recover and sequence isolates. |
+| [`ester-library-synthesis`](https://doi.org/10.1039/d2cc05670d) | S2 | P + D | fails (setup) | MIT | Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction. Robot work: 96-well library synthesis, quench, solvent/salt screen. Reported result: 96-well esterification library synthesised on OT-2 with yields/conversions measured by LC-MS. |
+| [`flat-agar-celegans-ot2`](https://doi.org/10.57844/arcadia-h01v-2nxt) | S2 | P + D | fails (setup) | MIT | Flat agar and optimized media enable high-throughput C. elegans imaging in 96-well plates. Robot work: C. elegans bleach synchronisation, OP50 agar spotting, worm plating for imaging. Reported result: Pub reports flat-agar 96-well imaging quality (focus/worm detection) enabled by robot-prepared plates. |
+| [`formulations-prep-shampoo`](https://www.nature.com/articles/s41597-024-03573-w) | S2 | P + D | fails (setup) | none | Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset. Robot work: viscous liquid formulation preparation with gravimetric verification. Reported result: Gravimetric analysis of robot-prepared formulations and downstream property measurements form the published dataset. |
+| [`gfp-codon-burden-ot2`](https://doi.org/10.1186/s13036-025-00521-z) | S2 | P + D | 7/15 files pass | MIT | Codon usage modulates the relationship between the burden and yield of protein overexpression. Robot work: bacterial growth/induction burden assay (IPTG titration, GFP + OD plate-reader). Reported result: J Biol Eng 2025 (preprint 10.1101/2024.11.28.625058) reports growth-rate burden vs GFP yield across codon-deoptimised strains; raw plate-reader data and processed data are in the repo. |
+| [`greenaway-halogenation`](https://chemrxiv.org/engage/chemrxiv/article-details/15000393) | S2 | P + D | fails (setup) | BSD-3-Clause | An automated platform for tailored late-stage halogenation of pharmaceuticals. Robot work: reaction array setup, quench, NMR/LC-MS sample prep. Reported result: Screening arrays dispensed by OT-2 gave halogenation conversions/selectivities measured by NMR and LC-MS across substrate panels. |
+| [`greenaway-mocs`](https://doi.org/10.1002/anie.202424270) | S2 | P + D | fails (setup) | none | Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages. Robot work: solution-phase screening array + host-guest assay. Reported result: Automated screen identified assembled cages confirmed by MS/NMR and host-guest binding measured across the array. |
+| [`greenaway-pocs`](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc06133g) | S2 | P + D | fails (setup) | none | Streamlining the automated discovery of porous organic cages. Robot work: cage synthesis plate + analytical transfer protocols. Reported result: Automated workflow produced porous organic cages characterised by HRMS/NMR, with hit rates reported vs manual discovery. |
+| [`lucks-cellfree-biosensor`](https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1) | S2 | P + D | fails (setup) | none | Semi-automated production of cell-free biosensors. Robot work: cell-free reaction assembly (384-well biosensor build). Reported result: A full 384-well plate of fluoride-sensing cell-free reactions assembled robotically matched expected colorimetric/fluorescent detection performance. |
+| [`lysostaphin-turbidity`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12836826/) | S2 | P + D | fails (setup) | AGPL-3.0 | Turbid but accurate: automating lysostaphin quantification including uncertainty quantification. Robot work: antibacterial activity turbidity assay (serial dilution + OD lysis kinetics). Reported result: Turbidity assay quantified lysostaphin over a 0.63-10 mg/L dynamic range with Bayesian uncertainty quantification using autoclaved S. carnosus indicator cells. |
+| [`msd-biochem-assays-ot2`](https://doi.org/10.1016/j.slast.2024.100205) | S2 | P + D | passes | Apache-2.0 | Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler. Robot work: Bradford and PicoGreen standard curves / quantitation assays. Reported result: SLAS Technology 2024 paper compares OT-2 Bradford/PicoGreen standard curves and sample quantitation to manual (linearity, CV, accuracy). |
+| [`plant-phenotyping-ot2`](https://doi.org/10.1002/aisy.202500624) | S2 | P + D | fails (setup) | MIT | Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience. Robot work: plate filling and treatment dosing for plant phenotyping. Reported result: Automated phenotyping screen measured growth responses used to select stress-resilient conditions. |
+| [`sapp-dmx-protein-design`](https://doi.org/10.1038/s41467-026-76740-9) | S2 | P + D | fails (setup) | MIT | Accelerating protein design by scaling experimental characterization. Robot work: SEC fraction pooling and normalisation for protein characterisation. Reported result: High-throughput expression/characterisation of designed proteins; thousands of designs assayed with the automated pipeline. |
+| [`cayman-his-elisa`](https://dx.doi.org/10.17504/protocols.io.n92ld4x3nl5b) | S3 | P + D | fails (setup) | MIT | An Opentrons OT-2 workflow for the Cayman His-tag detection ELISA kit. Robot work: ELISA sample/standard loading, plate washing, substrate addition. Reported result: Standard curves and His-tag quantification generated from the automated ELISA runs in the Arcadia protocol record. |
+| [`massspecpreppy`](https://doi.org/10.1002/pmic.202300294) | S3 | P + D | 3/10 files pass | GPL-3.0 | MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics. Robot work: BCA assay, reduction/alkylation, SP3 digestion, Evotip loading. Reported result: BCA recovery 101.3% (SD 7.8) for the automated workflow vs 96.3% manual; 94.5% of protein groups passed thresholds for OT-2 digestion. |
+| [`roboctab`](https://www.mdpi.com/2223-7747/14/15/2263) | S3 | P + D | fails (setup) | none | High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping. Robot work: CTAB plant DNA extraction. Reported result: DNA yield/purity and genotyping call rates from robot-extracted samples compared with manual CTAB extraction. |
+| [`tidytron`](https://doi.org/10.1016/j.slast.2023.08.007) | S3 | P + D | 3/15 files pass | Apache-2.0 | TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 robots. Robot work: plasticware wash-and-reuse / tip and plate cleaning. Reported result: Carryover after wash validated by qPCR/transformation and fluorescence assays showing no detectable cross-contamination vs fresh plasticware. |
+| [`hyrad-adna-capture`](https://doi.org/10.1111/1755-0998.13518) | S4 | P + D | passes | none | Performance and automation of ancient DNA capture with RNA hyRAD probes. Robot work: hybridization capture + magnetic bead washes (magnetic module, thermocycler). Reported result: Capture efficiency and on-target read fractions for automated vs manual hybridization reported for ancient DNA libraries. |
+| [`ant-cloning`](https://pubs.acs.org/doi/10.1021/acssynbio.0c00240) | S5 | P + D | 7/10 files pass | none | Automated cloning by natural transformation (ANT) OT-2 workflow. Robot work: PCR, digestion, overlap-extension PCR, natural transformation, plating. Reported result: Cloning efficiency and correct-assembly rates for automated natural transformation reported in the paper. |
+| [`beckham-enzyme-pipeline`](https://www.nature.com/articles/s41598-024-64938-0) | S5 | P + D | 2/15 files pass | none (no LICENSE file) | Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline. Robot work: E. coli transformation, inoculation, expression, lysis, enzyme assay. Reported result: Robot-assisted pipeline screened enzyme variant libraries; activity/expression measured and compared with manual handling. |
+| [`culturomics-isolation`](https://doi.org/10.1002/imo2.70037) | S5 | P + D | 2/11 files pass | none | Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex communities. Robot work: microvolume DNA extraction, two-step amplicon PCR, bead purification, pooling. Reported result: Isolates recovered and phylogenetically identified from automated plates; sequencing success rates reported vs manual pipeline. |
+| [`damplab-moclo-transformation`](https://academic.oup.com/synbio/article/7/1/ysac004/6542944) | S5 | P + D | no protocol file | BSD-3-Clause | A linear programming-based strategy to save pipette tips in automated DNA assembly (with DAMP Lab MoClo/transformation workflow). Robot work: MoClo Golden Gate assembly + E. coli transformation + plating. Reported result: Tip-saving assembly strategy evaluated on OT-2 runs; assembly/transformation success measured against standard tip usage. |
+| [`exfab-qiaseq-flex`](https://dx.doi.org/10.17504/protocols.io.n2bvjer3pgk5) | S5 | P + D | passes | GPL-3.0 | Automated QIAseq FX DNA Library Preparation on the Opentrons Flex. Robot work: NGS library preparation (fragmentation, adapter ligation, bead cleanup, PCR). Reported result: Protocol entry reports libraries prepared for Illumina short-read sequencing of bee gut samples (sequencing-ready yields). |
+| [`jubiotech-ot2-autoclone`](https://doi.org/10.1007/s00253-022-12017-7) | S5 | P + D | 2/7 files pass | AGPL-3.0 | Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation. Robot work: Golden Gate assembly, heat-shock transformation, plasmid prep, plating. Reported result: Automated strain construction produced verified C. glutamicum secretion strains characterised in microbioreactor cultivations. |
+| [`chemputer-peptide`](https://www.nature.com/articles/s41467-025-62344-2) | SD | P + D | not run | Zenodo (check) | Universal peptide synthesis via solid-phase methods fused with chemputation. Robot work: Self-driving lab campaign. Reported result: Synthesised multiple peptides (incl. semaglutide-type) with purity/yield reported. |
+| [`panda-bear`](https://pubs.rsc.org/en/content/articlehtml/2024/mh/d4mh00797b) | SD | P + D | not run | GPL-3.0 | PANDA: a self-driving lab for studying electrodeposited polymer films. Robot work: Self-driving lab campaign. Reported result: BO campaign optimised PEDOT:PSS electrochromic switching; data reported. |
+| [`sdl-demo-clslab`](https://www.cell.com/matter/fulltext/S2590-2385(22)00651-1) | SD | P + D | not run | MIT | What is a minimal working example for a self-driving laboratory? (SDL-Demo / CLSLab:Light). Robot work: Self-driving lab campaign. Reported result: Optimisation of LED mixing to match target spectra; simulator vs hardware comparison reported. |
+
+## Partial (108)
+
+| Candidate | Level | Spec | Simulator | Licence | Description |
+|---|---|---|---|---|---|
+| [`chibio-2020`](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000794) | BR | P + D | not run | none (no LICENSE file) | In situ characterisation and manipulation of biological systems with Chi.Bio. Robot work: Closed-loop culture control. Reported result: Turbidostat growth, optogenetic feedback control and fluorescence measurements demonstrated with reported traces. |
+| [`evolver-ddr-elife`](https://elifesciences.org/articles/67175) | BR | P + D | not run | MIT | Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community (eVOLVER). Robot work: Closed-loop culture control. Reported result: Fluctuating dilution regimes run on eVOLVER with community composition measured by sequencing. |
+| [`photobioreactor-fluorescence`](https://www.mdpi.com/2079-6374/15/3/128) | BR | P + D | not run | unverified | Integration of Fluorescence Spectroscopy into a Photobioreactor for the Monitoring of Cyanobacteria. Robot work: Closed-loop culture control. Reported result: Cyanobacterial growth monitored by fluorescence with reported correlation to OD. |
+| [`pioreactor`](https://docs.pioreactor.com) | BR | P + D | not run | MIT | Pioreactor open-source bioreactor software (used in published studies). Robot work: Closed-loop culture control. Reported result: No first-party results paper; third-party papers (e.g., 10.1186/s12934-025-02670-8) use it for culture experiments. |
+| [`reacsight`](https://www.nature.com/articles/s41467-022-31033-9) | BR | P + D | not run | check Zenodo | Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight. Robot work: Closed-loop culture control. Reported result: Automated cytometry-based optogenetic control of yeast populations and co-cultures with reported dynamics. |
+| [`brightfield-biofilm`](https://journals.asm.org/doi/10.1128/mbio.00448-26) | IM | P + D | not run | none | Label-free microscopy enables high-throughput identification of genes controlling biofilm development. Robot work: Microscope acquisition. Reported result: Genome-wide biofilm screen with hit genes reported. |
+| [`culturomics-colony-picking`](https://www.nature.com/articles/s41587-023-01674-2) | IM | P + D | not run | unverified | High-throughput microbial culturomics using automation and machine learning (CAMII colony picker). Robot work: Microscope acquisition. Reported result: Isolated >26,000 gut isolates with morphology-guided picking efficiency reported. |
+| [`daxi-lightsheet`](https://www.nature.com/articles/s41592-022-01417-2) | IM | P + D | not run | CC BY (repo) | DaXi: high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy. Robot work: Microscope acquisition. Reported result: Zebrafish/drosophila volumetric imaging reported. |
+| [`fish-fluidics`](https://www.sciencedirect.com/science/article/pii/S246806722200088X) | IM | P + D | not run | unverified | An open source 16-channel fluidics system for automating sequential FISH-based imaging. Robot work: Microscope acquisition. Reported result: seqFISH rounds automated with imaging results. |
+| [`imswitch`](https://joss.theoj.org/papers/10.21105/joss.03394) | IM | P + D | not run | GPL-3.0 | ImSwitch: generalizing microscope control in Python. Robot work: Microscope acquisition. Reported result: Software paper; underpins etSTED and UC2 experiments. |
+| [`openframe-openaf`](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13219) | IM | P + D | not run | BSD | openFrame: modular open microscopy platform with single-shot optical autofocus. Robot work: Microscope acquisition. Reported result: Autofocus accuracy/stability characterised and used in HCA imaging. |
+| [`phage-cocktails-robotics`](https://www.nature.com/articles/s41467-026-68684-x) | IM | P + D | not run | check Zenodo | High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails. Robot work: Microscope acquisition. Reported result: Phage cocktails designed and validated with plaque/plate-reader data. |
+| [`pysted`](https://www.nature.com/articles/s42256-024-00903-w) | IM | P + D | not run | CC (Attribution, check NC) | Development of AI-assisted microscopy frameworks through realistic simulation with pySTED. Robot work: Microscope acquisition. Reported result: RL policies trained in simulation were deployed on a real STED microscope with image quality reported. |
+| [`ac-training-lab`](https://github.com/AccelerationConsortium/ac-training-lab) | OR | P + D | not run | MIT | Acceleration Consortium Training Lab (remote-access SDL modules incl. Hello-World, sample transfer). Robot work: Workcell orchestration / scheduling. Reported result: Educational SDL modules; no single results paper verified. |
+| [`chemos-2020`](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229862) | OR | P + D | not run | Apache-2.0 | ChemOS: An orchestration software to democratize autonomous discovery. Robot work: Workcell orchestration / scheduling. Reported result: Demonstrates closed-loop optimisation on a cocktail-mixing robot and HPLC calibration, with reported optimisation traces. |
+| [`madsci-ad-sdl`](https://doi.org/10.21105/joss.09416) | OR | P + D | not run | MIT | MADSci: A modular Python-based framework to enable autonomous science. Robot work: Workcell orchestration / scheduling. Reported result: Framework; experiments reported via ANL RPL deployments but no single peer-reviewed results paper verified. |
+| [`mobile-robots-dai-2024`](https://www.nature.com/articles/s41586-024-08173-7) | OR | P + D | not run | Zenodo (check per record) | Autonomous mobile robots for exploratory synthetic chemistry. Robot work: Workcell orchestration / scheduling. Reported result: Supramolecular/structural diversification chemistry run autonomously with UPLC-MS/NMR-based decisions; hits reported. |
+| [`star-hardwarex`](https://www.sciencedirect.com/science/article/pii/S2468067224000178) | OR | P + D | not run | check Zenodo | Sequential Treatment Application Robot (STAR) for high-replication marine experimentation. Robot work: Workcell orchestration / scheduling. Reported result: Marine organism treatment experiments with high replication reported. |
+| [`zhao-autonomous-enzyme`](https://www.nature.com/articles/s41467-025-61209-y) | OR | P + D | not run | MIT | A generalized platform for artificial intelligence-powered autonomous enzyme engineering (iBioFAB). Robot work: Workcell orchestration / scheduling. Reported result: Engineered AtHMT and YmPhytase variants with 16-26x improvements in 4 rounds. |
+| [`chemos2-atlas`](https://pubs.rsc.org/en/content/articlehtml/2025/dd/d4dd00115j) | OT | P + D | not run | MIT | Atlas: a brain for self-driving laboratories (BO library used in ChemOS 2.0 campaigns). Robot work: Other automation. Reported result: BO planners benchmarked on emulators and deployed on SDL campaigns (e.g., electrochemistry with ChemOS 2.0). |
+| [`covid-mastermix-omix`](https://pmc.ncbi.nlm.nih.gov/articles/PMC11639134/) | OT | D (needs a written oracle) | not run | none | Development and validation of automated methods for COVID-19 PCR Master Mix preparation. Robot work: Other automation. Reported result: Automated PCR master mix preparation matched manual pipetting accuracy in a diagnostic lab (Ct value comparisons, gravimetric checks). |
+| [`duckbot-jubilee`](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0296717) | OT | P + D | not run | MIT | The Duckbot: A system for automated imaging and manipulation of duckweed. Robot work: Other automation. Reported result: Automated growth assays measured duckweed area/growth across treatments. |
+| [`icfree-cfps`](https://doi.org/10.1016/j.isci.2025.113599) | OT | P + D | not run | MIT | An AI-driven workflow for the accelerated optimization of cell-free protein synthesis. Robot work: Other automation. Reported result: Iterative ML rounds improved cell-free protein yields measured on plate reader across generated compositions. |
+| [`labdroid-cell-culture`](https://elifesciences.org/articles/77007) | OT | P + D | not run | none | Robotic search for optimal cell culture in regenerative medicine (LabDroid Maholo, iPSC-RPE). Robot work: Other automation. Reported result: BO over 7 culture parameters improved iPSC-RPE differentiation scores (pigmentation) in 111 days. |
+| [`llm-rdf-synthesis`](https://www.nature.com/articles/s41467-024-54457-x) | OT | P + D | not run | MIT (per README badge) | An automatic end-to-end chemical synthesis development platform powered by large language models. Robot work: Other automation. Reported result: End-to-end synthesis campaigns executed with reported yields and optimised conditions. |
+| [`memplex-printing`](https://www.nature.com/articles/s41467-025-59471-1) | OT | P + D | not run | MIT | Designer artificial environments for membrane protein synthesis. Robot work: Other automation. Reported result: Thousands of cell-free membrane-protein reactions printed and measured; formulations identified. |
+| [`myra-cfe-platform`](https://academic.oup.com/synbio/article/doi/10.1093/synbio/ysag010) | OT | P + D | not run | none | A liquid handling platform for standardized quantification of cell-free enzymatic activity. Robot work: Other automation. Reported result: Standardised enzymatic activity quantification reproducible across operators/platforms reported in the paper. |
+| [`polymerization-planner`](https://doi.org/10.1021/acspolymersau.5c00067) | OT | P + D | not run | MIT | Automation-Assisted Photoinduced Atom Transfer Radical Polymerization. Robot work: Other automation. Reported result: Polymerisations run from planner recipes characterised by GPC (conversion, dispersity). |
+| [`sdl-guide-gormley`](https://pubs.rsc.org/en/content/articlehtml/2026/dd/d5dd00525f) | OT | P + D | not run | MIT | A user's guide to your first self-driving liquid handling lab. Robot work: Other automation. Reported result: Closed-loop campaign optimised enzyme assay conditions with plate-reader readouts. |
+| [`spatial-tx-bravo`](https://pmc.ncbi.nlm.nih.gov/articles/PMC7158132/) | OT | D (needs a written oracle) | not run | none | Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues. Robot work: Other automation. Reported result: Automated ST library prep cut prep time by 35%, increased samples per run and showed near-zero technical variability between preparations. |
+| [`teemi`](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011929) | OT | P + D | not run | MIT | teemi: open-source literate programming for iterative DBTL cycles. Robot work: Other automation. Reported result: Yeast strain library built and screened with titres reported. |
+| [`aquarium`](https://academic.oup.com/synbio/article/8/1/ysad005/7069301) | PL | P + D | not run | MIT | Aquarium laboratory operating system (UW BIOFAB) - used in SD2 robustness studies. Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Aquarium-run yeast logic circuit experiments with cytometry outcomes reported. |
+| [`autoprotocol-python`](https://autoprotocol.org) | PL | P + D | not run | BSD-3-Clause (LICENSE.rst) | Autoprotocol-python (Strateos/Transcriptic protocol IR). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Specification; experimental results come from cloud-lab papers (e.g., SD2 replication papers). |
+| [`coscientist`](https://www.nature.com/articles/s41586-023-06792-0) | PL | P + D | not run | (LICENSE present,… | Autonomous chemical research with large language models (Coscientist). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Suzuki/Sonogashira couplings executed and confirmed by GC-MS; plate-reader colour tasks executed. |
+| [`sample-protein-sdl`](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926838/) | PL | P + D | not run | check Zenodo | Self-driving laboratories to autonomously navigate the protein fitness landscape (SAMPLE). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Four agents converged on glycoside hydrolases >12 C more thermostable. |
+| [`sd2-yeast-replication`](https://academic.oup.com/synbio/article/7/1/ysac018/6703309) | PL | P + D | not run | none | Highly-automated, high-throughput replication of yeast-based logic circuit design assessments (SD2/Strateos/Aquarium). Robot work: Protocol program (XDL, LabOP, Autoprotocol). Reported result: Logic-circuit assays replicated across labs with cytometry results compared. |
+| [`aliquot-niaid`](https://github.com/QVEU/ALIQUOT) | S1 | E only (no paper) | not run | none | ALIQUOT: Automated Liquid handling Infection Quantification Using OpenTrons (NIH/NIAID QVEU). Robot work: virus infection quantification: serial dilution, fix, immunostain (OT-2 + Flex). |
+| [`labscriptai-protein-eng`](https://www.biorxiv.org/content/10.1101/2025.09.30.679666v1.full) | S1 | P + D | not run | none | Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows. Robot work: LLM protocol generation; cell-free GFP variant characterisation; enzyme screening; fluorescence calibration. Reported result: Fluorescence standard curves CV<5%, R2>0.999; 318 GFP variants characterised (best 5.0x avGFP); enzyme double mutants >3x catalytic efficiency. |
+| [`olh-turbidostat-plr`](https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full) | S1 | P + D | not run | none | A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments. Robot work: turbidostat / continuous culture; pipetting accuracy calibration. Reported result: OLH pipetting MAE 4.1 vs 7.2 uL manual (p<0.005); closed-loop turbidostat held ~200 cultures at OD setpoints. |
+| [`aml-drug-synergy-pyhamilton`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10449086/) | S2 | P + D | not run | none | High-throughput approaches to uncover synergistic drug combinations in leukemia. Robot work: drug combination dilution matrix and dosing for synergy screening (leukemia cells). Reported result: Multidimensional drug-combination screens identified synergistic combinations in leukemia (H3K27 modification-related), with viability readouts and synergy scores. |
+| [`artic-normalisation-esr`](https://github.com/ESR-NZ/opentrons_protocols) | S2 | E only (no paper) | not run | none | ESR-NZ ARTIC normalisation/end-repair/barcoding (OT-2). Robot work: SARS-CoV-2 ARTIC DNA normalisation + nanopore end-repair/barcoding. |
+| [`auto-sp-proteomics`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12355475/) | S2 | D (needs a written oracle) | not run | n/a (no repo) | AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications. Robot work: proteomics BCA, digestion and PTM enrichment. Reported result: AUTO-SP automated BCA, digestion and PTM enrichment on PDX breast tumour tissue, with protein/PTM IDs comparable to manual. |
+| [`detectr-covid-ot2`](https://github.com/tsdobbs/mammoth-COVID19-assay-OT2) | S2 | E only (no paper) | not run | none | Mammoth DETECTR COVID-19 assay on OT-2. Robot work: CRISPR-Cas12 diagnostic (RNP prep + DETECTR reaction). |
+| [`dtu-synbio-automation`](https://github.com/DALSA-Lab/dtu_synbio_lab_automation) | S2 | P + D | not run | MIT | DTU Synbio lab automation protocol collection. Robot work: teaching/library protocols (agar plating, liquid-class optimisation, parameterised transfers). Reported result: No published results; teaching and internal-use repository. |
+| [`evotron-evolver-sampling`](https://www.nature.com/articles/s41467-022-32392-z) | S2 | P + D | not run | none | Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback. Robot work: automated sampling from eVOLVER bioreactors into plates. Reported result: Closed-loop optogenetic control held co-culture ratios at setpoints, measured by cytometry/OD from robot-sampled timepoints. |
+| [`exposomics-384-flex`](https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols) | S2 | P + D | not run | MIT | Opentrons Flex 384-well protein-precipitation sample preparation for nontargeted exposomics. Robot work: protein precipitation / dilution in 384-well format for LC-HRMS. Reported result: README reports up to 288 biological samples plus QC per plate feeding multiple LC-HRMS assays, but no peer-reviewed results found. |
+| [`flex-genomics-di-omics`](https://github.com/di-omics/ot-flex-automation) | S2 | P + D | not run | none | Opentrons Flex whole-genome / methylation / TIP-seq workflows (di-omics). Robot work: NGS library prep on Flex with off-deck handoffs. Reported result: README tracks validation status per protocol but no publication. |
+| [`hydrogel-crosslink-ot2`](https://github.com/JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-) | S2 | E only (no paper) | not run | none | Semi-autonomous synthesis and modelling of chemically cross-linked hydrogels (OT-2). Robot work: materials: hydrogel formulation synthesis. |
+| [`imperial-colony-picker`](https://github.com/Imperial-Opentrons-Users/automated-colony-picker) | S2 | P + D | not run | none | Automated colony picker add-on for the OT-2 (Imperial SSB MRes; cited by Slowpoke). Robot work: colony PCR reagent prep and colony resuspension. Reported result: Vision-guided colony picking demonstrated on OT-2; results reported only in the project write-up and via the Slowpoke citation. |
+| [`ipsc-robot-pyhamilton`](https://doi.org/10.1101/2020.12.18.423371) | S2 | P + D | not run | none | Automated hiPSC culture and sample preparation for 3D live cell microscopy. Robot work: iPSC culture: media exchange, seeding, imaging scan. Reported result: Code implements Allen Institute iPSC culture protocols (bioRxiv 2020.12.18.423371); robot-specific results not in repo. |
+| [`krisp-sars2-pooling`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8423848/) | S2 | P + D | not run | MIT | Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. Robot work: SARS-CoV-2 hypercube sample pooling. Reported result: Infected samples reliably detected in pools of 27 and 81 with minimal sensitivity loss for individual Ct up to 32. |
+| [`metclo-ot2`](https://doi.org/10.1007/978-1-0716-0908-8_9) | S2 | P + D | not run | none | MetCloOT2: Automated MetClo assembly on Opentrons OT-2 (MSc project, based on Lin & O Callaghan 2018/2020). Robot work: DNA assembly (MetClo methylation-based Golden Gate). Reported result: Underlying MetClo method papers (NAR 2018; Methods Mol Biol 2020) report manual assembly results; OT-2 implementation is an MSc project without published validation. |
+| [`myrplate-flex-casting`](https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15) | S2 | P + D | not run | MIT | myrPlate engineered connective tissue casting on Opentrons Flex. Robot work: collagen/cell suspension casting into 48-well tissue plates. Reported result: README describes casting engineered connective tissues; no publication located. |
+| [`nioz-ot2-database`](https://github.com/MolLabNIOZ/OT2) | S2 | E only (no paper) | not run | none | MolLabNIOZ/OT2 protocol database (NIOZ molecular ecology). Robot work: amplicon PCR setup, Qubit quantification, dilution, pooling. |
+| [`openblend-media`](https://doi.org/10.1002/bit.27947) | S2 | P + D | not run | MIT | Modular development enables rapid design of media for alternative hosts. Robot work: combinatorial media blending into microplates. Reported result: Blended media designs were tested in growth experiments for alternative microbial hosts, with growth rates reported per formulation. |
+| [`ot2-cherrypick`](https://chemrxiv.org/doi/full/10.26434/chemrxiv.15000637/v1) | S2 | P + D | not run | GPL-3.0 | OT2-CherryPick: A Zero-Install Web Platform for Orchestrating Complex Liquid Handling on the Opentrons OT-2. Robot work: CSV-driven cherry-picking / liquid transfer generator. Reported result: ChemRxiv preprint describing a GUI/CSV cherry-picking platform; validation is mainly simulation/operational, check for gravimetric data. |
+| [`ot2-yeast-spot-assay`](https://doi.org/10.1016/j.slast.2022.12.001) | S2 | P + D | not run | none | Automation of yeast spot assays using an affordable liquid handling robot. Robot work: yeast serial dilution spot assay on agar (3D-printed Petri mount, z-adjust). Reported result: Automated spot assays of budding yeast reproduced manual growth phenotypes, imaged with a flatbed scanner (spot intensity quantified). |
+| [`pac832-galr1-ot2`](https://github.com/douglasyao/pac-832-supplementary-data) | S2 | E only (no paper) | not run | none | PAC-832: A selective small-molecule antagonist of galanin receptor 1 (GalR1) - supplementary data and OT-2 protocols. Robot work: cell-based GPCR pharmacology assays (cAMP, acetylcholine release) dose-response plating. Reported result: Repo includes raw and processed cAMP/ACh assay data for PAC-832 vs galanin; paper DOI not yet resolved (likely preprint). |
+| [`pasta-spatial`](https://pmc.ncbi.nlm.nih.gov/articles/PMC13539481/) | S2 | P + D | not run | none | PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology. Robot work: spatial proteomics staining (tyramide-oligo amplification cycles on slides). Reported result: High-plex protein and RNA codetection on FFPE tissue via cyclical tyramide-oligonucleotide amplification and imaging (Nature Methods figures). |
+| [`peg-solubility-assay`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8578320/) | S2 | P + D | not run | none | An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement. Robot work: protein solubility assay (PEG titration, plate prep and transfer). Reported result: Relative solubility of proteins/antibodies quantified from PEG-precipitation midpoints using ~200 ug material; accuracy compared against established methods. |
+| [`pozzo-ot2-doe`](https://github.com/pozzo-research-group/OT2Protocols) | S2 | P + D | not run | MIT | Pozzo group OT-2 design-of-experiments protocols. Robot work: formulation DoE sample preparation. Reported result: Results appear in separate group publications, not this repo. |
+| [`prism-protocol-gen`](https://doi.org/10.1039/d6dd00004e) | S2 | P + D | not run | MIT | PRISM: Protocol Refinement through Intelligent Simulation Modeling. Robot work: LLM protocol generation + simulation validation; PCR master mix/sample prep. Reported result: Digital Discovery 2026: LLM-generated, simulation-refined protocols executed on OT-2 (PCR prep). |
+| [`pvlab-solubility-dropcast-ot2`](https://github.com/PV-Lab/Robotic_Liquid_Handling) | S2 | E only (no paper) | not run | MIT | PV-Lab Robotic_Liquid_Handling (MIT AMLS OT-2 solubility testing / drop casting). Robot work: materials: solubility testing, thin-film drop casting. |
+| [`retro-10x-ot2`](https://github.com/retrobiosciences/opentrons-10x) | S2 | E only (no paper) | not run | none | OT-2 10x scRNA-seq library prep (Retro Biosciences). Robot work: 10x Genomics single-cell library prep. |
+| [`robotic-titration-cv-ot2`](https://doi.org/10.1039/d4dd00334a) | S2 | P + D | not run | MIT | High-throughput robotic colourimetric titrations using computer vision. Robot work: chemistry: colourimetric acid-base titration with webcam endpoint detection. Reported result: Digital Discovery paper reports titration accuracy vs manual/reference concentrations using OT-2 + webcam colour analysis. |
+| [`rtwizard-antigen-ot2`](https://github.com/BenHinnant/rtWIZARD) | S2 | E only (no paper) | not run | none | rtWIZARD: OT-2 running 42 rapid antigen tests in parallel. Robot work: lateral-flow rapid antigen test loading (ASF, PPA). |
+| [`sdl-enzyme-flex`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12503018/) | S2 | D (needs a written oracle) | not run | MIT | Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab. Robot work: self-driving enzymatic reaction optimisation (pH, temperature, cosubstrate). Reported result: ML-driven Opentrons Flex platform optimised enzymatic reaction conditions after >10,000 simulated campaigns selected the best algorithm; experimental campaigns improved activity. |
+| [`trypanosomatid-drug-combo-ot2`](https://github.com/FranAguero07/OT2_protocols) | S2 | E only (no paper) | not run | none | OT-2 protocols for drug combination screening (Trypanosomatics Lab, UNSAM). Robot work: drug dilution/combination matrix, cell lysis, 384-well transfer (luciferase readout). Reported result: README states protocols are described in the lab paper (not cited by DOI). |
+| [`vadr-vacuum-miniprep-flex`](https://doi.org/10.64898/2026.09.16.746974) | S2 | P + D | not run | none | An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2. Robot work: plasmid miniprep with 3D-printed vacuum manifold. Reported result: bioRxiv 2026 reports improved DNA isolation yields with the open-source vacuum manifold on Opentrons Flex (link between repo and preprint inferred from content/date; verify). |
+| [`viscous-liquid-bo-ot2`](https://doi.org/10.1039/d3dd00255a) | S2 | P + D | not run | MIT | Optimization of liquid handling parameters for viscous liquid transfers with pipetting robots, a sticky situation. Robot work: liquid-class optimisation (viscous liquids, gravimetric, Bayesian optimisation). Reported result: Digital Discovery 2024 reports gravimetric transfer error and speed after multi-objective BO for viscous liquids on OT-2 and Sartorius rLine. |
+| [`worm-food-preference`](https://github.com/slhogle/c_elegans_food_preference_protocol) | S2 | P + D | not run | GPL-3.0 | C. elegans food preference protocol (bacteria and worm spotting on OT-2). Robot work: spotting bacteria and worms onto agar plates. Reported result: Protocol reproduces a published behavioural assay; no new results in the repo. |
+| [`agentex-genetic-codes`](https://doi.org/10.1038/s41586-026-10949-y) | S3 | P + D | not run | none | Automated prototyping of genetic codes. Robot work: in vitro translation reaction assembly, RNA purification. Reported result: Automated prototyping produced and characterised reassigned genetic codes with mass-spec/translation readouts. |
+| [`bean-kasp-anthracnose`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10546687/) | S3 | P + D | not run | none | Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR. Robot work: plant DNA extraction + KASP/PACE allele-specific PCR genotyping. Reported result: Automated DNA extraction and KASP assays genotyped common bean lines at four anthracnose resistance markers with clear allele clustering, matching expected genotypes. |
+| [`cfrna-pipeline`](https://doi.org/10.1038/s41596-023-00855-2) | S3 | P + D | not run | none | An inexpensive semi-automated sample processing pipeline for cell-free RNA (extraction). Robot work: cell-free RNA extraction and cleanup. Reported result: RNA yields and sequencing library quality from the semi-automated pipeline compared with manual extraction. |
+| [`damplab-taqpath-ot2`](https://doi.org/10.17504/protocols.io.brhvm366) | S3 | P + D | not run | none | Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex RT-PCR (BU DAMP Lab). Robot work: MagMAX RNA extraction + TaqPath RT-qPCR setup. |
+| [`har1eyk-starlet-protein-extraction`](https://github.com/har1eyk/hamilton-starlet-scripts) | S3 | E only (no paper) | not run | none | hamilton-starlet-scripts (PyLabRobot STARlet protein extraction / Orange G volume tests). Robot work: protein extraction; volume QC (Orange G). |
+| [`opentrons-covid19-dev`](https://www.protocols.io/groups/opentrons-covid19-testing/publications) | S3 | P + D | not run | Apache-2.0 | Opentrons/covid19 (OT-2 COVID-19 RT-qPCR station development repo, Opentrons + Open Medicine Institute). Robot work: SARS-CoV-2 RNA extraction + RT-qPCR setup stations A/B/C. Reported result: Experiment folders contain LOD/contamination study notes; formal results only on protocols.io, no peer-reviewed paper. |
+| [`ot2-proteomics-thesis`](https://github.com/martineingolfsrud/Opentrons-OT-2-performance-assessment) | S3 | E only (no paper) | not run | none | Automated Versus Manual Proteomics Sample Preparation: A Comparative Evaluation of Liquid Handling Workflows (MSc thesis). Robot work: proteomics: BCA assay + SP3 digestion. Reported result: Thesis raw data in repo comparing OT-2 vs human BCA/SP3 performance; not peer reviewed. |
+| [`tape-organoid-barcoding`](https://doi.org/10.1038/s41592-020-0737-8) | S3 | P + D | not run | none | Cell-type-specific signaling networks in heterocellular organoids (TOBis barcoding / robotic organoid extraction). Robot work: mass-cytometry barcode production/aliquoting, organoid extraction. Reported result: TOBis barcoded organoids profiled by mass cytometry; signalling networks resolved per cell type. |
+| [`ufdutton-16s-flex`](https://github.com/UFDuttonLab/lab_automation_opentrons) | S3 | E only (no paper) | not run | none | UF Dutton Lab Opentrons 16S microbiome workflow (OT-2 + Flex). Robot work: microbiome DNA extraction + 16S/shotgun library prep. |
+| [`ht-hcr-sea-urchin`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12516323/) | S4 | P + D | not run | none | Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos. Robot work: whole-mount in situ HCR on embryos in 96-well plates. Reported result: Processed 192 probe sets in 32 h; produced localisation data for 101 genes across three developmental stages. |
+| [`tmt-bead-platform-ot2`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8210952/) | S4 | D (needs a written oracle) | not run | n/a (no repo) | A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation. Robot work: TMTpro isobaric-tag proteomics sample prep. Reported result: Robot-prepared TMTpro16-plex triplicates quantified similar numbers of proteins/peptides with good reproducibility vs manual. |
+| [`ai4pd-flex-protein-purification`](https://github.com/AI4PDLab/Opentrons_Flex_Protocols) | S5 | E only (no paper) | not run | MIT | Opentrons Flex protein purification and molecular biology scripts (AI4PD Lab). Robot work: protein expression, Ni-NTA purification, TEV digestion, Golden Gate, miniprep. |
+| [`amplicon-seq-bisanz`](https://github.com/jbisanz/AmpliconSeq) | S5 | E only (no paper) | not run | none | AmpliconSeq (16S amplicon library OT-2 scripts, Bisanz lab). Robot work: 16S amplicon library prep (extraction wash, PCR, indexing, pooling, AMPure). |
+| [`angelovangel-ot2-ngs`](https://github.com/angelovangel/opentrons) | S5 | E only (no paper) | not run | none | angelovangel/opentrons (KAUST Bioscience core NGS/Sanger OT-2 + Flex protocols). Robot work: Sanger PCR setup, ONT rapid library, DNA normalisation, PacBio Kinnex PCR. |
+| [`biomationscripter`](https://biomationscripterlib.readthedocs.io) | S5 | P + D | not run | MIT | BiomationScripter: Python library for scripting bio-automation protocols. Robot work: protocol-generation library (templates for PCR, dilution, transformation). Reported result: No wet-lab results tied to a publication found. |
+| [`ecoli-protein-expr-purif-ot2`](https://github.com/nortonbakerbc/opentrons) | S5 | E only (no paper) | not run | none | OT-2 assisted recombinant protein expression and purification in E. coli (Norton-Baker). Robot work: protein expression: transformation, inoculation, lysis, purification transfers. Reported result: README says protocols are described in a paper (citation not resolved in README head); likely reports expression/purification yields. |
+| [`evogen-ot-library`](https://github.com/anttonalberdi/EvoGenOT) | S5 | E only (no paper) | not run | none | EvoGenOT (UCPH EvoGenomics Opentrons protocol library). Robot work: DNA/RNA co-extraction (D-Rex), BEST library build, bead purification. |
+| [`locost-covid-nanopore-ot2`](https://github.com/JDMirza/Opentrons_LoCost_Covid19) | S5 | E only (no paper) | not run | none | Opentrons_LoCost_Covid19 (ARTIC LoCost nanopore library prep on OT-2). Robot work: SARS-CoV-2 nanopore library prep (dilution, end-repair, barcode ligation, pooling). |
+| [`ot2-moclo-jove`](https://github.com/emernic/OT2_MoClo_JoVE) | S5 | E only (no paper) | not run | MIT | Modular Cloning with the OT2 (OT2_MoClo_JoVE). Robot work: MoClo Golden Gate, heat-shock transformation, plating, colony picking, bead miniprep. Reported result: Repo targets a JoVE article (not resolved in Crossref); JoVE articles typically include representative results. |
+| [`parseq-pyhamilton`](https://doi.org/10.1101/2023.12.12.571337) | S5 | P + D | not run | none | parSEQ: Probe and Rescue Sequencing for Advanced Variant Retrieval from DNA Pool. Robot work: variant library sequencing pipeline: barcoding PCR, cherry picking, Illumina/nanopore library prep. Reported result: bioRxiv 2023 parSEQ preprint reports retrieval of sequence-verified variants from pooled DNA libraries using the Hamilton pipeline. |
+| [`polar-sarscov2-ot2`](https://doi.org/10.17504/protocols.io.bearjad6) | S5 | P + D | not run | MIT | POLAR: Pathogen-Oriented Low-cost Assembly & Re-sequencing SARS-CoV-2 (OT-2 automation). Robot work: viral RNA magbead extraction + SARS-CoV-2 amplicon library prep. |
+| [`pudu-synbio-ot2`](https://github.com/RudgeLab/PUDU) | S5 | E only (no paper) | not run | MIT | PUDU (Protocol Unified Design Unit) - OT-2 synthetic biology workflows. Robot work: Golden Gate / Loop assembly, transformation, plating, iGEM GFP/OD calibration. |
+| [`roborna-nirvana`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10663496/) | S5 | P + D | not run | none | An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Robot work: SARS-CoV-2 magnetic-bead RNA extraction + RT-qPCR + nanopore variant sequencing. Reported result: Automated extraction showed high reproducibility with no cross-contamination; limit of detection, sensitivity and specificity comparable to commercial assays; NIRVANA identified circulating variants. |
+| [`a-lab-2023`](https://www.nature.com/articles/s41586-023-06734-w) | SD | P + D | not run | none (ARROWS); see repos | An autonomous laboratory for the accelerated synthesis of novel materials (A-Lab). Robot work: Self-driving lab campaign. Reported result: Claimed 41/58 novel compounds synthesized in 17 days (phase claims later contested). |
+| [`ada-thin-films`](https://www.science.org/doi/10.1126/sciadv.aaz8867) | SD | P + D | not run | MIT | Self-driving laboratory for accelerated discovery of thin-film materials (Ada). Robot work: Self-driving lab campaign. Reported result: Optimised hole-transport-layer pseudomobility via closed-loop BO; data released per campaign. |
+| [`afion-plasmonic`](https://www.nature.com/articles/s41467-025-56788-9) | SD | P + D | not run | none | Self-driving lab for the photochemical synthesis of plasmonic nanoparticles (AFION). Robot work: Self-driving lab campaign. Reported result: Targeted Ag nanoparticle morphologies/spectra achieved autonomously with reported spectra. |
+| [`ahtech-electrochem`](https://www.science.org/doi/10.1126/sciadv.adu4391) | SD | P + D | not run | MIT | A high-throughput experimentation platform for data-driven discovery in electrochemistry (AHTech). Robot work: Self-driving lab campaign. Reported result: Thousands of CVs on redox mediators with discovered reactivity trends reported. |
+| [`bear-mechanics`](https://www.nature.com/articles/s41467-024-48534-4) | SD | P + D | not run | (LICENSE present,… | Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership (BEAR). Robot work: Self-driving lab campaign. Reported result: Record 75% energy-absorbing efficiency structures discovered; >25,000 experiments. |
+| [`chemcrow`](https://www.nature.com/articles/s42256-024-00832-8) | SD | P + D | not run | MIT | Augmenting large language models with chemistry tools (ChemCrow). Robot work: Self-driving lab campaign. Reported result: Executed syntheses of DEET and three thioureas plus a chromophore on RoboRXN, with characterisation. |
+| [`chemputer-modules-acscs`](https://pubs.acs.org/doi/10.1021/acscentsci.3c00304) | SD | P + D | not run | unverified | Robotic Modules for the Programmable Chemputation of Molecules and Materials. Robot work: Self-driving lab campaign. Reported result: Several syntheses executed on new modules with yields reported. |
+| [`clio-electrolytes`](https://www.nature.com/articles/s41467-022-32938-1) | SD | P + D | not run | none | Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation (Clio). Robot work: Self-driving lab campaign. Reported result: Found electrolyte with 13% higher conductivity in 42 experiments; pouch-cell validation. |
+| [`helao-async`](https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00193h) | SD | P + D | not run | MIT | HELAO-async: autonomous electrochemistry/high-throughput experimentation orchestration (Caltech/TRI). Robot work: Self-driving lab campaign. Reported result: Used for autonomous electrocatalyst/OER composition screening with reported datasets. |
+| [`organa`](https://arxiv.org/abs/2401.06949) | SD | P + D | not run | none | ORGANA: a robotic assistant for automated chemistry experimentation and characterization. Robot work: Self-driving lab campaign. Reported result: Solubility, pH, recrystallisation and electrochemistry (quinone) experiments executed with reported user-study times and measured values. |
+| [`polybot-pedot`](https://www.nature.com/articles/s41467-024-55655-3) | SD | P + D | not run | MIT | Autonomous platform for solution processing of electronic polymers (Polybot). Robot work: Self-driving lab campaign. Reported result: Autonomously optimised PEDOT:PSS film conductivity/defects over closed-loop campaigns; conductivities reported. |
+| [`raft-polymerization-platform`](https://pubs.rsc.org/en/content/articlehtml/2023/dd/d2dd00100d) | SD | P + D | not run | check Zenodo | A fully automated platform for photoinitiated RAFT polymerization. Robot work: Self-driving lab campaign. Reported result: Automated photo-RAFT polymerisations with Mn/Đ characterisation reported. |
+| [`robochem`](https://www.science.org/doi/10.1126/science.adj1817) | SD | P + D | not run | MIT | Automated self-optimization, intensification, and scale-up of photocatalysis in flow (RoboChem). Robot work: Self-driving lab campaign. Reported result: 19 photocatalytic transformations self-optimised; yields often exceeded literature. |
+| [`solubility-hein`](https://www.cell.com/iscience/fulltext/S2589-0042(21)00144-0) | SD | P + D | not run | unverified | Automated solubility screening platform using computer vision. Robot work: Self-driving lab campaign. Reported result: Solubility of compounds determined by CV turbidity with comparison to HPLC. |
+
+## No (58)
+
+| Candidate | Level | Spec | Simulator | Licence | Description |
+|---|---|---|---|---|---|
+| [`bio-spec-hardwarex`](https://www.sciencedirect.com/science/article/pii/S2468067225000690) | BR | D (needs a written oracle) | not run | CC BY (hardware, per… | BIO-SPEC: An open-source bench-top parallel bioreactor system. Robot work: Closed-loop culture control. Reported result: Validation growth experiments reported in HardwareX. |
+| [`takahashi-turbidostat`](https://pubs.acs.org/doi/10.1021/sb500165g) | BR | D (needs a written oracle) | not run | unverified | A low cost, customizable turbidostat for use in synthetic circuit characterization. Robot work: Closed-loop culture control. Reported result: Circuit characterisation in turbidostats with growth/fluorescence data. |
+| [`archemist`](https://arxiv.org/abs/2204.13571) | OR | D (needs a written oracle) | not run | unverified | ARChemist: Autonomous Robotic Chemistry System Architecture (Fakhruldeen et al.). Robot work: Workcell orchestration / scheduling. Reported result: Solubility screening and crystallisation workflows demonstrated. |
+| [`mobile-robot-burger-2020`](https://www.nature.com/articles/s41586-020-2442-2) | OR | D (needs a written oracle) | not run | n/a | A mobile robotic chemist (Burger et al.). Robot work: Workcell orchestration / scheduling. Reported result: 688 experiments over 8 days found photocatalyst mixtures 6x more active. |
+| [`adept-framework`](https://www.nature.com/articles/s42004-026-01932-9) | OT | D (needs a written oracle) | not run | n/a | The ADePT framework for assessing autonomous laboratory robotics. Robot work: Other automation. Reported result: Assessment framework; useful for rubric design, not tasks. |
+| [`autopots-proteome`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8140400/) | OT | D (needs a written oracle) | not run | n/a (no repo) | Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling. Robot work: Other automation. Reported result: autoPOTS quantified proteomes from low-input/single-cell-scale samples using an unmodified low-cost pipetting robot. |
+| [`autorelacs`](https://pmc.ncbi.nlm.nih.gov/articles/PMC7381599/) | OT | D (needs a written oracle) | not run | MIT | AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq. Robot work: Other automation. Reported result: AutoRELACS generated ChIP-seq data comparable to the manual RELACS protocol across many samples. |
+| [`baybe`](https://pubs.rsc.org/en/content/articlehtml/2025/dd/d5dd00050e) | OT | P + D | not run | Apache-2.0 | BayBE: Bayesian Back End for design of experiments. Robot work: Other automation. Reported result: Campaign API with benchmarks; industrial case studies reported, few with released wet-lab data. |
+| [`bioclonebot`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10955647/) | OT | D (needs a written oracle) | not run | see OSF (HardwareX requires… | BioCloneBot: A versatile, low-cost, and open-source automated liquid handler. Robot work: Other automation. Reported result: Validated accuracy and repeatability across liquid handling tasks. |
+| [`catib-screening`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10894497/) | OT | D (needs a written oracle) | not run | GPL-3.0 | "High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization". Robot work: Other automation. Reported result: Generated 63 BsGDH CatIB variants; automated screening workflow validated and used to rank variant activities in parallel. |
+| [`diy-ot-linear-motion-qpcr`](https://pmc.ncbi.nlm.nih.gov/articles/PMC7424513/) | OT | D (needs a written oracle) | not run | n/a (no repo) | Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting. Robot work: Other automation. Reported result: Benchmarking showed micropipetting speed/positional accuracy adequate for qPCR setup reproducibility. |
+| [`diy-stem-lhr`](https://pmc.ncbi.nlm.nih.gov/articles/PMC9645590/) | OT | D (needs a written oracle) | not run | n/a (no repo) | DIY liquid handling robots for integrated STEM education and life science research. Robot work: Other automation. Reported result: Qualitative teacher study plus demonstration experiments. |
+| [`egf-sequeduct`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10877595/) | OT | D (needs a written oracle) | not run | GPL-3.0 | Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing. Robot work: Other automation. Reported result: Biofoundry-scale validation of assembled plasmids via nanopore long-read sequencing with automated reports. |
+| [`evobot`](https://doi.org/10.1177/2472630316689285) | OT | D (needs a written oracle) | not run | n/a (no repo) | New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot. Robot work: Other automation. Reported result: New capabilities demonstrated for long-running artificial-life experiments. |
+| [`findus`](https://doi.org/10.1177/2472630319877374) | OT | D (needs a written oracle) | not run | GPL-3.0 | FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences. Robot work: Other automation. Reported result: Pipetting errors <0.3%; showcase biology and chemistry applications. |
+| [`flyspresso-embryo-ihc`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8119710/) | OT | D (needs a written oracle) | not run | not checked | An open-source semi-automated robotics pipeline for embryo immunohistochemistry. Robot work: Other automation. Reported result: Automated embryo fixation, colorimetric/antibody staining and adaptive confocal imaging demonstrated. |
+| [`illumina-dnaprep-flowbot`](https://pmc.ncbi.nlm.nih.gov/articles/PMC11001922/) | OT | D (needs a written oracle) | not run | n/a (no repo) | Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot. Robot work: Other automation. Reported result: Automated libraries had comparable yields (median 1.5-fold diff), similar assembly quality and 100% cgMLST concordance; hands-on time 25 vs 125 min. |
+| [`labdroid-phenol-chloroform`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8931447/) | OT | D (needs a written oracle) | not run | CC-BY-4.0 | Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing. Robot work: Other automation. Reported result: Routine extraction of >100 kb gDNA from algae, bacteria, insects and human cells; validated by pulse-field electrophoresis and nanopore read N50. |
+| [`lego-lhr-stem`](https://pmc.ncbi.nlm.nih.gov/articles/PMC5360201/) | OT | D (needs a written oracle) | not run | n/a (no repo) | Liquid-handling Lego robots and experiments for STEM education and research. Robot work: Other automation. Reported result: Activities tested with school students; build and experiment instructions provided. |
+| [`maple-fly-robot`](https://pmc.ncbi.nlm.nih.gov/articles/PMC6193762/) | OT | D (needs a written oracle) | not run | not checked | MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping. Robot work: Other automation. Reported result: Automated virgin collection and social-behaviour experiments revealing persistent idiosyncrasies. |
+| [`miniaturized-16s-mosquito`](https://pmc.ncbi.nlm.nih.gov/articles/PMC6222042/) | OT | D (needs a written oracle) | not run | protocols.io (CC-BY) | High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. Robot work: Other automation. Reported result: Miniaturised 5 uL reactions matched standard 25 uL composition; validated on 46 fish x 5 body sites over seven months. |
+| [`mngs-384-miniaturized`](https://pmc.ncbi.nlm.nih.gov/articles/PMC6328170/) | OT | D (needs a written oracle) | not run | n/a (no repo) | Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. Robot work: Other automation. Reported result: ERCC spike-ins showed miniaturised prep fidelity equivalent to full-volume preps at much lower cost/time. |
+| [`pipette-show`](https://pubs.acs.org/doi/10.1021/acssynbio.1c00494) | OT | P + D | not run | MIT | Pipette Show: An Open Source Web Application to Support Pipetting into Microplates. Robot work: Other automation. Reported result: Error rates for manual plate filling with vs without the app. |
+| [`polymer-protein-hybrids`](https://onlinelibrary.wiley.com/doi/10.1002/adma.202201809) | OT | P + D | not run | none | Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids. Robot work: Other automation. Reported result: Enzyme-stabilising copolymers designed and assayed. |
+| [`proteoautonet`](https://doi.org/10.1038/s41467-026-68484-3) | OT | P + D | not run | none | ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning. Robot work: Other automation. Reported result: Co-elution networks derived from robot-processed samples validated against known complexes. |
+| [`snails-slow-pipetting`](https://pmc.ncbi.nlm.nih.gov/articles/PMC7953553/) | OT | D (needs a written oracle) | not run | none | Consistent ultra-long DNA sequencing with automated slow pipetting. Robot work: Other automation. Reported result: Across six libraries SNAILS preserved more >100 kb reads and increased average read length vs manual slow pipetting. |
+| [`summit-flow`](https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmtd.202000051) | OT | P + D | not run | MIT | Summit: benchmarking machine learning methods for reaction optimisation. Robot work: Other automation. Reported result: Emulators trained on literature flow-chemistry data; no new wet-lab experiments. |
+| [`tox-pipetting-robot`](https://pmc.ncbi.nlm.nih.gov/articles/PMC5473567/) | OT | D (needs a written oracle) | not run | n/a (no repo) | A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays. Robot work: Other automation. Reported result: Tested precision of automated pipetting for online toxicity bioassays. |
+| [`transfection-reagent-agnostic`](https://doi.org/10.1002/cpz1.968) | OT | D (needs a written oracle) | not run | n/a (no repo) | A Novel, Fully Automated, and Reagent-Agnostic Transient Transfection Protocol. Robot work: Other automation. Reported result: HeLa transfection efficiency 40.9-73.3% and A549 42.2-54%, comparable to manual. |
+| [`endylab-opentrons`](https://github.com/EndyLab/opentrons) | S1 | P + D | not run | none | Endy Lab Opentrons protocol collection. Robot work: PCR setup, dilution series, calibration. Reported result: No linked publication. |
+| [`kedar-balance-integration`](https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance) | S1 | P + D | not run | none | Opentrons OT-2 mass-balance integration (application note supplement). Robot work: gravimetric calibration with external balance. Reported result: Gravimetric accuracy of dispensed volumes reported in the application note. |
+| [`cellfree-biosensor-ot2`](https://doi.org/10.1021/acssynbio.4c00703) | S2 | D (needs a written oracle) | not run | n/a (no repo) | Semiautomated Production of Cell-Free Biosensors. Robot work: cell-free biosensor reaction assembly (LacZ colorimetric / fluorescent). Reported result: Compared manual vs semi-automated OT-2 assembly of cell-free reactions; robotic assembly reduced variability in colorimetric and fluorescent outputs. |
+| [`combinatorial-barcode-dna`](https://pmc.ncbi.nlm.nih.gov/articles/PMC9917336/) | S2 | D (needs a written oracle) | not run | CC-BY-4.0 | Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications. Robot work: oligo mixing for combinatorial DNA barcode library assembly. Reported result: Built 256- and 512-member modular barcode libraries from <50 oligos; OT-2 used for oligo mixing in Gen_2 library. |
+| [`covid-fosh-review`](https://pmc.ncbi.nlm.nih.gov/articles/PMC9521367/) | S2 | D (needs a written oracle) | not run | unknown | High-throughput and automated screening for COVID-19. Robot work: review of open-source automated COVID-19 testing. Reported result: Review of case studies (China, Spain, UK); no new wet-lab data. |
+| [`curcumin-formulation-sdl`](https://pmc.ncbi.nlm.nih.gov/articles/PMC13576497/) | S2 | D (needs a written oracle) | not run | none | Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator. Robot work: drug formulation solubility screening (excipient mixing). Reported result: Found 7 curcumin formulations with solubility >10 mg/mL after sampling 256 of 7776 candidates. |
+| [`duckweed-hte`](https://pmc.ncbi.nlm.nih.gov/articles/PMC10361482/) | S2 | D (needs a written oracle) | not run | MIT | Accelerated high-throughput imaging and phenotyping system for small organisms. Robot work: modified OT-2 loading duckweed into well plates for plant-microbe growth phenotyping. Reported result: Study of 6,000 experimental units across 2,000 treatments with time-resolved growth data; system scales to 11,520 units. |
+| [`gpcr-livecell-ot2`](https://pmc.ncbi.nlm.nih.gov/articles/PMC9994309/) | S2 | D (needs a written oracle) | not run | n/a (no repo) | GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System. Robot work: automated compound addition during live-cell cAMP imaging. Reported result: Measured GPR68 cAMP dynamics vs extracellular pH and ogerin modulation using OT-2-integrated microscopy. |
+| [`hydra-hydrogel-plates`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12749810/) | S2 | D (needs a written oracle) | not run | none | Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing. Robot work: hydrogel coating of 96/384-well plates for cell culture HTS. Reported result: HYDRA produced meniscus-free hydrogel coatings validated by imaging-based anticancer dose-response assays and long-term microscopy. |
+| [`marchantia-agro-transformation`](https://pmc.ncbi.nlm.nih.gov/articles/PMC11993085/) | S2 | D (needs a written oracle) | not run | n/a (no repo) | Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation. Robot work: Agrobacterium-mediated plant (Marchantia) transformation. Reported result: Semi-automated protocol showed transformation efficiency similar to manual manipulation. |
+| [`mxene-aerogel-al`](https://pmc.ncbi.nlm.nih.gov/articles/PMC11144242/) | S2 | D (needs a written oracle) | not run | none (data Zenodo… | Machine intelligence accelerated design of conductive MXene aerogels with programmable properties. Robot work: materials mixture preparation (MXene/CNF/gelatin) for active learning. Reported result: OT-2 prepared 264 mixtures; 162 conductive aerogels fabricated/characterised over 8 active-learning cycles to train an ANN for inverse design. |
+| [`newcastle-neg-opentrons`](https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons) | S2 | P + D | not run | none | Newcastle Network Ecology Group OT-2 protocol and labware collection. Robot work: mixed lab protocols and custom labware definitions. Reported result: No linked publication found. |
+| [`nfkb-luciferase-ot2`](https://doi.org/10.1016/j.slast.2024.100155) | S2 | D (needs a written oracle) | not run | n/a (no repo) | Luciferase reporter assay for NF-kB activation automated by an open-source liquid handling platform. Robot work: cell seeding, transfection and luciferase reporter assay. Reported result: OT-2 Python protocols for HeLa seeding, NF-kB reporter transfection and luciferase readout gave quantifiable activation signals with good sample-handling quality. |
+| [`opentrons-physicalai-hf`](https://huggingface.co/datasets/Opentrons/PhysicalAI) | S2 | P + D | not run | unstated | Opentrons/PhysicalAI (Hugging Face dataset of Flex teleoperation episodes). Robot work: Flex plate-handoff manipulation episodes (imitation learning data). Reported result: Inference session summaries record on-robot execution of plate handoffs to a BioTek reader. |
+| [`ot2eye`](https://doi.org/10.1016/j.slast.2026.100410) | S2 | D (needs a written oracle) | not run | MIT | OT2Eye: Detection of labware conditions to monitor and extend affordable liquid-handling robots. Robot work: labware/tip detection from OT-2 camera images. Reported result: High accuracy identifying plates and tip racks and their deck positions, and tip presence/absence. |
+| [`plastic-substitutes-al`](https://pmc.ncbi.nlm.nih.gov/articles/PMC11186784/) | S2 | D (needs a written oracle) | not run | BSD | Machine intelligence-accelerated discovery of all-natural plastic substitutes. Robot work: nanocomposite film mixture preparation for active learning. Reported result: OT-2 prepared 286 CNF/MMT/gelatin/glycerol nanocomposites to train models discovering all-natural plastic substitutes. |
+| [`pr-pr`](https://doi.org/10.1021/sb4001728) | S2 | D (needs a written oracle) | not run | n/a (no repo) | PR-PR: cross-platform laboratory automation system. Robot work: cross-platform protocol language (Golden Gate, Kunkel mutagenesis, Gibson). Reported result: Modified Golden Gate assembly run across liquid-handling robot, microfluidic and manual platforms; Kunkel and Gibson also implemented. |
+| [`radiolabeling-psma-ot2`](https://doi.org/10.1002/jlcr.4085) | S2 | D (needs a written oracle) | not run | n/a (no repo) | Automated radiolabeling and handling of 177 Lu- and 225 Ac-PSMA-617 using a robotic pipettor. Robot work: radiochemistry (177Lu/225Ac-PSMA-617 labelling). Reported result: Robotic pipettor performed radiometal labelling with reduced operator exposure and synthesis times (radiochemical yields/purity reported). |
+| [`synthetic-cells-robotics`](https://pmc.ncbi.nlm.nih.gov/articles/PMC12078883/) | S2 | D (needs a written oracle) | not run | unknown (repo not found) | Scaling Up Synthetic Cell Production Using Robotics and Machine Learning Toward Therapeutic Applications. Robot work: synthetic cell production scale-up. Reported result: Robotic scale-up increased synthetic-cell batch size 30-fold; luciferase SCs monitored in mice. |
+| [`xchem-opentrons`](https://github.com/xchem/opentrons) | S2 | P + D | not run | Apache-2.0 | XChem Opentrons reaction liquid-handling toolkit. Robot work: reaction dispensing arrays for crystallographic screening. Reported result: No single paper ties these scripts to reported results. |
+| [`swabseq-flex`](https://doi.org/10.1016/j.diagmicrobio.2026.117519) | S3 | D (needs a written oracle) | not run | n/a (no repo) | Automated implementation of the SwabSeq COVID-19 diagnostic assay on the opentrons flex liquid-handling robot. Robot work: SwabSeq NGS COVID-19 diagnostic (RT-PCR barcoding, pooling, SPRI cleanup). Reported result: Flex workflow completed in ~2.5 h with complete agreement on negatives, very high agreement on positives and no discordant calls vs manual. |
+| [`bead-digestion-ann`](https://doi.org/10.1016/j.talanta.2024.125988) | S4 | D (needs a written oracle) | not run | n/a (no repo) | Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Robot work: proteomics paramagnetic bead digestion. Reported result: ANN-optimised OT-2 bead digestion showed high reproducibility across plasma, Arabidopsis, E. coli and mouse cortex; identified 385 unique rat bile proteins. |
+| [`kitfree-rna-extraction`](https://pmc.ncbi.nlm.nih.gov/articles/PMC8636496/) | S4 | D (needs a written oracle) | not run | n/a (no repo) | A high-throughput pipeline for scalable kit-free RNA extraction. Robot work: kit-free magnetic-bead RNA extraction for SARS-CoV-2 RT-qPCR. Reported result: Semi-automated kit-free extraction validated by SARS-CoV-2 RT-qPCR without loss of diagnostic sensitivity/accuracy. |
+| [`protein-corona-ot2`](https://pmc.ncbi.nlm.nih.gov/articles/PMC7483600/) | S4 | D (needs a written oracle) | not run | n/a (no repo) | Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data. Robot work: protein corona formation and magnetic isolation for proteomics. Reported result: Automated corona isolation with magnetic-core nanoparticles; compared low-cost proteomics workflows. |
+| [`sp3-magbead-protocol-repo`](https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol) | S4 | P + D | not run | MIT | Automated magnetic bead-based digestion protocols for Opentrons OT-2 (proteomics CNB-CBM). Robot work: SP3 bead digestion. Reported result: None published. |
+| [`ai-chemist-ustc`](https://academic.oup.com/nsr/article/9/10/nwac190/6694179) | SD | D (needs a written oracle) | not run | n/a | An all-round AI-Chemist with a scientific mind. Robot work: Self-driving lab campaign. Reported result: OER catalysts discovered autonomously. |
+| [`aurora-materials`](https://pubs.acs.org/doi/10.1021/acsami.5c02605) | SD | P + D | not run | vendor | AURORA - An Automatic Robotic Platform for Materials Discovery. Robot work: Self-driving lab campaign. Reported result: Electrochemical materials screening reported. |
+| [`cloudlab-chiral-perovskite`](https://www.nature.com/articles/s41467-020-15728-5) | SD | D (needs a written oracle) | not run | n/a | Autonomous discovery of optically active chiral inorganic perovskite nanocrystals through an intelligent cloud lab. Robot work: Self-driving lab campaign. Reported result: Chiral perovskite NCs with CD responses discovered. |
+| [`sdl-nano-acsnano`](https://pubs.acs.org/doi/10.1021/acsnano.4c17504) | SD | D (needs a written oracle) | not run | n/a | A Self-Driving Lab for Nano- and Advanced Materials Synthesis. Robot work: Self-driving lab campaign. Reported result: Perspective/platform review. |
diff --git a/research/expansion/DOCKER_SIM.md b/research/expansion/DOCKER_SIM.md
new file mode 100644
index 0000000..8ab8541
--- /dev/null
+++ b/research/expansion/DOCKER_SIM.md
@@ -0,0 +1,82 @@
+# Simulating the experimental candidates in Docker (2026-10-13)
+
+Image `t2w-sim` (`docker/sim/`): Opentrons 7.5.0 (the benchmark's grader version) and PyLabRobot 0.2.2.
+Protocols ran with `--network none`, read-only code and a non-root user. Each repo's custom labware JSON was passed to the simulator.
+
+**795 Opentrons protocol files in 69 repos: 203 pass `opentrons_simulate`, 592 fail.** 32 repos have at least one passing protocol.
+
+Hamilton: the har1eyk STARlet Automated Protein Extraction protocol (PyLabRobot) runs end to end on PyLabRobot's simulated backend (`docker/sim/hamilton_ape.py`): 936 liquid moves, 164 tip pickups, 10 CoRe-gripper plate moves to the magnet and back.
+
+3D replay videos (not committed) are rendered on the host with `tools/replay_candidate.py` and `tools/hamilton_replay.py`.
+
+| Repo | Pass | Fail |
+|---|---|---|
+| `tidytron` | 35 | 2 |
+| `gfp-codon-burden-ot2` | 21 | 21 |
+| `pvlab-solubility-dropcast-ot2` | 15 | 5 |
+| `angelovangel-ot2-ngs` | 13 | 9 |
+| `evogen-ot-library` | 13 | 12 |
+| `opentrons-covid19-dev` | 12 | 40 |
+| `nioz-ot2-database` | 11 | 191 |
+| `biomationscripter` | 8 | 11 |
+| `newcastle-neg-opentrons` | 8 | 26 |
+| `ant-cloning` | 7 | 3 |
+| `beckham-enzyme-pipeline` | 6 | 15 |
+| `dtu-synbio-automation` | 6 | 4 |
+| `ecoli-protein-expr-purif-ot2` | 6 | 15 |
+| `locost-covid-nanopore-ot2` | 6 | 0 |
+| `pudu-synbio-ot2` | 5 | 23 |
+| `artic-normalisation-esr` | 4 | 7 |
+| `massspecpreppy` | 3 | 7 |
+| `amplicon-seq-bisanz` | 2 | 3 |
+| `culturomics-isolation` | 2 | 9 |
+| `detectr-covid-ot2` | 2 | 0 |
+| `imperial-colony-picker` | 2 | 0 |
+| `jubiotech-ot2-autoclone` | 2 | 5 |
+| `msd-biochem-assays-ot2` | 2 | 0 |
+| `trypanosomatid-drug-combo-ot2` | 2 | 1 |
+| `ufdutton-16s-flex` | 2 | 15 |
+| `worm-food-preference` | 2 | 0 |
+| `damplab-taqpath-ot2` | 1 | 1 |
+| `exfab-qiaseq-flex` | 1 | 0 |
+| `hyrad-adna-capture` | 1 | 0 |
+| `labop` | 1 | 2 |
+| `openblend-media` | 1 | 1 |
+| `prism-protocol-gen` | 1 | 0 |
+| `ac-training-lab` | 0 | 1 |
+| `ai4pd-flex-protein-purification` | 0 | 7 |
+| `aliquot-niaid` | 0 | 13 |
+| `blots-ot2` | 0 | 1 |
+| `cayman-his-elisa` | 0 | 4 |
+| `ester-library-synthesis` | 0 | 3 |
+| `evotron-evolver-sampling` | 0 | 2 |
+| `exposomics-384-flex` | 0 | 2 |
+| `flat-agar-celegans-ot2` | 0 | 3 |
+| `flex-genomics-di-omics` | 0 | 10 |
+| `formulations-prep-shampoo` | 0 | 1 |
+| `greenaway-halogenation` | 0 | 9 |
+| `greenaway-mocs` | 0 | 5 |
+| `greenaway-pocs` | 0 | 6 |
+| `hydrogel-crosslink-ot2` | 0 | 1 |
+| `labscriptai-protein-eng` | 0 | 11 |
+| `llm-rdf-synthesis` | 0 | 1 |
+| `lucks-cellfree-biosensor` | 0 | 1 |
+| `lysostaphin-turbidity` | 0 | 1 |
+| `metclo-ot2` | 0 | 1 |
+| `myrplate-flex-casting` | 0 | 3 |
+| `ot2-cherrypick` | 0 | 1 |
+| `ot2-proteomics-thesis` | 0 | 12 |
+| `ot2-yeast-spot-assay` | 0 | 3 |
+| `pac832-galr1-ot2` | 0 | 31 |
+| `pasta-spatial` | 0 | 1 |
+| `peg-solubility-assay` | 0 | 2 |
+| `plant-phenotyping-ot2` | 0 | 2 |
+| `polar-sarscov2-ot2` | 0 | 2 |
+| `retro-10x-ot2` | 0 | 1 |
+| `roboctab` | 0 | 2 |
+| `robotic-titration-cv-ot2` | 0 | 3 |
+| `roche-pipetting-performance-ot2` | 0 | 2 |
+| `rtwizard-antigen-ot2` | 0 | 7 |
+| `sapp-dmx-protein-design` | 0 | 1 |
+| `tape-organoid-barcoding` | 0 | 7 |
+| `vadr-vacuum-miniprep-flex` | 0 | 1 |
diff --git a/research/expansion/SUMMARY.md b/research/expansion/SUMMARY.md
new file mode 100644
index 0000000..e4adc4e
--- /dev/null
+++ b/research/expansion/SUMMARY.md
@@ -0,0 +1,51 @@
+# Benchmark expansion: merged candidate search (2026-10-12)
+
+Four research passes looked for (paper, public robot code, reported wet-lab results) triples:
+web deep research (Europe PMC full text + GitHub), Amass BioMedCore full-text search (1,850 credits),
+a GitHub code sweep (2,271 repos, PyLabRobot first), and a non-liquid-handling pass (imaging,
+protocol languages, bioreactors, schedulers, arms). Per-source files: `*_candidates.jsonl`, `*_notes.md`.
+Merged and de-duplicated by DOI and GitHub repo: `merged_candidates.jsonl` (`found_by` lists the sources).
+
+## Counts
+
+| | Candidates |
+|---|---|
+| Raw rows across the 4 sources | 328 |
+| Unique after merging | 263 |
+| Already in the corpus (`docs/task-sources.md`) | 53 |
+| **New** | **210** |
+| New, ready | **44** (25 liquid handling, 19 non-liquid-handling) |
+| New, partial | 108 |
+| New, no usable code | 58 |
+| New and found by more than one source | 38 |
+
+"Ready" = open paper text + public code that should run in a simulator or dry-run as-is or with labware
+fixes + reported wet-lab results. It was judged from reading code; none of the new protocols has been run
+in `opentrons_simulate` yet. 9 of the 44 ready candidates have no or unclear code licence (reference-only).
+
+## How much bigger the benchmark could be
+
+Counting an easy + hard variant per experiment (2 tasks per candidate, conservative; the agents' own
+per-paper estimates are higher because many papers contain several experiments):
+
+| Scenario | Tasks | vs today |
+|---|---|---|
+| Today | 11 | 1x |
+| + 12 corpus papers that already have pipeline IR but no task (25 experiments) | ~61 | 5.5x |
+| + 44 new ready candidates | ~149 (agents' estimate ~251) | 14x (23x) |
+| + 108 new partial candidates | ~365 (agents' estimate ~458) | 33x (42x) |
+
+**Ready to execute on today's grader:** the 25 liquid-handling ready candidates (24 OT-2, 1 Flex) fit the
+existing Opentrons simulator + run-log grader, about 50 tasks. The 19 non-liquid-handling ready candidates
+(imaging, protocol languages such as XDL/LabOP, scheduling) need new graders.
+
+## Findings worth knowing
+
+- Code, not papers, is the bottleneck: Amass returned 4,019 papers, but most published robot protocols
+  never release the script. Recall levelled off (the last 20 queries added 4 papers).
+- PyLabRobot: about 50 public repos use it, but only one has a paper with wet-lab results
+  (Chory lab turbidostat, custom hardware, no licence). PLR tasks would need porting Opentrons/PyHamilton triples.
+- The Opentrons Protocol Library (833 protocols) cites no research papers, so it is not a source of triples.
+- Closest existing benchmark: AEGIS (24 MIT OT-2 protocols with injected bugs). LabScript-AI and the
+  KAISA-LSE GPT-generated-protocol study are related work.
+- Highest-value single find: Cronin lab ACRA, 100+ literature-to-XDL pairs executed on the Chemputer.
diff --git a/research/expansion/VERIFIED.md b/research/expansion/VERIFIED.md
new file mode 100644
index 0000000..5bd9b83
--- /dev/null
+++ b/research/expansion/VERIFIED.md
@@ -0,0 +1,39 @@
+# Simulator verification of the 25 ready liquid-handling candidates (2026-10-12)
+
+Each repo was shallow-cloned and every file with `def run` and an Opentrons import/apiLevel (max 15 per repo) was run
+through `opentrons_simulate` (Opentrons 7.5.0) in an empty temp dir with a 120 s timeout, with any custom labware JSON in the repo passed via `-L`.
+Files using network, shell or file-deletion calls would have been skipped; none did.
+
+**Result:** 128 protocol files found, 30 pass as-is, in 10 of 25 repos (3 fully, 7 partly). 14 repos fail every file; 1 had no protocol file.
+
+Failures (98 files): 43 custom labware referenced by an absolute path on the author's machine, 24 API version newer than 7.5 supports,
+15 extra Python packages, 5 missing input files (CSV/JSON), 10 other (indentation, index errors), 1 syntax.
+Most are fixable by vendoring the labware JSON and inputs, or by simulating with a newer Opentrons release.
+
+| Candidate | Status | Passed / run | Licence |
+|---|---|---|---|
+| `ant-cloning` | partly_verified | 7/10 | none |
+| `gfp-codon-burden-ot2` | partly_verified | 7/15 | MIT |
+| `massspecpreppy` | partly_verified | 3/10 | GPL-3.0 |
+| `tidytron` | partly_verified | 3/15 | Apache-2.0 |
+| `beckham-enzyme-pipeline` | partly_verified | 2/15 | none (no LICENSE file) |
+| `culturomics-isolation` | partly_verified | 2/11 | none |
+| `jubiotech-ot2-autoclone` | partly_verified | 2/7 | AGPL-3.0 |
+| `msd-biochem-assays-ot2` | verified | 2/2 | Apache-2.0 |
+| `exfab-qiaseq-flex` | verified | 1/1 | GPL-3.0 |
+| `hyrad-adna-capture` | verified | 1/1 | none |
+| `blots-ot2` | failed | 0/1 | none |
+| `cayman-his-elisa` | failed | 0/4 | MIT |
+| `damplab-moclo-transformation` | no_protocol_found | 0/0 | BSD-3-Clause |
+| `ester-library-synthesis` | failed | 0/3 | MIT |
+| `flat-agar-celegans-ot2` | failed | 0/3 | MIT |
+| `formulations-prep-shampoo` | failed | 0/1 | none |
+| `greenaway-halogenation` | failed | 0/9 | BSD-3-Clause |
+| `greenaway-mocs` | failed | 0/5 | none |
+| `greenaway-pocs` | failed | 0/6 | none |
+| `lucks-cellfree-biosensor` | failed | 0/1 | none |
+| `lysostaphin-turbidity` | failed | 0/1 | AGPL-3.0 |
+| `plant-phenotyping-ot2` | failed | 0/2 | MIT |
+| `roboctab` | failed | 0/2 | none |
+| `roche-pipetting-performance-ot2` | failed | 0/2 | GPL-3.0 |
+| `sapp-dmx-protein-design` | failed | 0/1 | MIT |
diff --git a/research/expansion/amass_candidates.jsonl b/research/expansion/amass_candidates.jsonl
new file mode 100644
index 0000000..d15e1eb
--- /dev/null
+++ b/research/expansion/amass_candidates.jsonl
@@ -0,0 +1,109 @@
+{"id": "massspecpreppy", "title": "MassSpecPreppy-An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications", "doi": "10.1002/pmic.202300294", "paper_url": "https://doi.org/10.1002/pmic.202300294", "year": 2023, "venue": "Proteomics", "open_access_license": "cc-by (Wiley Proteomics OA, verify)", "code_url": "https://github.com/stemicha/MassSpecPreppy", "code_files": ["OT2_protocols_template/Mass_Spec_Preppy__OT2_part4_post_EvoTip_loading.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_sequential.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well_without_red_alk.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay_take3_HS.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay_take3_slow_retract.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_EvoTip_loading.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_vial_elution.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_mix.py"], "code_license": "GPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics sample prep (BCA, SP3 digestion, Evotip loading)", "results_evidence": "BCA assay average recovery 101.3% (SD 7.82%) vs 96.3% manual; 94.5% of protein groups passed significance for OT-2 digestion vs 95% manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "10 OT-2 apiLevel .py templates (BCA, SP3 digestion, Evotip loading) generated by Shiny app; GPL-3.0; quantitative validation; overlaps thematically with proteomics-digestion-workflow but distinct paper/code.", "est_tasks": 6, "source_agent": "amass", "amass_ids": ["AMBC_XpNyVYaPbRFaGhr2QlXH8oh5ucp"]}
+{"id": "beckham-enzyme-pipeline", "title": "Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline", "doi": "10.1038/s41598-024-64938-0", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11196671/", "year": 2024, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/beckham-lab/opentrons", "code_files": ["Misc/Magbead_wash_elution/MagBead_Wash_Elution_OT2.py", "1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "1-Transformation/Transformation_cherrypicking/Generate_transformation_cherrypicking_protocol.py", "1-Transformation/Transformation_cherrypicking/2024-03-18_Transformation_cherrypicking_OT2.py", "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2_old.py", "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2.py", "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2_test_plateCandD.py", "4-Transfer/Transfer_plate-to-plate/Transfer_plate-to-plate_4x24_to_1x96_OT2.py", "2-Inoculation/Inculation_swap_rows_for_multichannel/Inoculation_swap_rows_1x96_to_4x24_OT2.py", "2-Inoculation/Inoculation_platetoplate/Inoculation_1x96_to_4x24_OT2.py", "2-Inoculation/Inoculation_cherrypicking/Generate_inoculation_cherrypicking_protocol.py", "3-Lysis/Lysis_buffer_addition/Lysis_buffer_addition_OT2.py", "3-Lysis/Lysis_4-plate_aspiration/Lysis_4-plate_aspiration_OT2.py", "3-Lysis/Lysis_1-plate_aspiration/Lysis_1-plate_aspiration_OT2.py", "5-Purification/Transfer_off_mag_beads/Transfer_off_MagBeads_OT2.py", "5-Purification/Purification_pipetting_only/Purification_pipetting_only_OT2.py", "5-Purification/Purification_with_shaker/Purification_with_shaker_OT2.py", "7-Normalization/Calculate_Volumes_to_Normalize.py", "7-Normalization/2024-03-29_Normalization_OT2.py", "8-DSF/DSF_setup_OT2.py", "6-Quantification/BCA_assay_OT2.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "transformation, protein expression and Ni-bead purification of 96 enzymes", "results_evidence": "Purified 96 PET hydrolases in parallel with yields up to 400 ug, reproducible purity, thermostability and activity benchmark dataset.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "21 OT-2 apiLevel scripts (transformation, cherry-picking, mag-bead wash/elution, transfers) but repo has no LICENSE; otherwise strong.", "est_tasks": 8, "source_agent": "amass", "amass_ids": ["AMBC_BlS5kMf4ztlWBtPPCnmSR0WVgO8"]}
+{"id": "tidytron", "title": "TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 lab robots", "doi": "10.1016/j.slast.2023.08.007", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12212179/", "year": 2023, "venue": "SLAS technology", "open_access_license": "cc-by", "code_url": "https://github.com/PlantSynBioLab/TidyTron", "code_files": ["scripts/p10/p10_DNAclean_no_neuts.py", "scripts/p10/p10_Ecoliclean_1-2-1.py", "scripts/p10/p10_DNAclean_no_neuts_multichan.py", "scripts/p10/p10_Ecoliclean_1-1_multichan.py", "scripts/p10/p10_Ecoliclean_3-3-3_multichan.py", "scripts/p10/p10_Ecoliclean_1-1.py", "scripts/p10/p10_Ecoliclean_1-2-1_multichan.py", "scripts/p10/p10_DNAclean_neutralizers.py", "scripts/p10/p10_Ecoliclean_3-3-3.py", "scripts/p10/p10_DNAclean_neutralizers_multichan.py", "scripts/p1000/p1000_Ecoliclean_3-3-3.py", "scripts/p1000/p1000_DNAclean_no_neuts.py", "scripts/p1000/p1000_Ecoliclean_1-1.py", "scripts/p1000/p1000_Ecoliclean_1-2-1.py", "scripts/p1000/p1000_DNAclean_neutralizers.py", "scripts/plate/integrated_tipclean_plateclean_RT.py", "scripts/plate/integrated_tipclean_plateclean_RT_multi.py", "scripts/plate/integrated_tipclean_plateclean_HOT.py", "scripts/plate/integrated_tipclean_plateclean_HOT_multi.py", "scripts/p300/p300_Ecoliclean_1-2-1_multichan.py", "scripts/p300/p300_DNAclean_no_neuts.py", "scripts/p300/p300_DNAclean_neutralizers.py", "scripts/p300/p300_DNAclean_neutralizers_multichan.py", "scripts/p300/p300_Ecoliclean_3-3-3_multichan.py", "scripts/p300/p300_Ecoliclean_3-3-3.py", "scripts/p300/p300_Ecoliclean_1-1.py", "scripts/p300/p300_DNAclean_no_neuts_multichan.py", "scripts/p300/p300_Ecoliclean_1-1_multichan.py", "scripts/p300/p300_Ecoliclean_1-2-1.py", "scripts/optimization_scripts/DNAcleaning optimization.py", "scripts/optimization_scripts/integrated_tipclean_plateclean_RT_multi.py", "scripts/optimization_scripts/plate_clean_optimization.py", "scripts/optimization_scripts/DNAcleaning.py", "scripts/optimization_scripts/fig1C_10ul_tip_cleaning_optimization.py", "scripts/optimization_scripts/fig1D_96rack_variation_10ul_tip_cleaningproject.py", "scripts/optimization_scripts/fig1A_B_p10_tip.py", "scripts/optimization_scripts/integrated_tipclean_plateclean_HOT_multi.py"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plasticware decontamination / tip and plate washing", "results_evidence": "Validated cleaning of tips and plates contaminated with DNA, E. coli and S. cerevisiae (qPCR/growth-based residual contamination measured across cleaning solutions and contact times).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "37 OT-2 apiLevel scripts, Apache-2.0, OA SLAS Technology, quantitative validation; repetitive variants so a few distinct tasks.", "est_tasks": 4, "source_agent": "amass", "amass_ids": ["AMBC_VZZYciJKR3AVWynhK7tRyLwMqZV"]}
+{"id": "krisp-sars2-pooling", "title": "Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing", "doi": "10.1038/s41598-021-96934-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8423848/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/krisp-kwazulu-natal/efficient-SARS-CoV-2-pooled-testing-strategy-code", "code_files": ["scripts/pooling27_300pip.py", "scripts/pooling27_50pip.py", "scripts/pooling81_50pip.py", "scripts/pooling81_300pip.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "SARS-CoV-2 hypercube sample pooling", "results_evidence": "Infected samples reliably detected in pools of 27 and 81 with minimal sensitivity loss for individual Ct up to 32.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "4 pooling scripts use the deprecated Opentrons v1 API (from opentrons import robot); would need porting to v2; MIT.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Kt4JG1AeKTTljzD16AIh1saLcLf"]}
+{"id": "openblend-media", "title": "Modular development enables rapid design of media for alternative hosts", "doi": "10.1002/bit.27947", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9298315/", "year": 2021, "venue": "Biotechnology and bioengineering", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/abiedermann/openblend_public", "code_files": ["openblend_plates.py", "plate_builder.py", "run_plate_prep.py", "cal_protocol.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "media blending / design of experiments", "results_evidence": "Modular blended media improved Pichia pastoris biomass accumulation and heterologous protein titre in mL-scale batch fermentations.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Python package generates OT-2 plate-prep protocols (opentrons imports; one apiLevel calibration file); needs wrapper to produce a standalone simulate-able protocol; MIT.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Z6bmqGnumWlGkqT380EkIxGMIbS"]}
+{"id": "roboctab", "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping", "doi": "10.3390/plants14152263", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12348566/", "year": 2025, "venue": "Plants (Basel, Switzerland)", "open_access_license": "cc-by", "code_url": "https://github.com/tomstamour/RoboCTAB", "code_files": ["RoboCTAB_OT2.py", "RoboCTAB_Flex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plant DNA extraction (CTAB) for genotyping", "results_evidence": "DNA yield and quality from leaves and roots sufficient for SNP genotyping/sequencing; compared tissue types for yield.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean OT-2 and Flex versions of the CTAB script (good OT-2 vs Flex pair) but repo has no LICENSE file.", "est_tasks": 4, "source_agent": "amass", "amass_ids": ["AMBC_S2FodXDUCy94XapVqSKJA7lsf1H"]}
+{"id": "pasta-spatial", "title": "PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology", "doi": "10.1038/s41592-026-03200-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13539481/", "year": 2026, "venue": "Nature methods", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/SizunJiangLab/PASTA", "code_files": ["automation/PASTA_oligoHRP_automation.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "spatial proteomics staining (tyramide-oligo amplification cycles on slides)", "results_evidence": "High-plex protein and RNA codetection on FFPE tissue via cyclical tyramide-oligonucleotide amplification and imaging (Nature Methods figures).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single OT-2 apiLevel 2.7 script for oligo-HRP staining cycles; no LICENSE; custom slide labware likely needed.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_8AMU8xpBC4bYAOyoUy4ljNomnML"]}
+{"id": "pipette-opt-dna-assembly", "title": "A linear programming-based strategy to save pipette tips in automated DNA assembly", "doi": "10.1093/synbio/ysac004", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9074407/", "year": 2022, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "cc-by", "code_url": "https://github.com/KSechkar/pipette_opt", "code_files": ["src/ppopt/estimate_runtimes/estimate_runtimes.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA assembly reaction setup with tip-saving optimisation", "results_evidence": "Algorithm reduced pipette tip consumption in randomly generated and real-life modular DNA assembly scenarios (computational; runtime estimated via opentrons simulate).", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Mainly an optimiser; robot code is a runtime-estimation wrapper plus related DAMPLAB/OT2-MoClo-Transformation-Ecoli templates in v1 API (BSD); no wet-lab validation of the optimised runs.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_FWl11HjtE3lKjjh4oLSkI1YqJw"]}
+{"id": "reacsight", "title": "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight", "doi": "10.1038/s41467-022-31033-9", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9188569/", "year": 2022, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/konst-ac/reacsight-project", "code_files": ["OT2/flaskr_withLib.py"], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "bioreactor sampling / cytometry loading, reactive control", "results_evidence": "Real-time optogenetic control of yeast gene expression, competition assays under nutrient scarcity, and dynamic control of two-strain consortium composition.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "OT-2 driven via Flask server using opentrons.execute and smoothie driver internals (not a protocol file); hardware-integrated (bioreactors, cytometer); repo here is a later project fork, original code on Zenodo 10.5281/zenodo.4776009; no license.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_NFUrVUFmrASp5tcgz1qZ1YNekjL"]}
+{"id": "peg-solubility-assay", "title": "An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement", "doi": "10.1038/s41598-021-01126-4", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8578320/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://gitlab.developers.cam.ac.uk/ch/sormanni/peg-solubility-assay", "code_files": ["PEG_Assay_Step1.py", "PEG_Assay_Step2.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein solubility assay (PEG titration, plate prep and transfer)", "results_evidence": "Relative solubility of proteins/antibodies quantified from PEG-precipitation midpoints using ~200 ug material; accuracy compared against established methods.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Two OT-2 API v2 scripts (step1 PEG gradient setup, step2 transfer after centrifugation) with clear paper protocol; no LICENSE; may need aluminium-block labware definitions.", "est_tasks": 4, "source_agent": "amass", "amass_ids": ["AMBC_J9kXwo9tekw77p29y6R0RRYa3n"]}
+{"id": "y1h-yeast-lap", "title": "Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast", "doi": "10.1002/cpz1.70059", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11580771/", "year": 2024, "venue": "Current protocols", "open_access_license": "cc-by (Current Protocols OA, verify)", "code_url": "https://github.com/BiocomputationLab/LAPrepository", "code_files": ["LAPEntries/LAP-PCR-OT2-2.0.0/ScriptPCR_v200.py", "LAPEntries/LAP-PCR-OT2-1.0.0/ScriptPCR.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-2.0.0/CounterSelectionScript_v200.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.0.0/CounterSelectionScript.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.0.0/ScriptPlateGenerationAndIncubation_v200.py", "LAPEntries/LAP-CellMediaInoculation-OT2-1.0.0/ScriptPlateGenerationAndIncubation.py", "LAPEntries/LAP-MoCloAssembly-OT2-2.0.0/ScriptMoCloConstructAssembly_v200.py", "LAPEntries/LAP-MoCloAssembly-OT2-1.0.1/ScriptMoCloConstructAssembly_v101.py", "LAPEntries/LAP-CellMediaInoculation-OT2-2.0.0/ScriptPlateGenerationAndIncubation_v200.py", "LAPEntries/LAP-MoCloAssembly-OT2-1.0.0/ScriptMoCloConstructAssembly.py", "LAPEntries/LAP-CustomReagentMixingMultiSinglePip-OT2-1.0.0/ScriptMixingReagents_v100.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.1.0/CounterSelectionScript_v110.py", "LAPEntries/LAP-NplateMerging-OT2-2.0.0/ScriptMergePlates_v200.py", "LAPEntries/LAP-NplateMerging-OT2-1.0.0/ScriptMergePlates.py", "SetFunctions/define_tiprack.py", "SetFunctions/check_tip_and_pick.py", "SetFunctions/setting_labware.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "yeast transformation / arrayed library inoculation (Y1H screening)", "results_evidence": "Robotized yeast one-hybrid workflow for screening arrayed Arabidopsis TF libraries against promoter fragment baits (interaction readouts reported).", "wet_lab_validated": true, "duplicate_of_existing": "lap-transposon-genotyping (same LAPrepository code repo; different paper)", "readiness": "partial", "readiness_reason": "Uses LAP-CellMediaInoculation-OT2 scripts (apiLevel) driven by Excel variables files; repo has no license file; repo already in corpus via lap-transposon-genotyping.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_3uwG18vtShB9zqOfI0Cku0a0czs"]}
+{"id": "ht-hcr-sea-urchin", "title": "Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos", "doi": "10.1242/dev.204814", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12516323/", "year": 2025, "venue": "Development (Cambridge, England)", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/ylee-sio/HL_HTHCR", "code_files": ["HL_HTHCRv16.json"], "code_license": "none", "robot_platform": "flex", "api": "other", "protocol_category": "whole-mount in situ HCR on embryos in 96-well plates", "results_evidence": "Processed 192 probe sets in 32 h; produced localisation data for 101 genes across three developmental stages.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocol is an Opentrons Flex Protocol Designer JSON (schema v8), not Python; could be exported/converted; no license.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Wz78wSUCdhU6RWyec7626bqjRZZ"]}
+{"id": "bean-kasp-anthracnose", "title": "Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR", "doi": "10.1186/s13007-023-01071-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10546687/", "year": 2023, "venue": "Plant methods", "open_access_license": "cc-by", "code_url": "https://github.com/McGillHaricots/peas-andlove", "code_files": ["protocols/Extraction & PACE Assay Part 2 (thermocycling_Co-42(1)).json", "protocols/PACE Assay (dual marker no dna).json", "protocols/... (Opentrons JSON protocols)"], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "plant DNA extraction + KASP/PACE allele-specific PCR genotyping", "results_evidence": "Automated DNA extraction and KASP assays genotyped common bean lines at four anthracnose resistance markers with clear allele clustering, matching expected genotypes.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocols are Opentrons Protocol Designer JSON files inside a large mixed lab repo, not Python; no license.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_RvNHz2cHbnDsOx9V5pABxjs3t2d"]}
+{"id": "shampoo-formulations-ot2", "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset", "doi": "10.1038/s41597-024-03573-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11222379/", "year": 2024, "venue": "Scientific data", "open_access_license": "cc-by", "code_url": "https://github.com/sustainable-processes/formulations-prep", "code_files": ["OpentronsProtocol_FormulationSamples.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "liquid formulation preparation (viscous ingredients, gravimetric checks)", "results_evidence": "Dataset of 812 shampoo formulations (294 stable) with phase stability, turbidity and rheology measurements prepared on semi-automated OT-2 platform.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "One OT-2 apiLevel protocol plus balance-automation notebook; no license; viscous-liquid custom labware likely; chemistry rather than biology.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_R4FOoj3BF9Yc4ZVhWkMLJeEn1pS"]}
+{"id": "lysostaphin-turbidity", "title": "Turbid but accurate: automating lysostaphin quantification including uncertainty quantification", "doi": "10.1186/s12934-025-02911-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12836826/", "year": 2026, "venue": "Microbial cell factories", "open_access_license": "cc-by", "code_url": "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025", "code_files": ["code/Turbidity_assay_OT_8samples.py"], "code_license": "AGPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "antibacterial activity turbidity assay (serial dilution + OD lysis kinetics)", "results_evidence": "Turbidity assay quantified lysostaphin over a 0.63-10 mg/L dynamic range with Bayesian uncertainty quantification using autoclaved S. carnosus indicator cells.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Single self-contained OT-2 apiLevel script (Turbidity_assay_OT_8samples.py) matching the paper; OA paper; licence AGPL-3.0 (clear, but like APEX cannot be vendored).", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Fuaep5GZ3DJGlqCuFCqpNgo1dwp"]}
+{"id": "cybergenetic-coculture", "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback", "doi": "10.1038/s41467-022-32392-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9381578/", "year": 2022, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/santkumar/evotron", "code_files": [], "code_license": "other-open (Zenodo 10.5281/zenodo.6908131)", "robot_platform": "tecan", "api": "other", "protocol_category": "automated bioreactor sampling / optogenetic closed-loop co-culture control", "results_evidence": "Platform stabilised two-strain E. coli community ratio across multiple parallel co-cultures with closed-loop optogenetic control.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Evotron software (Tecan Freedom EVO integration, non-Python robot scripts); no simulate-able liquid-handling protocol.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_84pEeTIu8u42WOCdvFB2fZZqsoC"]}
+{"id": "covid-mastermix-omix", "title": "Development and validation of automated methods for COVID-19 PCR Master Mix preparation", "doi": "10.1016/j.slast.2024.100195", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11639134/", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by", "code_url": "https://github.com/Donald-OMIX/Liquid_Handler_Methods", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "PCR master mix preparation (diagnostic COVID-19)", "results_evidence": "Automated PCR master mix preparation matched manual pipetting accuracy in a diagnostic lab (Ct value comparisons, gravimetric checks).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Methods are proprietary binary .pkg/.dfx liquid-handler method packages (non-Python); useful as paper-only reference task.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_F2lqGDVrkmw72Y3hIXeAkI354m8"]}
+{"id": "pylabrobot-paper", "title": "PyLabRobot: An Open-Source, Hardware Agnostic Interface for Liquid-Handling Robots and Accessories", "doi": "10.1101/2023.07.10.547733", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10369895/", "year": 2023, "venue": "bioRxiv : the preprint server for biology", "open_access_license": "cc-by (bioRxiv, verify)", "code_url": "https://github.com/PyLabRobot/pylabrobot", "code_files": ["(library; demos in rickwierenga/plr-game-of-life, pylabrobot-art-studio)"], "code_license": "MIT", "robot_platform": "pylabrobot", "api": "pylabrobot", "protocol_category": "hardware-agnostic liquid-handling interface (Hamilton STAR, Tecan EVO, OT-2)", "results_evidence": "Validated via unit tests and application demos (browser simulator, position calibration, path teaching); no biological assay results.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT library with simulator, useful as an execution backend for PLR tasks but no paper-specific wet-lab protocol to reproduce.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_1j8eO8dsJWaiiSG8DhA3CmhWjU8"]}
+{"id": "coscientist", "title": "Autonomous chemical research with large language models", "doi": "10.1038/s41586-023-06792-0", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10733136/", "year": 2023, "venue": "Nature", "open_access_license": "cc-by", "code_url": "https://github.com/gomesgroup/coscientist", "code_files": [], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "LLM-generated OT-2 protocols (plate colouring, UV-Vis, cross-coupling)", "results_evidence": "GPT-4 agent planned and executed Pd-catalysed cross-coupling optimisation and OT-2 liquid-handling tasks with GC-MS/UV-Vis confirmation.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo is a placeholder (no .py code released, agent code withheld); generated protocols only in SI; relevant as related LLM-to-robot work.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_HzNJIL493Lx8JDNpbaXQBofSd25"]}
+{"id": "roborna-nirvana", "title": "An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing", "doi": "10.1038/s41598-023-47190-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10663496/", "year": 2023, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/strubelab/roboRNA", "code_files": ["EvoScripts/roboRNA_everything.exd"], "code_license": "none", "robot_platform": "tecan", "api": "other", "protocol_category": "SARS-CoV-2 magnetic-bead RNA extraction + RT-qPCR + nanopore variant sequencing", "results_evidence": "Automated extraction showed high reproducibility with no cross-contamination; limit of detection, sensitivity and specificity comparable to commercial assays; NIRVANA identified circulating variants.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Tecan Freedom EVOware .exd scripts (non-Python) with deck images and protocol summary; no license; good paper-only task for porting to OT-2/PLR.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Vnwuovs621rAfxFbZZ7xtkq9lKj"]}
+{"id": "facs-automation", "title": "An open-source FACS automation system for high-throughput cell biology", "doi": "10.1371/journal.pone.0299402", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10956866/", "year": 2024, "venue": "PloS one", "open_access_license": "cc-by", "code_url": "https://github.com/czbiohub-sf/2023-facs-automation-pub", "code_files": [], "code_license": "BSD", "robot_platform": "other", "api": "other", "protocol_category": "FACS sample handling and autonomous sorting/gating", "results_evidence": "Walkaway sequential FACS of many samples with algorithmic gating; reduced operator variation and hands-on time (sort purity/yield reported).", "wet_lab_validated": true, "duplicate_of_existing": "opencell-automation (same CZ Biohub group, separate paper)", "readiness": "no", "readiness_reason": "Python GUI-automation of instrument software and Hamilton/robot arm integration; no liquid-handling protocol file.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_2ng2mytae0v23coWE16OdsGd9pR"]}
+{"id": "openworkstation", "title": "OpenWorkstation: A modular open-source technology for automated in vitro workflows", "doi": "10.1016/j.ohx.2020.e00152", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9041211/", "year": 2020, "venue": "HardwareX", "open_access_license": "cc-by", "code_url": "https://github.com/SebastianEggert/OpenWorkstation", "code_files": [], "code_license": "CC-BY-SA-4.0 (Zenodo 10.5281/zenodo.3986643)", "robot_platform": "other", "api": "other", "protocol_category": "open hardware pipetting/transport workstation for in vitro cell culture", "results_evidence": "Demonstrated automated pipetting of liquids and viscous substances and vessel transport for in vitro workflows.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Firmware/hardware project (GitHub repo empty on default branch; code in Zenodo zip); no protocol-level Python.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_LWZtC25gR5OCg827KO54GIuZX52"]}
+{"id": "snails-slow-pipetting", "title": "Consistent ultra-long DNA sequencing with automated slow pipetting", "doi": "10.1186/s12864-021-07500-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7953553/", "year": 2021, "venue": "BMC genomics", "open_access_license": "cc-by", "code_url": "https://github.com/dholab/SNAILS", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "ultra-long nanopore library prep slow pipetting (3D-printer based)", "results_evidence": "Across six libraries SNAILS preserved more >100 kb reads and increased average read length vs manual slow pipetting.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Python scripts emit G-code for a modified 3D printer; not a liquid-handler API.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_7qRIj7wDrr98JaRqTAYKUMqfbjA"]}
+{"id": "autorelacs", "title": "AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq", "doi": "10.1038/s41598-020-69443-8", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7381599/", "year": 2020, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/FrancescoFerrari88/AutoRELACS", "code_files": [], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "ChIP-seq barcoding library prep (Biomek i7)", "results_evidence": "AutoRELACS generated ChIP-seq data comparable to the manual RELACS protocol across many samples.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo holds analysis notebooks only; Biomek i7 methods not released as code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_SYmOf482v5ytfvMV1Xbdpqc2FV1"]}
+{"id": "icfree-cfps-al", "title": "An AI-driven workflow for the accelerated optimization of cell-free protein synthesis", "doi": "10.1016/j.isci.2025.113599", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12529354/", "year": 2025, "venue": "iScience", "open_access_license": "cc-by", "code_url": "https://github.com/brsynth/icfree-ml", "code_files": [], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "cell-free protein synthesis optimisation (active learning, Echo acoustic dispensing)", "results_evidence": "2- to 9-fold increase in colicin M and E1 yield in E. coli and HeLa CFPS within four active-learning cycles.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "icfree generates Echo picklists (CSV), not robot Python; MIT.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_KuYx7k5s0alo6KdAQylfEHmxkKx"]}
+{"id": "myra-arg-cellfree", "title": "A liquid handling platform for standardized quantification of cell-free enzymatic activity encoded by antimicrobial resistance genes", "doi": "10.1093/synbio/ysag010", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13561876/", "year": 2026, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "cc-by", "code_url": "https://github.com/Mo42-mb/Myra_automation", "code_files": ["example_output/1-MyraScript-genes-interactive.py", "example_output/2-MyraScript-MM.py"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "cell-free expression of antibiotic resistance genes + antibiotic IC50 assay", "results_evidence": "No statistical difference Myra vs manual pipetting; aac(3)-IIa raised gentamicin IC50 >150-fold and arr-3 raised rifampicin IC50 ~20-fold.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "R script generates Myra (Bio Molecular Systems) Python-like scripts, not Opentrons/PLR; no license; logic portable to OT-2.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_QDvyBiXgpiNAe5oUqD0elPUHuZX"]}
+{"id": "labdroid-phenol-chloroform", "title": "Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing", "doi": "10.12688/f1000research.109251.1", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8931447/", "year": 2022, "venue": "F1000Research", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.5733820", "code_files": [], "code_license": "CC-BY-4.0", "robot_platform": "other", "api": "other", "protocol_category": "HMW genomic DNA phenol-chloroform extraction (Maholo LabDroid)", "results_evidence": "Routine extraction of >100 kb gDNA from algae, bacteria, insects and human cells; validated by pulse-field electrophoresis and nanopore read N50.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Proprietary LabDroid job files (.PRJ); humanoid robot not a liquid handler API.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_5RmeQb0DTzqBED9vaGn7r1LhEBe"]}
+{"id": "egf-sequeduct", "title": "Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing", "doi": "10.1021/acssynbio.3c00589", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10877595/", "year": 2024, "venue": "ACS synthetic biology", "open_access_license": "cc-by", "code_url": "https://github.com/Edinburgh-Genome-Foundry/Sequeduct", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "nanopore plasmid assembly QC (analysis pipeline)", "results_evidence": "Biofoundry-scale validation of assembled plasmids via nanopore long-read sequencing with automated reports.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Analysis pipeline only; no robot code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Orw4zCCJAZKmeiuONAxiZlV2SA1"]}
+{"id": "sdl-enzyme-flex", "title": "Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab", "doi": "10.1002/bit.70038", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12503018/", "year": 2025, "venue": "Biotechnology and bioengineering", "open_access_license": "cc-by", "code_url": "https://github.com/putzsebastian/sdl-enzymes-optimization", "code_files": [], "code_license": "MIT", "robot_platform": "flex", "api": "other", "protocol_category": "self-driving enzymatic reaction optimisation (pH, temperature, cosubstrate)", "results_evidence": "ML-driven Opentrons Flex platform optimised enzymatic reaction conditions after >10,000 simulated campaigns selected the best algorithm; experimental campaigns improved activity.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Repo has optimisation scripts only (no Flex protocol). Same author's KAISA-LSE_SDL-Platform and automation-isotherms-complexes repos contain Opentrons apiLevel protocols, incl. an LLM protocol-generation replication study (MIT) worth a look.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_UlURib8c7yzycxPTXEqd9KsArMa"]}
+{"id": "curcumin-formulation-sdl", "title": "Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator", "doi": "10.1039/d5dd00171d", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13576497/", "year": 2025, "venue": "Digital discovery", "open_access_license": "cc-by", "code_url": "https://github.com/shorthouse-lab/Ros_SDformulation", "code_files": [], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "drug formulation solubility screening (excipient mixing)", "results_evidence": "Found 7 curcumin formulations with solubility >10 mg/mL after sampling 256 of 7776 candidates.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo has Bayesian-optimisation notebooks only; OT-2 protocol not released; no license (Zenodo CC-BY).", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_PnLa1CsDtEMYEsgnfmLycDR2B5o"]}
+{"id": "sdl-guide-gormley", "title": "A user's guide to your first self-driving liquid handling lab", "doi": "10.1039/d5dd00525f", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13071554/", "year": 2026, "venue": "Digital discovery", "open_access_license": "cc-by", "code_url": "https://github.com/GormleyLab/Pipette-Liquid-Handler", "code_files": [], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "DIY self-driving liquid handling lab tutorial (colour mixing/active learning)", "results_evidence": "Tutorial SDL built from low-cost hardware demonstrating active-learning optimisation of mixtures.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom DIY pipetting rig controller (serial/G-code), not Opentrons/PLR; MIT.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_2OCErX4yZcta0GaW6nMF47qMdtI"]}
+{"id": "ot2-yeast-spot-assay", "title": "Automation of yeast spot assays using an affordable liquid handling robot", "doi": "10.1016/j.slast.2022.12.001", "paper_url": "https://doi.org/10.1016/j.slast.2022.12.001", "year": 2022, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": "https://github.com/bioinfo-tsukuba/ot2_spot_assay", "code_files": ["ot2_execute/compiler/compile_after_plate_reader_for_paper.py", "ot2_execute/compiler/compile_predispense.py", "ot2_execute/compiler/compile_after_plate_reader.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "yeast serial dilution spot assay on agar (3D-printed Petri mount, z-adjust)", "results_evidence": "Automated spot assays of budding yeast reproduced manual growth phenotypes, imaged with a flatbed scanner (spot intensity quantified).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Compiler scripts generate OT-2 apiLevel protocols from plate-reader data; needs custom Petri-dish labware definition; no license.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_Z44qoWuOtzrQkgx2l6lRuw0NcNX"]}
+{"id": "bead-digestion-ann", "title": "Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network", "doi": "10.1016/j.talanta.2024.125988", "paper_url": "https://doi.org/10.1016/j.talanta.2024.125988", "year": 2024, "venue": "Talanta", "open_access_license": "paywalled (Talanta)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics paramagnetic bead digestion", "results_evidence": "ANN-optimised OT-2 bead digestion showed high reproducibility across plasma, Arabidopsis, E. coli and mouse cortex; identified 385 unique rat bile proteins.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code found; paywalled.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_F15HwF4NineYWeVZrQQDYlLOWJW"]}
+{"id": "nfkb-luciferase-ot2", "title": "Luciferase reporter assay for NF-kB activation automated by an open-source liquid handling platform", "doi": "10.1016/j.slast.2024.100155", "paper_url": "https://doi.org/10.1016/j.slast.2024.100155", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell seeding, transfection and luciferase reporter assay", "results_evidence": "OT-2 Python protocols for HeLa seeding, NF-kB reporter transfection and luciferase readout gave quantifiable activation signals with good sample-handling quality.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Python protocols described but no repository located (may be in SI); worth checking SLAS supplementary.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_6JPEUNa4CkA8mVKu3EfuFiMaZlK"]}
+{"id": "ot2-biochem-assays-pharma", "title": "Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler", "doi": "10.1016/j.slast.2024.100205", "paper_url": "https://doi.org/10.1016/j.slast.2024.100205", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "biochemical assay pipetting accuracy vs Tecan EVO", "results_evidence": "Two biochemical assays on OT-2 showed accurate pipetting with low covariance compared with Tecan EVO.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code located.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_ZMfCdr8ok9pUyzM9pRuUpNIgBB"]}
+{"id": "radiolabeling-psma-ot2", "title": "Automated radiolabeling and handling of 177 Lu- and 225 Ac-PSMA-617 using a robotic pipettor", "doi": "10.1002/jlcr.4085", "paper_url": "https://doi.org/10.1002/jlcr.4085", "year": 2024, "venue": "Journal of labelled compounds & radiopharmaceuticals", "open_access_license": "unknown/likely paywalled", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "radiochemistry (177Lu/225Ac-PSMA-617 labelling)", "results_evidence": "Robotic pipettor performed radiometal labelling with reduced operator exposure and synthesis times (radiochemical yields/purity reported).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code; niche radiochemistry.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CuOYvsMA0ArgHxEYefJckQamsBl"]}
+{"id": "cfrna-extraction-pipeline", "title": "An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction", "doi": "10.1038/s41596-023-00855-2", "paper_url": "https://doi.org/10.1038/s41596-023-00855-2", "year": 2023, "venue": "Nature protocols", "open_access_license": "paywalled (Nature Protocols)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free RNA extraction from plasma (96 samples)", "results_evidence": "RT-qPCR with synthetic spike-in showed RNA quality comparable to manual; +12x throughput, -11x time, -3x cost; 96 samples in 4.5 h.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code not found via Amass text (paywalled); Nature Protocols likely has GitHub/SI scripts - worth a manual check.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_3LhuNKDG0LIwIE4QXn4GlgrjzmP"]}
+{"id": "cellfree-biosensor-ot2", "title": "Semiautomated Production of Cell-Free Biosensors", "doi": "10.1021/acssynbio.4c00703", "paper_url": "https://doi.org/10.1021/acssynbio.4c00703", "year": 2025, "venue": "ACS synthetic biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free biosensor reaction assembly (LacZ colorimetric / fluorescent)", "results_evidence": "Compared manual vs semi-automated OT-2 assembly of cell-free reactions; robotic assembly reduced variability in colorimetric and fluorescent outputs.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code repository located.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_2gr7aV8pMyf5se5ktlfFCQkZdNX"]}
+{"id": "swabseq-flex", "title": "Automated implementation of the SwabSeq COVID-19 diagnostic assay on the opentrons flex liquid-handling robot", "doi": "10.1016/j.diagmicrobio.2026.117519", "paper_url": "https://doi.org/10.1016/j.diagmicrobio.2026.117519", "year": 2026, "venue": "Diagnostic microbiology and infectious disease", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "SwabSeq NGS COVID-19 diagnostic (RT-PCR barcoding, pooling, SPRI cleanup)", "results_evidence": "Flex workflow completed in ~2.5 h with complete agreement on negatives, very high agreement on positives and no discordant calls vs manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Flex protocol code not located (check SI); high-value Flex target if found.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_QpaAmsl6M7rjKC75l8yL5odts5x"]}
+{"id": "marchantia-agro-transformation", "title": "Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation", "doi": "10.1111/tpj.70118", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11993085/", "year": 2025, "venue": "The Plant journal : for cell and molecular biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Agrobacterium-mediated plant (Marchantia) transformation", "results_evidence": "Semi-automated protocol showed transformation efficiency similar to manual manipulation.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link in full text.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_QTLDXogx16ZOAstLvfRPprCJmTV"]}
+{"id": "transfection-reagent-agnostic", "title": "A Novel, Fully Automated, and Reagent-Agnostic Transient Transfection Protocol", "doi": "10.1002/cpz1.968", "paper_url": "https://doi.org/10.1002/cpz1.968", "year": 2024, "venue": "Current protocols", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "automated transient transfection of adherent cells", "results_evidence": "HeLa transfection efficiency 40.9-73.3% and A549 42.2-54%, comparable to manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code located; platform unclear from abstract.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_69n4c5dgMmotdIjN4UtUde64nHh"]}
+{"id": "illumina-dnaprep-flowbot", "title": "Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot", "doi": "10.1038/s41598-024-58963-2", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11001922/", "year": 2024, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "Illumina DNA library prep for WGS (flowbot ONE)", "results_evidence": "Automated libraries had comparable yields (median 1.5-fold diff), similar assembly quality and 100% cgMLST concordance; hands-on time 25 vs 125 min.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Flow Robotics protocol file available only on request; good paper-only porting task.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_6hmaeTZsbAf0xOYBT4JLJPyjYE0"]}
+{"id": "tmt-bead-platform-ot2", "title": "A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation", "doi": "10.1021/jasms.1c00077", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8210952/", "year": 2021, "venue": "Journal of the American Society for Mass Spectrometry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "TMTpro isobaric-tag proteomics sample prep", "results_evidence": "Robot-prepared TMTpro16-plex triplicates quantified similar numbers of proteins/peptides with good reproducibility vs manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Paper states open-source OT-2 templates are provided (likely SI), but no repository URL extracted; needs manual SI retrieval.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_E2Bo8H8BA9wM9XBVa6wJnkVtnJF"]}
+{"id": "autopots-proteome", "title": "Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling", "doi": "10.1021/acs.analchem.0c04240", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8140400/", "year": 2020, "venue": "Analytical chemistry", "open_access_license": "author manuscript (PMC)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "low-input one-pot proteomics prep in 384-well plates", "results_evidence": "autoPOTS quantified proteomes from low-input/single-cell-scale samples using an unmodified low-cost pipetting robot.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code; robot is OT-2 per full text but protocol not released.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_9SKC53Uk2sKzNuvdXAm8dqYRnks"]}
+{"id": "protein-corona-ot2", "title": "Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data", "doi": "10.1007/s00216-020-02726-1", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7483600/", "year": 2020, "venue": "Analytical and bioanalytical chemistry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein corona formation and magnetic isolation for proteomics", "results_evidence": "Automated corona isolation with magnetic-core nanoparticles; compared low-cost proteomics workflows.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Protocol only in ESM text; no code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_B5qpdBu6SwPc7FpkHe7KMJcgnUZ"]}
+{"id": "kitfree-rna-extraction", "title": "A high-throughput pipeline for scalable kit-free RNA extraction", "doi": "10.1038/s41598-021-02742-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8636496/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "kit-free magnetic-bead RNA extraction for SARS-CoV-2 RT-qPCR", "results_evidence": "Semi-automated kit-free extraction validated by SARS-CoV-2 RT-qPCR without loss of diagnostic sensitivity/accuracy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link in full text.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_67rBmQVGvZfNxbJQxDsiuEoRZew"]}
+{"id": "mxene-aerogel-al", "title": "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties", "doi": "10.1038/s41467-024-49011-8", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11144242/", "year": 2024, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/oshin71/Programmable-MXene-Aerogel", "code_files": [], "code_license": "none (data Zenodo BSD-3-Clause-Clear)", "robot_platform": "ot2", "api": "other", "protocol_category": "materials mixture preparation (MXene/CNF/gelatin) for active learning", "results_evidence": "OT-2 prepared 264 mixtures; 162 conductive aerogels fabricated/characterised over 8 active-learning cycles to train an ANN for inverse design.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo is empty/data only; OT-2 scripts not released; materials science.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_SpCNFN4CK5sOluCy0KLQ4t2mTLD"]}
+{"id": "plastic-substitutes-al", "title": "Machine intelligence-accelerated discovery of all-natural plastic substitutes", "doi": "10.1038/s41565-024-01635-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11186784/", "year": 2024, "venue": "Nature nanotechnology", "open_access_license": "cc-by", "code_url": "https://github.com/chentl/MatAL", "code_files": [], "code_license": "BSD", "robot_platform": "ot2", "api": "other", "protocol_category": "nanocomposite film mixture preparation for active learning", "results_evidence": "OT-2 prepared 286 CNF/MMT/gelatin/glycerol nanocomposites to train models discovering all-natural plastic substitutes.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "MatAL contains ML code only; no OT-2 protocol; BSD.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_XSTjitcXORpdBVLgqh3351fcD7e"]}
+{"id": "hydra-hydrogel-plates", "title": "Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing", "doi": "10.1038/s44172-025-00575-3", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12749810/", "year": 2025, "venue": "Communications engineering", "open_access_license": "cc-by", "code_url": "https://github.com/Synthetic-Physiology-Lab/hydra-hts-hydrogel-analysis", "code_files": [], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "hydrogel coating of 96/384-well plates for cell culture HTS", "results_evidence": "HYDRA produced meniscus-free hydrogel coatings validated by imaging-based anticancer dose-response assays and long-term microscopy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo contains image-analysis scripts only; OT-2 protocol not released.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_Ht5d4BDlmKuczCVx9dH7zd50pLf"]}
+{"id": "duckweed-hte", "title": "Accelerated high-throughput imaging and phenotyping system for small organisms", "doi": "10.1371/journal.pone.0287739", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10361482/", "year": 2023, "venue": "PloS one", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.8060938", "code_files": [], "code_license": "MIT", "robot_platform": "ot2", "api": "other", "protocol_category": "modified OT-2 loading duckweed into well plates for plant-microbe growth phenotyping", "results_evidence": "Study of 6,000 experimental units across 2,000 treatments with time-resolved growth data; system scales to 11,520 units.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Zenodo holds R analysis only; OT-2 loading protocol not found.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_1B9FNKPNZU8nO23095KgwBAzbKL"]}
+{"id": "combinatorial-barcode-dna", "title": "Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications", "doi": "10.3390/ijms24032549", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9917336/", "year": 2023, "venue": "International journal of molecular sciences", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.7415652", "code_files": [], "code_license": "CC-BY-4.0", "robot_platform": "ot2", "api": "other", "protocol_category": "oligo mixing for combinatorial DNA barcode library assembly", "results_evidence": "Built 256- and 512-member modular barcode libraries from <50 oligos; OT-2 used for oligo mixing in Gen_2 library.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Zenodo scripts are NUPACK/BLAST design scripts; zip download failed to verify any OT-2 code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_ELVDy0e7Q2jFGAgyKxmb8hYtJNp"]}
+{"id": "galaxy-synbiocad", "title": "The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering", "doi": "10.1038/s41467-022-32661-x", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9424320/", "year": 2022, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/brsynth (Galaxy-SynBioCAD tools; DNA-Bot generator)", "code_files": [], "code_license": "MIT (tools)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "pathway design to automated BASIC DNA assembly and transformation", "results_evidence": "Built a library of lycopene-producing E. coli strains across four sites using DNA-Bot generated OT-2 scripts; 83% success retrieving validated pathways.", "wet_lab_validated": true, "duplicate_of_existing": "dna-bot (OT-2 scripts are DNA-Bot generated)", "readiness": "partial", "readiness_reason": "Robot scripts are generated by DNA-Bot (already in corpus); new element is the lycopene library experiment.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_ChyB9zcT5J8Kd76qDJ3g2faQk1Y"]}
+{"id": "covid-fosh-review", "title": "High-throughput and automated screening for COVID-19", "doi": "10.3389/fmedt.2022.969203", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9521367/", "year": 2022, "venue": "Frontiers in medical technology", "open_access_license": "cc-by", "code_url": "https://www.protocols.io/groups/opentrons-covid19-testing", "code_files": [], "code_license": "unknown", "robot_platform": "ot2", "api": "other", "protocol_category": "review of open-source automated COVID-19 testing", "results_evidence": "Review of case studies (China, Spain, UK); no new wet-lab data.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Review article; points to Opentrons COVID protocols.io group.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_OaJc5wIMCiLR2rqrnf5sLmZb73s"]}
+{"id": "pharma-ot2-integration", "title": "Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment", "doi": "10.1016/j.slast.2024.100180", "paper_url": "https://doi.org/10.1016/j.slast.2024.100180", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "OT-2 integration in industrial pharma workflow (flexible pipetting protocols)", "results_evidence": "Two flexible pipetting protocols and medium-complexity assays developed with a software architecture wrapping OT-2.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Q0TUHQPGTKKntKEGkoPMxgyYHrv"]}
+{"id": "auto-sp-proteomics", "title": "AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications", "doi": "10.1021/acs.analchem.5c00886", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12355475/", "year": 2025, "venue": "Analytical chemistry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics BCA, digestion and PTM enrichment", "results_evidence": "AUTO-SP automated BCA, digestion and PTM enrichment on PDX breast tumour tissue, with protein/PTM IDs comparable to manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocols provided in Supporting Information (not a repo); need SI retrieval to confirm .py.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_MxqtygMHV1Ej6q6nLxjWToWK6jk"]}
+{"id": "gpcr-livecell-ot2", "title": "GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System", "doi": "10.1021/acssensors.2c01341", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9994309/", "year": 2023, "venue": "ACS sensors", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated compound addition during live-cell cAMP imaging", "results_evidence": "Measured GPR68 cAMP dynamics vs extracellular pH and ogerin modulation using OT-2-integrated microscopy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link found.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_q0Ggo2QEemYLff5LOgORAQYLI4"]}
+{"id": "diy-ot-linear-motion-qpcr", "title": "Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting", "doi": "10.1038/s41598-020-70465-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7424513/", "year": 2020, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "open-source DIY liquid handler for qPCR setup", "results_evidence": "Benchmarking showed micropipetting speed/positional accuracy adequate for qPCR setup reproducibility.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom hardware; no Opentrons/PLR code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_HoIJvKsIF5yFoutGHfRw4kxr5Dk"]}
+{"id": "diy-stem-lhr", "title": "DIY liquid handling robots for integrated STEM education and life science research", "doi": "10.1371/journal.pone.0275688", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9645590/", "year": 2022, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "educational DIY liquid handling robot (Snap4Arduino)", "results_evidence": "Qualitative teacher study plus demonstration experiments.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Block-based Arduino programming; not relevant API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_JOobtuYcydkFfO4xTZ7mNKDzWv4"]}
+{"id": "maple-fly-robot", "title": "MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping", "doi": "10.7554/eLife.37166", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6193762/", "year": 2018, "venue": "eLife", "open_access_license": "cc-by", "code_url": "https://github.com/FlySorterLLC/MAPLEControlSoftware", "code_files": [], "code_license": "not checked", "robot_platform": "other", "api": "other", "protocol_category": "Drosophila handling robot", "results_evidence": "Automated virgin collection and social-behaviour experiments revealing persistent idiosyncrasies.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom robot, not liquid handling.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_hU5OjLOIAJ8W8VBxIOTQR06Nlr"]}
+{"id": "synthetic-cells-robotics", "title": "Scaling Up Synthetic Cell Production Using Robotics and Machine Learning Toward Therapeutic Applications", "doi": "10.1002/adbi.202400671", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12078883/", "year": 2025, "venue": "Advanced biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/IdoGalil/syn", "code_files": [], "code_license": "unknown (repo not found)", "robot_platform": "tecan", "api": "other", "protocol_category": "synthetic cell production scale-up", "results_evidence": "Robotic scale-up increased synthetic-cell batch size 30-fold; luciferase SCs monitored in mice.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo URL dead; Tecan platform.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_ENm6Rp10P1W4yf8WWCUPVhWtn0V"]}
+{"id": "dup-hulp-rna-extraction", "title": "Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection", "doi": "10.1371/journal.pone.0246302", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7886139/", "year": 2021, "venue": "PloS one", "open_access_license": "see corpus", "code_url": "https://github.com/hulpopentrons/rna_extraction_ot2opentrons", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "hulp-rna-extraction", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'hulp-rna-extraction'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_6klQRhCNJYNnZchcfn8cisvhhvO"]}
+{"id": "dup-shotgun-proteomics-jove", "title": "Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot", "doi": "10.3791/63092", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8986016/", "year": 2021, "venue": "Journal of visualized experiments : JoVE", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "shotgun-proteomics-jove", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'shotgun-proteomics-jove'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_A9qKi019KhRueHfLKrLehGwAm8v"]}
+{"id": "dup-proteomics-digestion-workflow", "title": "Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics", "doi": "10.1016/j.mcpro.2024.100790", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11251069/", "year": 2024, "venue": "Molecular & cellular proteomics : MCP", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "proteomics-digestion-workflow", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'proteomics-digestion-workflow'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_DJEOKs7MNxMyVNZAFpE6NioOj4"]}
+{"id": "dup-pipetting-robot-nanoliter", "title": "Modification of a Low-Cost Pipetting Robot for Nanoliter Liquid Handling and Autosampling for Liquid Chromatography-Mass Spectrometry", "doi": "10.1002/jssc.70379", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13118588/", "year": 2026, "venue": "Journal of separation science", "open_access_license": "see corpus", "code_url": "https://github.com/rtklab-byu/openlc", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "pipetting-robot-nanoliter", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'pipetting-robot-nanoliter'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_JICUpy1Ar01vntisMXPgr7PPAn6"]}
+{"id": "dup-ot-mation", "title": "OT-Mation: an open-source code for parsing CSV files into Python scripts for control of OT-2 liquid-handling robotics", "doi": "10.1093/synbio/ysaf009", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12063526/", "year": 2025, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "see corpus", "code_url": "https://github.com/tphoward/ot-mation_repo", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "ot-mation", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'ot-mation'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_NCiEkN2Dc9ebxlxhNe3DdwPTeJE"]}
+{"id": "dup-actinomation", "title": "ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp", "doi": "10.1016/j.synbio.2025.03.005", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11999424/", "year": 2025, "venue": "Synthetic and systems biotechnology", "open_access_license": "see corpus", "code_url": "https://github.com/kedar", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "actinomation", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'actinomation'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_77MocSkO1RbfRmv3jKNi1ab0MCj"]}
+{"id": "dup-polymerisation-kinetics-robot", "title": "A robotic approach to polymerisation kinetics: a case study on copolymerisation parameter estimation", "doi": "10.1039/d6sc02232d", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13103962/", "year": 2026, "venue": "Chemical science", "open_access_license": "see corpus", "code_url": "https://github.com/prdmonash/a-robotic-approach-to-polymerization-kinetics-a-case-study-on-copolymerization-parameter-estimation", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "polymerisation-kinetics-robot", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'polymerisation-kinetics-robot'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_M8z99yDb5EkvjYFzUescLig11w1"]}
+{"id": "dup-apex-.5c00189", "title": "APEX: Automated Protein EXpression in Escherichia coli", "doi": "10.1021/acssynbio.5c00189", "paper_url": "https://doi.org/10.1021/acssynbio.5c00189", "year": 2025, "venue": "ACS synthetic biology", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "apex", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'apex'; recorded for dedup, not a new candidate. (different DOI/version of the same work)", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_L10Rrw6Qct5bmxMQZxINzp50vxX"]}
+{"id": "dup-slowpoke", "title": "Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex", "doi": "10.1021/acssynbio.5c00629", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12930513/", "year": 2026, "venue": "ACS synthetic biology", "open_access_license": "see corpus", "code_url": "https://github.com/tom-ellis-lab/slowpoke", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "slowpoke", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'slowpoke'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_LNZyRxr1lSEMWPy1Vdf6cr3yWaM"]}
+{"id": "dup-ht-mic", "title": "Development of a high-throughput minimum inhibitory concentration (HT-MIC) testing workflow", "doi": "10.3389/fmicb.2023.1079033", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10249070/", "year": 2023, "venue": "Frontiers in microbiology", "open_access_license": "see corpus", "code_url": "https://github.com/suman921/ht-mic", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "ht-mic", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'ht-mic'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_PlvV7JLJokbyIWF5oxnNLHphr3S"]}
+{"id": "dup-pipette-tool-change", "title": "Leveraging flexible pipette-based tool changes to transform liquid handling systems into dual-function sample preparation and imaging platforms", "doi": "10.1016/j.ohx.2025.e00653", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12181777/", "year": 2025, "venue": "HardwareX", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "pipette-tool-change", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'pipette-tool-change'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_BdogUnnIJ6d8G6DQNcIfOnauaqO"]}
+{"id": "dup-assemblytron", "title": "AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots", "doi": "10.1093/synbio/ysac032", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9832943/", "year": 2022, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "see corpus", "code_url": "http://doi.org/10.5281/zenodo.7250273", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "assemblytron", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'assemblytron'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_8xuxgObx5ypgVt6sA0FbA54CFPd"]}
+{"id": "dup-assemblytron-4220-7_8", "title": "Biofoundry-Assisted Golden Gate Cloning with AssemblyTron", "doi": "10.1007/978-1-0716-4220-7_8", "paper_url": "https://doi.org/10.1007/978-1-0716-4220-7_8", "year": 2025, "venue": "Methods in molecular biology (Clifton, N.J.)", "open_access_license": "see corpus", "code_url": "http://doi.org/10.5281/zenodo.7250273", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "assemblytron", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'assemblytron'; recorded for dedup, not a new candidate. (different DOI/version of the same work)", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_1JIgBBpQddQw7RVtolfypecj219"]}
+{"id": "dup-dna-bot", "title": "DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology", "doi": "10.1093/synbio/ysaa010", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7476404/", "year": 2020, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "see corpus", "code_url": "https://github.com/basic-dna-assembly/dna-bot/tree/oup_synbio", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "dna-bot", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'dna-bot'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_NmKFNEvS0wjBcYrMLAmr2nphJLQ"]}
+{"id": "dup-low-cost-pipetting-robot-slas", "title": "Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling", "doi": "10.1177/2472630320973591", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8143861/", "year": 2020, "venue": "SLAS technology", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "low-cost-pipetting-robot-slas", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'low-cost-pipetting-robot-slas'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Etubiyg36H4b1fVLvDugE61OFbs"]}
+{"id": "dup-lap-transposon-genotyping", "title": "Automated workflow for genotyping individual transposon library variants", "doi": "10.1186/s44330-025-00054-3", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7618916/", "year": 2026, "venue": "BMC methods", "open_access_license": "see corpus", "code_url": "https://github.com/biocomputationlab/laprepository", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "lap-transposon-genotyping", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'lap-transposon-genotyping'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_GaUhBNTZn866AJoqs4DdjHyuah0"]}
+{"id": "dup-covid19clinic", "title": "Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR", "doi": "10.1371/journal.pone.0252509", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8279358/", "year": 2021, "venue": "PloS one", "open_access_license": "see corpus", "code_url": "https://github.com/cdb-corebm/covid19clinic", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "covid19clinic", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'covid19clinic'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_M2MkI8RIGZLnSQ1BD4nrAQZreQd"]}
+{"id": "dup-opencell-automation", "title": "Open-source cell culture automation system with integrated cell counting for passaging microplate cultures", "doi": "10.1093/pnasnexus/pgaf385", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12750449/", "year": 2025, "venue": "PNAS nexus", "open_access_license": "see corpus", "code_url": "https://github.com/czbiohub-sf/2021-opencell-microscopy-automation", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "opencell-automation", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'opencell-automation'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_A9y1CexucKpkrG41mv7HHWXcrSy"]}
+{"id": "dup-pipetting-speed-ot2", "title": "Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq", "doi": "10.17912/micropub.biology.001566", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12117386/", "year": 2025, "venue": "microPublication biology", "open_access_license": "see corpus", "code_url": "https://github.com/bioinfo-tsukuba/ot2_pipspd_paper", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "pipetting-speed-ot2", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'pipetting-speed-ot2'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_RGU4qmDzfSwSXHM42J56x3dqbUw"]}
+{"id": "dup-protein-crystallization-ot2", "title": "Automation of protein crystallization scaleup via Opentrons-2 liquid handling", "doi": "10.1016/j.slast.2025.100268", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12229254/", "year": 2025, "venue": "SLAS technology", "open_access_license": "see corpus", "code_url": "https://github.com/jbderoo/opentrons2-protein-crystallization", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "protein-crystallization-ot2", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'protein-crystallization-ot2'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CDkn5snHqKQ1YO4dNo8xoEuxSfN"]}
+{"id": "dup-copick", "title": "Technical upgrade of an open-source liquid handler to support bacterial colony screening", "doi": "10.3389/fbioe.2023.1202836", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10315574/", "year": 2023, "venue": "Frontiers in bioengineering and biotechnology", "open_access_license": "see corpus", "code_url": "https://github.com/sysbio-cnb/copick", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "copick", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'copick'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_RkggefLR7wXfYye0lGqMvlR8Ke"]}
+{"id": "dup-moeller-hackflex", "title": "A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes", "doi": "10.1186/s13059-022-02777-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9558970/", "year": 2022, "venue": "Genome biology", "open_access_license": "see corpus", "code_url": "https://github.com/cumoellerlab/moeller_opentrons_protocol_library", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "moeller-hackflex", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'moeller-hackflex'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_MaWMpY96fowT57zJSiwCjv1KvaN"]}
+{"id": "dup-covid-diagnostic-capacity-2022", "title": "Optimization and adaptation of the diagnostic capacity for the performance of large volumes of SARS-CoV-2 RT-PCR", "doi": "10.1016/j.eimce.2022.05.001", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9127703/", "year": 2022, "venue": "Enfermedades infecciosas y microbiologia clinica (English ed.)", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "covid-diagnostic-capacity-2022", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'covid-diagnostic-capacity-2022'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_S5GHvIO0WeJq52cLQHfWVJVzhqy"]}
+{"id": "dup-covid-diagnostic-capacity-2021", "title": "Optimization and adaptation of the diagnostic capacity for the performance of large volumes of SARS-CoV-2 RT-PCR", "doi": "10.1016/j.eimc.2021.01.014", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7877244/", "year": 2021, "venue": "Enfermedades infecciosas y microbiologia clinica (English ed.)", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "covid-diagnostic-capacity-2021", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'covid-diagnostic-capacity-2021'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_OdVlxGttXtc1mrMiDYLJZWOV5oi"]}
+{"id": "dup-chory-2021-hamilton", "title": "Enabling high-throughput biology with flexible open-source automation", "doi": "10.15252/msb.20209942", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7993322/", "year": 2021, "venue": "Molecular systems biology", "open_access_license": "see corpus", "code_url": "https://github.com/dgretton/pyhamilton_population_dynamics", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'chory-2021-hamilton'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Z0QqQMnFRRHUJGhbxVGLSsavNDb"]}
+{"id": "dup-personal-pipetting-robots", "title": "Open-source personal pipetting robots with live-cell incubation and microscopy compatibility", "doi": "10.1038/s41467-022-30643-7", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9151679/", "year": 2022, "venue": "Nature communications", "open_access_license": "see corpus", "code_url": "https://github.com/csdgroup/phil", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "personal-pipetting-robots", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'personal-pipetting-robots'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_EUHMTk0r9F4O02hzFCYQA7Ed61h"]}
+{"id": "dup-sars-cov-2-rtqpcr-jove", "title": "Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots", "doi": "10.3791/63395", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9199378/", "year": 2022, "venue": "Journal of visualized experiments : JoVE", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "sars-cov-2-rtqpcr-jove", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'sars-cov-2-rtqpcr-jove'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_DZyA4PnsIe8DnhiCvLzdcTnLAds"]}
+{"id": "dup-botany-kiag066", "title": "BOTany methods: accessible automation for plant synthetic biology", "doi": "10.1093/plphys/kiag066", "paper_url": "https://doi.org/10.1093/plphys/kiag066", "year": 2026, "venue": "Plant physiology", "open_access_license": "see corpus", "code_url": "https://github.com/cvoiniciuc/botany", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "botany", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'botany'; recorded for dedup, not a new candidate. (different DOI/version of the same work)", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_5rGy5qncErBiV0p4UcnR6AdyaEz"]}
+{"id": "dup-infectious-disease-diagnostic-workflow", "title": "An Automated Versatile Diagnostic Workflow for Infectious Disease Detection in Low-Resource Settings", "doi": "10.3390/mi15060708", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11205418/", "year": 2024, "venue": "Micromachines", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "infectious-disease-diagnostic-workflow", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'infectious-disease-diagnostic-workflow'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_4Jr7X2fDzRWReAtldmDVqGS5JKk"]}
+{"id": "dup-sars-cov-2-magbead-extraction", "title": "SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP", "doi": "10.3390/v12080863", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7472728/", "year": 2020, "venue": "Viruses", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "sars-cov-2-magbead-extraction", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'sars-cov-2-magbead-extraction'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CCNZbFA2sV6RQLfqeerWgwiVdHB"]}
+{"id": "dup-sidekick", "title": "Sidekick: A Low-Cost Open-Source 3D-printed liquid dispensing robot", "doi": "10.1016/j.ohx.2022.e00319", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9168727/", "year": 2022, "venue": "HardwareX", "open_access_license": "see corpus", "code_url": "https://github.com/rodolfokeesey/liquid-handler", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "sidekick", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'sidekick'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_HMss8lpEbBDRaA8zrBq5FpGNP5R"]}
+{"id": "dup-auto-qpcr", "title": "Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data", "doi": "10.1038/s41598-021-99727-6", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8556264/", "year": 2021, "venue": "Scientific reports", "open_access_license": "see corpus", "code_url": "https://github.com/neuroeddu/auto-qpcr", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "auto-qpcr", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'auto-qpcr'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Qo3BjINV5mV7gE8itVvQtlwh8Co"]}
+{"id": "dup-maldi-surface-throughput", "title": "Customized Surface Design to Increase Throughput of Ambient Ionization Mass Spectrometry Lipidomics", "doi": "10.1021/jasms.3c00062", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12765230/", "year": 2023, "venue": "Journal of the American Society for Mass Spectrometry", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "maldi-surface-throughput", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'maldi-surface-throughput'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_TQC6jMfNFzVQSd7e84TLXQxW8OF"]}
+{"id": "aml-drug-synergy-pyhamilton", "title": "High-throughput approaches to uncover synergistic drug combinations in leukemia", "doi": "10.1016/j.slasd.2023.04.004", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10449086/", "year": 2023, "venue": "SLAS discovery : advancing life sciences R & D", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/stefangolas/drug_dilutions", "code_files": ["robot_method.py"], "code_license": "none", "robot_platform": "hamilton", "api": "other", "protocol_category": "drug combination dilution matrix and dosing for synergy screening (leukemia cells)", "results_evidence": "Multidimensional drug-combination screens identified synergistic combinations in leukemia (H3K27 modification-related), with viability readouts and synergy scores.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "pyhamilton script (needs Hamilton VENUS layout/.lay file, Windows); no license; could be ported to PLR/OT-2 as a serial-dilution matrix task.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_2wDq20Fozm18kEnjSpNC6xxLKdO"]}
+{"id": "catib-screening", "title": "\"High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization\"", "doi": "10.1186/s12934-024-02319-y", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10894497/", "year": 2024, "venue": "Microbial cell factories", "open_access_license": "cc-by", "code_url": "https://github.com/JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "semi-automated cloning of 63 CatIB variants and automated inclusion-body activity screening", "results_evidence": "Generated 63 BsGDH CatIB variants; automated screening workflow validated and used to rank variant activities in parallel.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Supplement repo has modelling notebooks only (GPL-3.0); robot methods (Tecan/OT-2 mix) not released as code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_6dJEL33HqVFIFPopNLW6tccMbse"]}
+{"id": "photo-atrp-automation", "title": "Automation-Assisted Photoinduced Atom Transfer Radical Polymerization", "doi": "10.1021/acspolymersau.5c00067", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12903423/", "year": 2025, "venue": "ACS polymers Au", "open_access_license": "cc-by", "code_url": "https://github.com/GormleyLab/polymerization_planner", "code_files": [], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "photoinduced ATRP polymerisation setup in well plates", "results_evidence": "Automation-assisted photo-ATRP generated high-throughput kinetics/dispersity data across ligands, initiators and monomers incl. MMA.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Planner generates volume tables; no robot protocol code; chemistry.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_4GfVPLKchWKr84K7MZOvdZ8oxw0"]}
+{"id": "findus", "title": "FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences", "doi": "10.1177/2472630319877374", "paper_url": "https://doi.org/10.1177/2472630319877374", "year": 2019, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology, verify)", "code_url": "https://github.com/FBarthels/FINDUS", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "DIY 3D-printed liquid handling workstation", "results_evidence": "Pipetting errors <0.3%; showcase biology and chemistry applications.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom firmware/GUI (GPL-3.0); not Opentrons/PLR.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_XhtKE5t0nOWiZV3YJgBgFJpKrAq"]}
+{"id": "bioclonebot", "title": "BioCloneBot: A versatile, low-cost, and open-source automated liquid handler", "doi": "10.1016/j.ohx.2024.e00516", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10955647/", "year": 2024, "venue": "HardwareX", "open_access_license": "cc-by", "code_url": "https://osf.io/qdp7v", "code_files": [], "code_license": "see OSF (HardwareX requires open licence)", "robot_platform": "other", "api": "other", "protocol_category": "DIY low-cost liquid handler", "results_evidence": "Validated accuracy and repeatability across liquid handling tasks.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom hardware/Arduino code (GitHub KoaCWells/BioCloneBot has no .py).", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_AwknKbU7IM88dQ9ywOSIu4JiHte"]}
+{"id": "ot2eye", "title": "OT2Eye: Detection of labware conditions to monitor and extend affordable liquid-handling robots", "doi": "10.1016/j.slast.2026.100410", "paper_url": "https://doi.org/10.1016/j.slast.2026.100410", "year": 2026, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": "https://github.com/bioinfo-tsukuba/ot2eye", "code_files": [], "code_license": "MIT", "robot_platform": "ot2", "api": "other", "protocol_category": "labware/tip detection from OT-2 camera images", "results_evidence": "High accuracy identifying plates and tip racks and their deck positions, and tip presence/absence.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Computer-vision tool, not a wet-lab protocol (MIT); possible verifier aid.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_67bEY0DCJ8NvYefU4Qifg3lJnc4"]}
+{"id": "evobot", "title": "New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot", "doi": "10.1177/2472630316689285", "paper_url": "https://doi.org/10.1177/2472630316689285", "year": 2017, "venue": "SLAS technology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "modular open-source liquid handling robot (droplet/artificial life experiments)", "results_evidence": "New capabilities demonstrated for long-running artificial-life experiments.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom robot software; code not verified.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_TYMC8o5BkU3fl3B2gzqtDi6PWI0"]}
+{"id": "lego-lhr-stem", "title": "Liquid-handling Lego robots and experiments for STEM education and research", "doi": "10.1371/journal.pbio.2001413", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5360201/", "year": 2017, "venue": "PLoS biology", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "educational Lego liquid handling robot", "results_evidence": "Activities tested with school students; build and experiment instructions provided.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Lego EV3 programs; not relevant API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_XmDWjWZyNFqYeaKBXEulafS1PTK"]}
+{"id": "pr-pr", "title": "PR-PR: cross-platform laboratory automation system", "doi": "10.1021/sb4001728", "paper_url": "https://doi.org/10.1021/sb4001728", "year": 2014, "venue": "ACS synthetic biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "tecan", "api": "other", "protocol_category": "cross-platform protocol language (Golden Gate, Kunkel mutagenesis, Gibson)", "results_evidence": "Modified Golden Gate assembly run across liquid-handling robot, microfluidic and manual platforms; Kunkel and Gibson also implemented.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "PR-PR DSL compiled to Tecan; historical; no Python protocol.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_XTiO9qwkOd5IRMZcuTRMPGZeqBC"]}
+{"id": "tox-pipetting-robot", "title": "A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays", "doi": "10.1371/journal.pone.0179636", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5473567/", "year": 2017, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "water-quality whole-organism bioassay robot", "results_evidence": "Tested precision of automated pipetting for online toxicity bioassays.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom open hardware; no Opentrons/PLR code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_A6M2tuF3phVX1rCESXk3NmVObNT"]}
+{"id": "modular-pipetting-imaging-uc2", "title": "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications", "doi": "10.1002/adbi.202101063", "paper_url": "https://doi.org/10.1002/adbi.202101063", "year": 2021, "venue": "Advanced biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "other", "protocol_category": "automated sample prep + imaging (Opentrons + OpenFlexure/UC2/ImJoy)", "results_evidence": "Demonstrated automated pipetting-imaging feedback pipeline with low-cost microscopes.", "wet_lab_validated": true, "duplicate_of_existing": "uc2-hi2 (related openUC2 group; different paper)", "readiness": "no", "readiness_reason": "Code not verified via Amass text; paywalled.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_DSCQ9BbNl9zmxKKsvmsPTC2Tvdi"]}
+{"id": "flyspresso-embryo-ihc", "title": "An open-source semi-automated robotics pipeline for embryo immunohistochemistry", "doi": "10.1038/s41598-021-89676-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8119710/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/janelia-pypi/hybridizer_python", "code_files": [], "code_license": "not checked", "robot_platform": "other", "api": "other", "protocol_category": "Drosophila embryo fixation and staining robotics", "results_evidence": "Automated embryo fixation, colorimetric/antibody staining and adaptive confocal imaging demonstrated.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom fluidics controller, not a liquid-handler API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_M7a5zpr9onHlfNo2rvYxjaoYQJ8"]}
+{"id": "spatial-tx-bravo", "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues", "doi": "10.1186/s12864-020-6631-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7158132/", "year": 2020, "venue": "BMC genomics", "open_access_license": "cc-by", "code_url": "https://github.com/jemten/Bravo_ST", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "Spatial Transcriptomics library prep (Agilent Bravo)", "results_evidence": "Automated ST library prep cut prep time by 35%, increased samples per run and showed near-zero technical variability between preparations.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Agilent VWorks Bravo protocol files (non-Python); no license; good paper-only porting target (bead cleanups, many steps).", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_7iUsjz95kTSaVU3lS34UgJNbiDH"]}
+{"id": "miniaturized-16s-mosquito", "title": "High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity", "doi": "10.1128/mSystems.00166-18", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6222042/", "year": 2018, "venue": "mSystems", "open_access_license": "cc-by", "code_url": "https://www.protocols.io/view/high-throughput-miniaturized-16s-rrna-amplicon-lib-u2ieyce", "code_files": [], "code_license": "protocols.io (CC-BY)", "robot_platform": "other", "api": "other", "protocol_category": "miniaturised 16S rRNA amplicon library prep (5 uL, Mosquito HV/Echo)", "results_evidence": "Miniaturised 5 uL reactions matched standard 25 uL composition; validated on 46 fish x 5 body sites over seven months.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Step-by-step protocols.io only (TTP Mosquito/Echo); paper-only task possible.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_PDQ9xjdqhxi9EVLaXrTUadiioCv"]}
+{"id": "mngs-384-miniaturized", "title": "Miniaturization and optimization of 384-well compatible RNA sequencing library preparation", "doi": "10.1371/journal.pone.0206194", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6328170/", "year": 2019, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "miniaturised 384-well mNGS RNA library prep (Mosquito HTS)", "results_evidence": "ERCC spike-ins showed miniaturised prep fidelity equivalent to full-volume preps at much lower cost/time.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Private protocols.io link; non-Python liquid handler.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_FgoF22qjQ8MieBA6wiWMAws9TF3"]}
+{"id": "oscar-ur-arm", "title": "OSCAR: A Modular Open-Source Robotic Platform for Biological Laboratories", "doi": "10.1021/acssynbio.5c00733", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13010791/", "year": 2026, "venue": "ACS synthetic biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/rodrigue-laboratory/oscar", "code_files": [], "code_license": "BSD (oscar_task)", "robot_platform": "other", "api": "other", "protocol_category": "robot-arm pipetting of plasmid assembly workflow (PCR, assembly, transformation)", "results_evidence": "OSCAR executed a representative plasmid assembly workflow from PCR through enzymatic assembly and transformation using human lab equipment.", "wet_lab_validated": true, "duplicate_of_existing": "pipette-tool-change (same Rodrigue lab pipette tool)", "readiness": "no", "readiness_reason": "ROS/C++ MoveIt task code for a UR arm; not a liquid-handler protocol API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_7CMiao3MoyrlOaW8MxiwS5SEj8j"]}
diff --git a/research/expansion/amass_notes.md b/research/expansion/amass_notes.md
new file mode 100644
index 0000000..eac4fc1
--- /dev/null
+++ b/research/expansion/amass_notes.md
@@ -0,0 +1,54 @@
+# Amass search: Text2WetLab expansion candidates
+
+Source agent: amass. Output: `amass_candidates.jsonl` (109 rows: 76 screened candidates + 33 rows that duplicate corpus papers, with ids starting `dup-`).
+
+## Credits
+- Start: 50,005. End: 48,155. **Spent: 1,850** (cap 8,000).
+- Cost: about 0.4 credits per record with `include=fulltext` (a 25-record query cost about 10 credits).
+- About 6% of queries returned HTTP 500 on the first try. They were retried at a smaller `limit` (20, then 10), and all but about 4 recovered.
+
+## Queries run (about 190 distinct, all on biomedcore with fulltext)
+- **Platform terms:** "Opentrons", "Opentrons OT-2 liquid handling robot" (one query per year, 2019 to 2026), "Opentrons Python protocol code available" (one query per year, 2019 to 2026), "open-source liquid handling robot automated protocol" (one query per year), "Opentrons Flex" (several), "PyLabRobot", "pyhamilton Hamilton robot Python", "Hamilton STAR open-source python script", "Hamilton Venus", "Tecan EVO/Fluent script", "Biomek", "Echo acoustic", "liquid handling robot Python API", "github liquid handling robot protocol", "liquid handling robot protocol deposited Zenodo", "scripts for the OT-2 are available on GitHub", "custom Opentrons protocol was written in Python".
+- **Domain terms (about 120 queries):** OT-2 or Opentrons combined with PCR setup, qPCR, RNA extraction, DNA extraction (plant, soil), Golden Gate/MoClo, Gibson, transformation, miniprep, NGS/Nextera/RNA-seq/nanopore/16S library prep, normalization/PicoGreen, serial dilution/dose response, ELISA/immunoassay/serology, cell culture/passaging/transfection/organoid, plating/colony picking, protein expression/purification/solubility/thermal stability, CRISPR, cell-free, MIC/antimicrobial, metabolomics/LC-MS/MALDI/proteomics, COVID/pooling/LAMP/wastewater, ddPCR, ChIP, phage/plaque, Bacillus/Pseudomonas/Streptomyces/Mycobacterium/Plasmodium, zebrafish/Drosophila/C. elegans, crystallization, formulation/hydrogel/polymer/perovskite/electrochemistry/nanoparticles, self-driving lab/Bayesian optimisation, education/colour mixing.
+- **Totals:** 4,019 unique records retrieved. 964 mention liquid handlers anywhere. 135 have a liquid-handling robot as the main subject; those were screened by hand.
+- **Recall:** it plateaued. The last 20 queries added only 4 new relevant papers. Amass's full text often strips hyperlinks, so code URLs were also pulled from the Europe PMC full-text XML of 97 PMC papers. That step found about 25 extra repo links. GitHub searches (`gh search repos`) found repos for papers without links: MassSpecPreppy, RoboCTAB, OT2Eye, ot2_spot_assay, pipette_opt, ReacSight and FINDUS.
+
+## Verification method
+- **GitHub REST API:** it was rate-limited (the 5,000/hr limit is shared with other agents). Repos were therefore checked with a shallow `git clone` instead.
+- **Robot code:** each repo's `.py` files were grepped for `from/import opentrons`, `apiLevel`, v1-style `robot.`/`instruments.P*`, `pylabrobot`, `pyhamilton` and Flex `robotType`.
+- **Licence:** read from the LICENSE file.
+- **Zenodo:** records were checked through the Zenodo API.
+- **GitLab:** the Cambridge GitLab (PEG assay) was checked through the GitLab API.
+- **Simulation:** `opentrons_simulate` is not installed here, so no candidate was simulated. "Ready" is a judgement from reading the code.
+
+## Counts (76 screened candidates, excluding the 33 `dup-` rows)
+- **Verified robot code** (repo or file checked, with Opentrons/PLR/pyhamilton .py or Opentrons JSON): 23. Of these, 17 have Opentrons Python API v2 code, 1 is v1-only (krisp pooling), 2 are Opentrons Protocol Designer JSON (HCR on Flex, bean KASP), 1 is pyhamilton, and 1 is the PyLabRobot library. Non-Python vendor code was also found: Tecan .exd (roboRNA), Agilent Bravo, Myra, binary .pkg methods and LabDroid jobs.
+- **Readiness:** 3 ready, 22 partial, 51 no.
+- **New vs duplicate:**
+  - 33 Amass hits were papers already in the corpus. They are recorded as `dup-<slug>` rows. They cover 32 corpus slugs, including both the bioRxiv and journal DOIs of APEX, BOTany and AssemblyTron.
+  - 5 screened candidates are new papers that share code or a group with corpus entries, so `duplicate_of_existing` is filled in: y1h-yeast-lap (LAPrepository), galaxy-synbiocad (DNA-Bot), facs-automation (CZ Biohub), oscar-ur-arm (pipette-tool-change), modular-pipetting-imaging-uc2 (UC2).
+  - The other 71 screened candidates are fully new.
+- **Wet-lab validated:** 70 of 76.
+
+## Top 15 candidates
+1. **massspecpreppy** (Proteomics 2023): 10 OT-2 v2 scripts for BCA, SP3 digestion and Evotip loading. BCA recovery was 101.3% vs 96.3% manual. GPL-3.0. Ready, about 6 tasks.
+2. **tidytron** (SLAS Tech 2023): 37 OT-2 v2 scripts for washing and reusing tips and plates, validated against DNA, E. coli and yeast contamination. Apache-2.0. Ready, about 4 tasks.
+3. **lysostaphin-turbidity** (Microb Cell Fact 2026): one self-contained OT-2 turbidity/dilution assay script, quantifying 0.63 to 10 mg/L lysostaphin. AGPL-3.0, so it cannot be vendored. Ready, about 2 tasks.
+4. **beckham-enzyme-pipeline** (Sci Rep 2024): 21 OT-2 v2 scripts for transformation, cherry-picking and mag-bead Ni purification of 96 PET hydrolases (up to 400 ug each). No LICENSE. Partial, about 8 tasks.
+5. **roboctab** (Plants 2025): CTAB plant DNA extraction script in both OT-2 and Flex versions, a natural OT-2-to-Flex pair. No LICENSE. Partial, about 4 tasks.
+6. **peg-solubility-assay** (Sci Rep 2021, Cambridge GitLab): two OT-2 v2 scripts for PEG-titration protein solubility from about 200 ug of protein. No LICENSE. Partial, about 4 tasks.
+7. **ot2-yeast-spot-assay** (SLAS Tech 2022, bioinfo-tsukuba): yeast spot-assay protocol generator with a custom Petri-dish mount. No LICENSE. Partial, about 3 tasks.
+8. **pasta-spatial** (Nat Methods 2026): OT-2 v2 script for cyclic tyramide-oligo staining. Needs custom slide labware. No LICENSE. Partial.
+9. **krisp-sars2-pooling** (Sci Rep 2021): hypercube pools of 27 and 81 samples, Ct up to 32 detected. MIT, but the code is v1 API and needs porting. Partial.
+10. **y1h-yeast-lap** (Curr Protoc 2024): yeast one-hybrid screening using LAP-CellMediaInoculation OT-2 scripts. The code repo is already in the corpus; the paper is new. Partial.
+11. **ht-hcr-sea-urchin** (Development 2025): Flex Protocol Designer JSON for 48-well whole-mount HCR; 101 genes imaged. The only validated Flex workflow with code found. Partial.
+12. **openblend-media** (Biotech Bioeng 2021): MIT package that generates OT-2 media-blending plates; improved Pichia titre. Partial.
+13. **bean-kasp-anthracnose** (Plant Methods 2023): OT-2 JSON protocols for DNA extraction and KASP genotyping. No license. Partial.
+14. **aml-drug-synergy-pyhamilton** (SLAS Discov 2023): pyhamilton drug-combination dilution matrix, the one Hamilton-Python candidate found. No license. Partial.
+15. **roborna-nirvana** (Sci Rep 2023): Tecan EVO magnetic-bead RNA extraction plus nanopore variant calling. Detection limit comparable to commercial kits. Non-Python, so it suits a paper-only port task. Partial.
+
+Honourable mentions:
+- **No code yet, but high value if the supplementary files hold scripts** (each marked "no" or "partial"): swabseq-flex (Opentrons Flex NGS diagnostic, 2026), cfrna-extraction-pipeline (Nat Protoc), nfkb-luciferase-ot2 (SLAS), tmt-bead-platform-ot2 and auto-sp-proteomics (templates in SI).
+- **Related LLM-to-protocol work:** putzsebastian/KAISA-LSE_SDL-Platform (MIT) contains an "LLM protocol-generation replication study" with hundreds of GPT-generated Opentrons protocols.
+
+Estimated task yield: ready plus partial candidates give about 64 tasks in total; the 3 ready candidates give about 12 of them.
diff --git a/research/expansion/fault_report.md b/research/expansion/fault_report.md
new file mode 100644
index 0000000..f5d065c
--- /dev/null
+++ b/research/expansion/fault_report.md
@@ -0,0 +1,41 @@
+### ecoli-heat-shock-transformation
+- **Opus 5.5**: 
+  - FAULT `mix` pipette-mixes tubes_1_5ml_1 A1 (oracle never mixes here)
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: 
+  - FAULT `mix` pipette-mixes tubes_1_5ml_1 A1 (oracle never mixes here)
+### opentrons-rna-extraction
+- **Opus 5.5**: 
+  - FAULT `volume` 100 uL Extraction plate (slot 4) -> Elution plate per well; oracle 80 uL
+  - note `timing` total waits 15 min vs oracle 28 min
+  - note `magnet` magnet engaged 2x vs oracle 7x
+- **Sonnet 5.5**: 
+  - FAULT `order` adds samples 1-24 (slot 10) to sample plate before NEST 12 Well Reservoir 15 mL A2 (slot 5) (oracle order differs)
+  - FAULT `volume` 79,680 uL total sample plate (slot 4) -> waste plate; oracle 75,600 uL (+5%)
+  - FAULT `volume` 100 uL sample plate (slot 4) -> elution plate per well; oracle 80 uL
+  - note `timing` total waits 15 min vs oracle 28 min
+  - note `magnet` magnet engaged 2x vs oracle 7x
+- **Fable 5.1**: 
+  - FAULT `volume` 100 uL extraction plate (slot 4) -> elution plate per well; oracle 80 uL
+  - note `timing` total waits 15 min vs oracle 28 min
+  - note `magnet` magnet engaged 2x vs oracle 7x
+### split-200ul-two-wells
+- **Opus 5.5**: no faults vs oracle
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: no faults vs oracle
+### a1-a12-100ul
+- **Opus 5.5**: no faults vs oracle
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: no faults vs oracle
+### colony-pcr-screening
+- **Opus 5.5**: no faults vs oracle
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: no faults vs oracle
+### golden-gate-assembly
+- **Opus 5.5**: no faults vs oracle
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: no faults vs oracle
+### ampure-bead-cleanup
+- **Opus 5.5**: no faults vs oracle
+- **Sonnet 5.5**: no faults vs oracle
+- **Fable 5.1**: no faults vs oracle
diff --git a/research/expansion/github_candidates.jsonl b/research/expansion/github_candidates.jsonl
new file mode 100644
index 0000000..d5d6cab
--- /dev/null
+++ b/research/expansion/github_candidates.jsonl
@@ -0,0 +1,77 @@
+{"id": "olh-turbidostat-plr", "title": "A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments", "doi": "10.64898/2026.03.02.709168", "paper_url": "https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full", "year": 2026, "venue": "bioRxiv", "open_access_license": "publisher TDM/other: https://www.biorxiv.org/about/FAQ#license", "code_url": "https://github.com/chory-lab/plr-turbidostat", "code_files": ["turbidostat.py", "simple_transfer.py", "tests/test_dilute_200ul.py", "tests/test_dilute_single_column.py", "tests/calibration.py"], "code_license": "none", "stars": 2, "last_push": "2026-05-07", "robot_platform": "pylabrobot", "api": "pylabrobot", "protocol_category": "turbidostat / continuous culture; pipetting accuracy calibration", "results_evidence": "OLH pipetting MAE 4.1 vs 7.2 uL manual (p<0.005); closed-loop turbidostat held ~200 cultures at OD setpoints.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyLabRobot code for a custom open liquid handler (OLH) + Byonoy reader; no license on turbidostat repo; full build package promised on publication; simulation needs custom backend.", "est_tasks": 4, "source_agent": "github", "also_code": ["https://github.com/chory-lab/olh-pylabrobot (MIT PLR fork with OLH backend)"]}
+{"id": "labscriptai-protein-eng", "title": "Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows", "doi": "10.1101/2025.09.30.679666", "paper_url": "https://www.biorxiv.org/content/10.1101/2025.09.30.679666v1.full", "year": 2025, "venue": "bioRxiv", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/KRATSZ/LabScript-AI", "code_files": ["labscriptai/planir/plr_sim.py", "labscriptai/webdemo/python/compile_hamilton.py", "labscriptai/plugins/mcp/opentrons-mcp/examples/flex_noop_protocol.py"], "code_license": "none", "stars": 131, "last_push": "2026-10-10", "robot_platform": "other", "api": "pylabrobot", "protocol_category": "LLM protocol generation; cell-free GFP variant characterisation; enzyme screening; fluorescence calibration", "results_evidence": "Fluorescence standard curves CV<5%, R2>0.999; 318 GFP variants characterised (best 5.0x avGFP); enzyme double mutants >3x catalytic efficiency.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Repo is an LLM agent/tooling, not the executed protocol scripts; no license; experiments span OT-2, Flex, Hamilton Vantage, Tecan Fluent; executed scripts would need extraction. Also a competitor system to Text2WetLab (useful as related work).", "est_tasks": 2, "source_agent": "github", "also_code": ["https://github.com/KRATSZ/labscriptai-ot (curated OT protocol library)"]}
+{"id": "har1eyk-starlet-protein-extraction", "title": "hamilton-starlet-scripts (PyLabRobot STARlet protein extraction / Orange G volume tests)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/har1eyk/hamilton-starlet-scripts", "code_files": ["Exp1021-Automated_Protein_Extraction/ape_96w_protocol.py", "Exp1021-Automated_Protein_Extraction/bpq_protocol.py"], "code_license": "none", "stars": 0, "last_push": "2026-07-03", "robot_platform": "hamilton", "api": "pylabrobot", "protocol_category": "protein extraction; volume QC (Orange G)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Genuine PLR STARlet protocols but no paper/results and no license.", "est_tasks": 1, "source_agent": "github"}
+{"id": "pioneer-ngs-plr", "title": "ngs_library_prep (Illumina library prep on Hamilton STARlet with PyLabRobot)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Pioneer-Research-Labs/ngs_library_prep", "code_files": ["methods/startup.py"], "code_license": "none", "stars": 12, "last_push": "2026-04-02", "robot_platform": "hamilton", "api": "pylabrobot", "protocol_category": "NGS library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "pioneer-ngs", "readiness": "partial", "readiness_reason": "Already in corpus (pioneer-ngs); no paper, no license.", "est_tasks": 0, "source_agent": "github"}
+{"id": "labop-pcr-plr", "title": "LabOP (Laboratory Open Protocol Language) PCR -> PyLabRobot example", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Bioprotocols/labop", "code_files": ["examples/protocols/pcr_pylabrobot/pcr_pylabrobot.py"], "code_license": "MIT", "stars": 51, "last_push": "2024-10-07", "robot_platform": "pylabrobot", "api": "pylabrobot", "protocol_category": "PCR setup (protocol-language compiler example)", "results_evidence": null, "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Compiler example, no wet-lab results; useful only as format reference.", "est_tasks": 0, "source_agent": "github"}
+{"id": "msd-biochem-assays-ot2", "title": "Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler", "doi": "10.1016/j.slast.2024.100205", "paper_url": "https://doi.org/10.1016/j.slast.2024.100205", "year": 2024, "venue": "SLAS Technology", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays", "code_files": ["Bradford_standard_curve.py", "PicoGreen_standard_curve_YW_validated.py"], "code_license": "Apache-2.0", "stars": 1, "last_push": "2024-08-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Bradford and PicoGreen standard curves / quantitation assays", "results_evidence": "SLAS Technology 2024 paper compares OT-2 Bradford/PicoGreen standard curves and sample quantitation to manual (linearity, CV, accuracy).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Two self-contained apiv2 scripts, Apache-2.0, open-access SLAS paper with validated assay results; standard labware.", "est_tasks": 4, "source_agent": "github"}
+{"id": "roboctab-dna-extraction", "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping", "doi": "10.3390/plants14152263", "paper_url": "https://www.mdpi.com/2223-7747/14/15/2263", "year": 2025, "venue": "Plants", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/tomstamour/RoboCTAB", "code_files": ["RoboCTAB_OT2.py", "RoboCTAB_Flex.py"], "code_license": "none", "stars": 2, "last_push": "2026-02-18", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plant DNA extraction (CTAB)", "results_evidence": "Plants 2025 reports DNA yield/purity and downstream genotyping success from robot-extracted plant DNA vs manual CTAB.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "OT-2 and Flex apiv2 scripts, CC BY MDPI paper with results; repo has no license file (flag), may need custom labware defs.", "est_tasks": 4, "source_agent": "github"}
+{"id": "arcadia-his-elisa-ot2", "title": "Automated Cayman His-tag ELISA on the Opentrons OT-2 (Arcadia Science pub)", "doi": "10.57844/arcadia-n03x-vb23", "paper_url": "https://thestacks.org/publications/resource-automated-cayman-his-tag-elisa", "year": 2026, "venue": "Arcadia Science (The Stacks pub) + protocols.io", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow", "code_files": ["scripts/ot2_p1000single_elisa_sample_loading_final.py", "scripts/ot2_p1000single_elisa_sample_loading_waste_chute.py", "scripts/ot2_p300multi_elisa_wash_substrate.py"], "code_license": "MIT", "stars": 3, "last_push": "2026-06-10", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "ELISA (sample/standard loading, plate washing, substrate addition)", "results_evidence": "Pub reports OT-2 ELISA standard curves (4PL fit) and back-calculated His-tagged protein concentrations, with an example analysis notebook on real run data.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT code, open pub + protocols.io, CSV plate map input; custom waste chute variant is optional.", "est_tasks": 4, "source_agent": "github"}
+{"id": "ant-cloning-ot2", "title": "Automating Cloning by Natural Transformation", "doi": "10.1021/acssynbio.0c00240", "paper_url": "https://doi.org/10.1021/acssynbio.0c00240", "year": 2020, "venue": "ACS Synthetic Biology", "open_access_license": "publisher TDM/other: https://doi.org/10.15223/policy-029", "code_url": "https://github.com/ljm176/ANTCloning", "code_files": ["Step 1_PCRSetup.py", "Step 2_Dilution and Digestion.py", "Step 3_OEPCR.py", "Step 4_Transformation.py", "Step 5_Plating.py", "Alternates/Step3_Gibson.py"], "code_license": "none", "stars": 1, "last_push": "2021-06-25", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cloning: PCR setup, DpnI digestion, overlap-extension PCR, natural transformation of Acinetobacter baylyi, plating", "results_evidence": "ACS Synth Biol 2020 reports transformation/cloning efficiencies and success rates for automated natural-transformation cloning in A. baylyi ADP1.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Five-step apiv2 pipeline with simulation notebook; no repo license; check paper OA status (ACS, possibly not OA). Same author as existing transporter-screening.", "est_tasks": 6, "source_agent": "github"}
+{"id": "tobis-cytof-barcoding-ot2", "title": "Multiplexed single-cell analysis of organoid signaling networks", "doi": "10.1038/s41596-021-00603-4", "paper_url": "https://doi.org/10.1038/s41596-021-00603-4", "year": 2021, "venue": "Nature Protocols", "open_access_license": "publisher TDM/other: https://www.springer.com/tdm", "code_url": "https://github.com/TAPE-Lab/OT-2_Code", "code_files": ["TOBis_Barcoding/Barcode_Production/126_Plex_Production_Protocol.py", "TOBis_Barcoding/Barcode_Production/35_Plex_Production_Protocol.py", "TOBis_Barcoding/Barcode_Aliquoting/35_Plex_Aliquoting/35_Plex_Aliquoting.py", "REPO/REPO_126_plex.py"], "code_license": "none", "stars": 1, "last_push": "2021-11-24", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "mass-cytometry barcode (TOBis) production and aliquoting", "results_evidence": "Nature Protocols 2021 (and Nat Methods 2020) report multiplexed CyTOF organoid signalling data using OT-2-produced 35/126-plex TOBis barcodes.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean apiv2 scripts but no license; Nature Protocols likely paywalled (check PMC); robot step is reagent prep so results are indirect.", "est_tasks": 4, "source_agent": "github"}
+{"id": "ot2-cherrypick", "title": "OT2-CherryPick: A Zero-Install Web Platform for Orchestrating Complex Liquid Handling on the Opentrons OT-2", "doi": "10.26434/chemrxiv.15000637", "paper_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15000637/v1", "year": 2026, "venue": "ChemRxiv", "open_access_license": "unknown (ChemRxiv; check)", "code_url": "https://github.com/HiteSit/OT2_CherryPick", "code_files": ["CherryPick_OT2.py"], "code_license": "GPL-3.0", "stars": 2, "last_push": "2026-06-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CSV-driven cherry-picking / liquid transfer generator", "results_evidence": "ChemRxiv preprint describing a GUI/CSV cherry-picking platform; validation is mainly simulation/operational, check for gravimetric data.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "GPL-3.0 protocol generator rather than a fixed experiment; results evidence unclear.", "est_tasks": 1, "source_agent": "github", "crossref_error": "HTTP Error 404: Not Found"}
+{"id": "cbgp-transposon-genotyping-ot2", "title": "High-throughput workflow for the genotypic characterization of transposon library variants (protocols.io, CBGP)", "doi": "10.17504/protocols.io.kqdg394jzg25/v1", "paper_url": "https://doi.org/10.17504/protocols.io.kqdg394jzg25/v1", "year": 2023, "venue": "protocols.io", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/Biocomputation-CBGP/OT2", "code_files": ["AntibioticPlatesGeneration/ScriptPlateGenerationAndIncubation.py", "ColonySelection/ColonySelectionScript.py", "MergingSamplesSourcePlates/ScriptMergeSamplesN1plate.py", "GoldenStandardAssembly/MoCloWithoutMixing.py"], "code_license": "none", "stars": 0, "last_push": "2023-08-22", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "antibiotic plate prep, colony selection, sample merging, MoClo assembly", "results_evidence": "protocols.io workflows from the CBGP group; wet-lab results are in the related transposon-genotyping paper already in corpus.", "wet_lab_validated": "unknown", "duplicate_of_existing": "lap-transposon-genotyping", "readiness": "partial", "readiness_reason": "Same group/workflow as existing lap-transposon-genotyping (BiocomputationLab); no license; custom 3D-printed labware.", "est_tasks": 2, "source_agent": "github"}
+{"id": "exfab-qiaseq-flex", "title": "QIAseq FX library prep on Opentrons Flex NGS workstation (ExFAB, protocols.io)", "doi": "10.17504/protocols.io.n2bvjer3pgk5/v1", "paper_url": "https://doi.org/10.17504/protocols.io.n2bvjer3pgk5/v1", "year": 2025, "venue": "protocols.io", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/exfab/Opentrons_Flex_ExFAB", "code_files": ["QIASeq FX 48x 6_24_25.py"], "code_license": "GPL-3.0", "stars": 0, "last_push": "2025-10-21", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "NGS library prep (bee gut libraries)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Flex script + protocols.io only; no paper with results.", "est_tasks": 1, "source_agent": "github"}
+{"id": "myrplate-ect-casting-flex", "title": "myrPlate engineered cardiac tissue casting on Opentrons Flex", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15", "code_files": ["myrPlate_tissue_casting_8Ch1ml_Fast_V15-ECTsFinal.py", "myrPlate-V15(aspiration).py", "myrPlate-V15(dispensing).py"], "code_license": "MIT", "stars": 1, "last_push": "2026-09-13", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "tissue engineering: cell-laden collagen casting", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT Flex script with run video; manuscript not yet linked; custom myrPlate labware.", "est_tasks": 1, "source_agent": "github"}
+{"id": "gfp-codon-burden-ot2", "title": "Codon usage modulates the relationship between the burden and yield of protein overexpression", "doi": "10.1186/s13036-025-00521-z", "paper_url": "https://doi.org/10.1186/s13036-025-00521-z", "year": 2025, "venue": "Journal of Biological Engineering", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/alexismhill3/gfp_deoptimization_burden", "code_files": ["wet_scripting/low_temp_day_1/generate_protocol.py", "wet_scripting/low_temp_day_1/base_protocol_multichannel.py", "wet_scripting/low_temp_day_1/complete_protocol.py", "wet_scripting/low_temp_day_2/complete_protocol.py", "wet_scripting/low_temp_day_3/complete_protocol.py"], "code_license": "MIT", "stars": 0, "last_push": "2025-04-30", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "bacterial growth/induction burden assay (IPTG titration, GFP + OD plate-reader)", "results_evidence": "J Biol Eng 2025 (preprint 10.1101/2024.11.28.625058) reports growth-rate burden vs GFP yield across codon-deoptimised strains; raw plate-reader data and processed data are in the repo.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT repo with apiLevel 2.18 protocols generated from plate-reader CSV, raw+processed data included, CC BY paper; generator needs input CSV but complete_protocol.py is concrete.", "est_tasks": 4, "source_agent": "github"}
+{"id": "pudu-synbio-ot2", "title": "PUDU (Protocol Unified Design Unit) - OT-2 synthetic biology workflows", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/RudgeLab/PUDU", "code_files": ["scripts/automated_ot2/Automated_Golden_Gate.py", "scripts/automated_ot2/run_Loop_assembly.py", "scripts/automated_ot2/run_Bacterial_Transformation.py", "scripts/automated_ot2/run_Plating.py", "scripts/automated_ot2/run_iGEM_gfp_od.py", "scripts/automated_ot2/run_iGEM_rgb_od.py"], "code_license": "MIT", "stars": 6, "last_push": "2026-07-14", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate / Loop assembly, transformation, plating, iGEM GFP/OD calibration", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, many apiv2 scripts (Rudge/Myers labs); no linked paper with results found in README.", "est_tasks": 2, "source_agent": "github"}
+{"id": "evogen-ot-library", "title": "EvoGenOT (UCPH EvoGenomics Opentrons protocol library)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/anttonalberdi/EvoGenOT", "code_files": ["Extractions/D-Rex/1_D-Rex_initial_v2.py", "Extractions/D-Rex/2_D-Rex_RNA_v2_part1.py", "Extractions/D-Rex/3_D-Rex_DNA_v2.py", "BEST_purification_14102020.py", "Library_Build/BEST/1_BEST_ER.v2.py"], "code_license": "none", "stars": 3, "last_push": "2023-03-10", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA/RNA co-extraction (D-Rex), BEST library build, bead purification", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Mixed v1/v2 scripts, no license; BEST library protocol is published (Car\u00f8e et al. 2018 MEE) but not linked from repo \u2014 would need tracing.", "est_tasks": 2, "source_agent": "github"}
+{"id": "artic-normalisation-esr", "title": "ESR-NZ ARTIC normalisation/end-repair/barcoding (OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/ESR-NZ/opentrons_protocols", "code_files": ["normalisation_artic.py", "normalisation_artic_multi.py", "NGS_normalisation.py"], "code_license": "none", "stars": 0, "last_push": "2020-06-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 ARTIC DNA normalisation + nanopore end-repair/barcoding", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper/license; reads plate-reader xlsx at runtime.", "est_tasks": 1, "source_agent": "github"}
+{"id": "amplicon-seq-bisanz", "title": "AmpliconSeq (16S amplicon library OT-2 scripts, Bisanz lab)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/jbisanz/AmpliconSeq", "code_files": ["ot2_scripts/1_ZymoMagWash.py", "ot2_scripts/2_PrimaryPCR.py", "ot2_scripts/3_CheryPickAndIndex_template.py", "ot2_scripts/4_PoolEquimolar_template.py", "ot2_scripts/O4_AmpureXPWash.py"], "code_license": "none", "stars": 8, "last_push": "2021-10-04", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "16S amplicon library prep (extraction wash, PCR, indexing, pooling, AMPure)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean pipeline with wet-lab markdown protocols but no paper/results, no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "lysostaphin-turbidity-ot2", "title": "Turbid but accurate: automating lysostaphin quantification including uncertainty quantification", "doi": "10.1186/s12934-025-02911-w", "paper_url": "https://doi.org/10.1186/s12934-025-02911-w", "year": 2026, "venue": "Microbial Cell Factories", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025", "code_files": ["code/Turbidity_assay_OT_8samples.py"], "code_license": "AGPL-3.0", "stars": 0, "last_push": "2026-08-26", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "enzyme activity assay (lysostaphin turbidity / bacteriolysis kinetics)", "results_evidence": "Microb Cell Fact 2026 reports automated turbidity-based lysostaphin quantification with Bayesian uncertainty quantification vs reference; raw data in repo.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Single apiv2 OT-2 script, raw data + manuscript in repo, CC BY journal; AGPL-3.0 code (cannot be vendored, link only).", "est_tasks": 2, "source_agent": "github"}
+{"id": "massspecpreppy-ot2", "title": "MassSpecPreppy\u2014An end\u2010to\u2010end solution for automated protein concentration determination and flexible sample digestion for proteomics applications", "doi": "10.1002/pmic.202300294", "paper_url": "https://doi.org/10.1002/pmic.202300294", "year": 2023, "venue": "PROTEOMICS", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/stemicha/MassSpecPreppy", "code_files": ["OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_mix.py"], "code_license": "GPL-3.0", "stars": 0, "last_push": "2026-09-10", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics: BCA protein assay + reduction/alkylation + SP3 digestion", "results_evidence": "Proteomics 2023 reports BCA accuracy and proteomics ID/quant reproducibility (CVs) for OT-2-prepared samples vs manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "GPL-3.0 template protocols (Shiny app fills parameters); open-access Proteomics paper with quantitative results; templates need parameter substitution.", "est_tasks": 6, "source_agent": "github"}
+{"id": "halogenation-pharma-ot2", "title": "An automated platform for tailored late-stage halogenation of pharmaceuticals", "doi": "10.26434/chemrxiv.15000393/v1", "paper_url": "https://doi.org/10.26434/chemrxiv.15000393/v1", "year": 2026, "venue": "ChemRxiv", "open_access_license": "unknown", "code_url": "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals", "code_files": ["opentrons_dispense_code/reaction_setup/protocol_1(stage1_screening).py", "opentrons_dispense_code/reaction_setup/protocol_2(stage2_0to6_chlor).py", "opentrons_dispense_code/reaction_setup/protocol_3(stage2_0to10_nis_nbs).py", "opentrons_dispense_code/nmr_sample_prep/nmr_sample_preparation.py"], "code_license": "BSD-3-Clause", "stars": 0, "last_push": "2026-08-10", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "chemistry: late-stage halogenation reaction setup screening + NMR sample prep", "results_evidence": "ChemRxiv 2026 reports automated halogenation screening of pharmaceuticals with conversion/selectivity outcomes measured by NMR/LCMS.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "BSD-3 code, multiple apiv2 reaction-setup protocols, open preprint; chemistry (non-bio) tasks; may use custom vial labware.", "est_tasks": 4, "source_agent": "github"}
+{"id": "robotic-titration-cv-ot2", "title": "High-throughput robotic colourimetric titrations using computer vision", "doi": "10.1039/d4dd00334a", "paper_url": "https://doi.org/10.1039/d4dd00334a", "year": 2025, "venue": "Digital Discovery", "open_access_license": "cc-by/3.0", "code_url": "https://github.com/yuanlee0325/HTE-robotic-titration-using-computer-vision", "code_files": ["folder4ot2/utils/titration_general.py"], "code_license": "MIT", "stars": 2, "last_push": "2025-03-31", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "chemistry: colourimetric acid-base titration with webcam endpoint detection", "results_evidence": "Digital Discovery paper reports titration accuracy vs manual/reference concentrations using OT-2 + webcam colour analysis.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, open RSC paper, but protocol is driven with camera loop/HTTP; needs refactor for opentrons_simulate.", "est_tasks": 2, "source_agent": "github"}
+{"id": "viscous-liquid-bo-ot2", "title": "Optimization of liquid handling parameters for viscous liquid transfers with pipetting robots, a sticky situation", "doi": "10.1039/d3dd00255a", "paper_url": "https://doi.org/10.1039/d3dd00255a", "year": 2024, "venue": "Digital Discovery", "open_access_license": "cc-by-nc/3.0", "code_url": "https://github.com/Quijanove/LiqTransferOptimizer", "code_files": ["BO_liquid_transfer.py", "Old scripts/Semi_automated_MOBO_OT2.py", "Old scripts/opentrons.py"], "code_license": "MIT", "stars": 3, "last_push": "2025-09-29", "robot_platform": "ot2", "api": "other", "protocol_category": "liquid-class optimisation (viscous liquids, gravimetric, Bayesian optimisation)", "results_evidence": "Digital Discovery 2024 reports gravimetric transfer error and speed after multi-objective BO for viscous liquids on OT-2 and Sartorius rLine.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, open paper; OT-2 controlled via HTTP/closed loop with balance, not a standalone apiv2 protocol.", "est_tasks": 2, "source_agent": "github"}
+{"id": "flat-agar-celegans-ot2", "title": "Flat agar and optimized media enable high-throughput C. elegans imaging in 96-well plates", "doi": "10.57844/arcadia-h01v-2nxt", "paper_url": "https://doi.org/10.57844/arcadia-h01v-2nxt", "year": 2026, "venue": "Arcadia Science (The Stacks pub)", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/Arcadia-Science/menisquish-flat-agar", "code_files": ["opentrons/bowie_celegans_bleach_sync_var-col_v1.py", "opentrons/hopsy_p20multi_op50_agar_spotting_centrifuge_v4.py", "opentrons/hopsy_p20multi_worm_plating_centrifuge_v4.py"], "code_license": "MIT", "stars": 0, "last_push": "2026-09-25", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "C. elegans bleach synchronisation, OP50 agar spotting, worm plating for imaging", "results_evidence": "Pub reports flat-agar 96-well imaging quality (focus/worm detection) enabled by robot-prepared plates.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT, three apiv2 protocols, open CC BY pub; may need custom plate labware defs.", "est_tasks": 4, "source_agent": "github"}
+{"id": "pasta-spatial-ot2", "title": "PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology", "doi": "10.1038/s41592-026-03200-z", "paper_url": "https://doi.org/10.1038/s41592-026-03200-z", "year": 2026, "venue": "Nature Methods", "open_access_license": "publisher TDM/other: https://www.springernature.com/gp/researchers/text-and-data-mining", "code_url": "https://github.com/SizunJiangLab/PASTA", "code_files": ["automation/PASTA_oligoHRP_automation.py"], "code_license": "none", "stars": 1, "last_push": "2026-05-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "spatial proteomics: oligo-HRP tyramide amplification staining cycles", "results_evidence": "Nature Methods 2026 (bioRxiv 10.1101/2025.04.30.651463) reports high-plex multimodal spatial imaging with PASTA signal amplification on tissues.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single apiv2 script but no repo license; Nat Methods may be paywalled (bioRxiv preprint open); robot does slide reagent handling (custom labware likely).", "est_tasks": 2, "source_agent": "github", "preprint_url": "https://www.biorxiv.org/content/10.1101/2025.04.30.651463"}
+{"id": "moc-screening-ot2", "title": "Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages Towards Accelerated Discovery", "doi": "10.1002/anie.202424270", "paper_url": "https://doi.org/10.1002/anie.202424270", "year": 2025, "venue": "Angewandte Chemie International Edition", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/GreenawayLab/development-automated-workflow-mocs", "code_files": ["Opentrons_Protocols/automated_synthesis_opentron_script.py", "Opentrons_Protocols/automated_screen_refined_opentron_script.py", "Opentrons_Protocols/automated_host_guest_assay_opentron_script.py", "Opentrons_Protocols/Solvent_benchmark_acetonitrile_automated_screen.py"], "code_license": "none", "stars": 3, "last_push": "2025-03-18", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "chemistry: metal-organic cage synthesis screening and host-guest assay", "results_evidence": "Angew Chem 2025 reports automated MOC assembly outcomes (MS/NMR) and host-guest binding results; data on Zenodo 10.5281/zenodo.14183035.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Five apiv2 scripts + Zenodo data; no repo license; check OA status of Angewandte article.", "est_tasks": 4, "source_agent": "github"}
+{"id": "opentrons-covid19-dev", "title": "Opentrons/covid19 (OT-2 COVID-19 RT-qPCR station development repo, Opentrons + Open Medicine Institute)", "doi": null, "paper_url": "https://www.protocols.io/groups/opentrons-covid19-testing/publications", "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Opentrons/covid19", "code_files": ["experiments/20200324-lod-study-1/station-C-qpcr-map.py", "experiments/20200319-end-to-end-qpcr-1/station-C-qpcr-map.py"], "code_license": "Apache-2.0", "stars": 12, "last_push": "2020-06-07", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 RNA extraction + RT-qPCR setup stations A/B/C", "results_evidence": "Experiment folders contain LOD/contamination study notes; formal results only on protocols.io, no peer-reviewed paper.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Apache-2.0, many dated experiment scripts; no paper; overlaps covid19clinic/hulp-rna-extraction topics.", "est_tasks": 2, "source_agent": "github"}
+{"id": "ot2-proteomics-thesis", "title": "Automated Versus Manual Proteomics Sample Preparation: A Comparative Evaluation of Liquid Handling Workflows (MSc thesis)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/martineingolfsrud/Opentrons-OT-2-performance-assessment", "code_files": ["BCA/bca_multichannel.py", "BCA/bca_singlechannel_v2.py", "SP3/sp3_multi.py", "SP3/sp3_version7_1.py"], "code_license": "none", "stars": 0, "last_push": "2026-06-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics: BCA assay + SP3 digestion", "results_evidence": "Thesis raw data in repo comparing OT-2 vs human BCA/SP3 performance; not peer reviewed.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Thesis (no DOI), no license; good raw data though.", "est_tasks": 2, "source_agent": "github"}
+{"id": "prism-protocol-gen", "title": "PRISM: Protocol Refinement through Intelligent Simulation Modeling", "doi": "10.1039/d6dd00004e", "paper_url": "https://doi.org/10.1039/d6dd00004e", "year": 2026, "venue": "Digital Discovery", "open_access_license": "cc-by-nc/3.0", "code_url": "https://github.com/ramanathanlab/PRISM", "code_files": ["ProtocolGenerator/Code/projects/prism/pcr_master_mix_and_sample_prep.py"], "code_license": "MIT", "stars": 5, "last_push": "2026-04-26", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "LLM protocol generation + simulation validation; PCR master mix/sample prep", "results_evidence": "Digital Discovery 2026: LLM-generated, simulation-refined protocols executed on OT-2 (PCR prep).", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Competitor/related-work system (LLM->robot protocols); one concrete generated PCR protocol; MIT.", "est_tasks": 1, "source_agent": "github"}
+{"id": "celegans-food-preference-ot2", "title": "C. elegans food preference assay (OT-2 bacteria and worm spotting)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/slhogle/c_elegans_food_preference_protocol", "code_files": ["02_spot_bacteria.py", "03_spot_worms.py"], "code_license": "GPL-3.0", "stars": 0, "last_push": "2024-11-29", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "C. elegans behaviour assay plate prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "GPL-3.0 scripts adapting Shtonda & Avery 2006; no own paper/results.", "est_tasks": 1, "source_agent": "github"}
+{"id": "shampoo-formulations-ot2", "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset", "doi": "10.1038/s41597-024-03573-w", "paper_url": "https://doi.org/10.1038/s41597-024-03573-w", "year": 2024, "venue": "Scientific Data", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/AniketChitre/formulations-prep", "code_files": ["OpentronsProtocol_FormulationSamples.py"], "code_license": "none", "stars": 1, "last_push": "2024-01-14", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscous liquid formulation preparation (shampoo dataset)", "results_evidence": "Scientific Data 2024 reports a high-throughput dataset of OT-2-prepared shampoo formulations with phase stability/rheology measurements and gravimetric composition checks.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Single apiv2 protocol, CC BY Sci Data paper with dataset; no repo license (flag); requires editing formulation list.", "est_tasks": 2, "source_agent": "github"}
+{"id": "parseq-pyhamilton", "title": "parSEQ:  Probe and Rescue Sequencing for Advanced Variant Retrieval from DNA Pool", "doi": "10.1101/2023.12.12.571337", "paper_url": "https://doi.org/10.1101/2023.12.12.571337", "year": 2023, "venue": "bioRxiv", "open_access_license": "unknown", "code_url": "https://github.com/finyl/parseq-pyhamilton", "code_files": ["parseqpyhamilton/methods/bpcr.py", "parseqpyhamilton/methods/cherry_picking.py", "parseqpyhamilton/methods/lib_illumina.py", "parseqpyhamilton/methods/lib_nanopore.py", "parseqpyhamilton/methods/plate_filling.py"], "code_license": "none", "stars": 2, "last_push": "2023-12-13", "robot_platform": "hamilton", "api": "other", "protocol_category": "variant library sequencing pipeline: barcoding PCR, cherry picking, Illumina/nanopore library prep", "results_evidence": "bioRxiv 2023 parSEQ preprint reports retrieval of sequence-verified variants from pooled DNA libraries using the Hamilton pipeline.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyHamilton (not PLR) code needs Hamilton VENUS; no license; could be ported to PLR STAR simulator with work.", "est_tasks": 3, "source_agent": "github"}
+{"id": "ipsc-robot-pyhamilton", "title": "Automated hiPSC culture and sample preparation for 3D live cell microscopy", "doi": "10.1101/2020.12.18.423371", "paper_url": "https://doi.org/10.1101/2020.12.18.423371", "year": 2020, "venue": "bioRxiv", "open_access_license": "publisher TDM/other: https://www.biorxiv.org/about/FAQ#license", "code_url": "https://github.com/stefangolas/iPSC-Robot", "code_files": ["Feed.py", "96w_Seed.py", "96w_Scan.py", "ipsc_utils.py"], "code_license": "none", "stars": 1, "last_push": "2022-12-16", "robot_platform": "hamilton", "api": "other", "protocol_category": "iPSC culture: media exchange, seeding, imaging scan", "results_evidence": "Code implements Allen Institute iPSC culture protocols (bioRxiv 2020.12.18.423371); robot-specific results not in repo.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyHamilton by PLR co-author S. Golas; linked preprint is the source protocol, not a validation of this code; no license; Celigo integration.", "est_tasks": 2, "source_agent": "github"}
+{"id": "pac832-galr1-ot2", "title": "PAC-832: A selective small-molecule antagonist of galanin receptor 1 (GalR1) - supplementary data and OT-2 protocols", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/douglasyao/pac-832-supplementary-data", "code_files": ["ot2_protocols/ach_assay/GalR1-SY5Y_PAC-832_only_ACh_part1.py", "ot2_protocols/ach_assay/GalR1-SY5Y_PAC-832_plus_galanin_ACh_plate1.py", "ot2_protocols/ach_assay/PTX_controls_ACh.py"], "code_license": "none", "stars": 1, "last_push": "2026-04-07", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-based GPCR pharmacology assays (cAMP, acetylcholine release) dose-response plating", "results_evidence": "Repo includes raw and processed cAMP/ACh assay data for PAC-832 vs galanin; paper DOI not yet resolved (likely preprint).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Many apiv2 scripts + raw data, but no license and paper not located; strong candidate once paper DOI found.", "est_tasks": 4, "source_agent": "github"}
+{"id": "polar-sarscov2-ot2", "title": "POLAR: Pathogen-Oriented Low-cost Assembly & Re-sequencing SARS-CoV-2 (OT-2 automation)", "doi": "10.17504/protocols.io.bearjad6", "paper_url": "https://doi.org/10.17504/protocols.io.bearjad6", "year": 2020, "venue": "protocols.io", "open_access_license": null, "code_url": "https://github.com/Zanecrc1/POLAR-SARS-CoV-2-Automation-for-OT-2", "code_files": ["Protocols/POLAR/POLAR_48_Samples.py", "Protocols/Zymo extraction/Zymo_extraction_48_sample_V1i.py"], "code_license": "MIT", "stars": 2, "last_push": "2020-08-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viral RNA magbead extraction + SARS-CoV-2 amplicon library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT apiv2 scripts but only protocols.io, no paper with automation results; overlaps existing magbead extraction papers.", "est_tasks": 2, "source_agent": "github"}
+{"id": "damplab-taqpath-ot2", "title": "Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex RT-PCR (BU DAMP Lab)", "doi": "10.17504/protocols.io.brhvm366", "paper_url": "https://doi.org/10.17504/protocols.io.brhvm366", "year": 2021, "venue": "protocols.io", "open_access_license": null, "code_url": "https://github.com/DAMPLAB/OT2-SARS-CoV2", "code_files": ["rna_extraction_magmax/rna_extraction_magmax.py", "qPCR_taqpath_multiplex/qPCR_taqpath_multiplex.py"], "code_license": "none", "stars": 2, "last_push": "2021-03-29", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "MagMAX RNA extraction + TaqPath RT-qPCR setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean apiv2 + simulation notebooks; protocols.io only; no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "isciii-covid-stations", "title": "BU-ISCIII opentrons_covid19 (ISCIII station A/B/C RT-PCR diagnostics)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/BU-ISCIII/opentrons_covid19", "code_files": ["calibration_check/stationA_protocol1_buffer_S3_calibration.py", "calibration_check/stationB_protocol1_extraction_S3_calibration.py", "calibration_check/stationC_protocol1_pcr_S3_calibration.py"], "code_license": "AGPL-3.0", "stars": 0, "last_push": "2021-02-08", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 sample prep, extraction, PCR setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "covid-diagnostic-capacity-2021", "readiness": "partial", "readiness_reason": "AGPL; covidWarriors lineage; likely code behind Spanish COVID diagnostic capacity papers already in corpus (no code known there) - check.", "est_tasks": 1, "source_agent": "github"}
+{"id": "aliquot-niaid", "title": "ALIQUOT: Automated Liquid handling Infection Quantification Using OpenTrons (NIH/NIAID QVEU)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/QVEU/ALIQUOT", "code_files": ["OT-2/Serial Dilution/1 Plate/Serial_Dilution_1plate.py", "OT-2/Fix/1 Plate/Fix_1_plate.py", "OT-2/Full Protocol/1 Plate/Fix_and_Stain_1_plate.py"], "code_license": "none", "stars": 1, "last_push": "2026-03-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "virus infection quantification: serial dilution, fix, immunostain (OT-2 + Flex)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Well-organised apiv2 scripts + R analysis; paper not linked yet; no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "ot2-moclo-jove", "title": "Modular Cloning with the OT2 (OT2_MoClo_JoVE)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/emernic/OT2_MoClo_JoVE", "code_files": ["ot2_moclo_jove/moclo_transform/data/moclo_transform_template.py", "ot2_moclo_jove/colony_picking/data/colony_pick_template.py", "ot2_moclo_jove/miniprep/data/miniprep_template.py"], "code_license": "MIT", "stars": 7, "last_push": "2019-05-07", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "MoClo Golden Gate, heat-shock transformation, plating, colony picking, bead miniprep", "results_evidence": "Repo targets a JoVE article (not resolved in Crossref); JoVE articles typically include representative results.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT but legacy APIv1 templates; JoVE likely paywalled; overlaps apex/slowpoke/assemblytron tasks.", "est_tasks": 2, "source_agent": "github"}
+{"id": "retro-10x-ot2", "title": "OT-2 10x scRNA-seq library prep (Retro Biosciences)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/retrobiosciences/opentrons-10x", "code_files": ["multi_8sample.py"], "code_license": "none", "stars": 13, "last_push": "2023-03-25", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "10x Genomics single-cell library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper/license; README warns protocol is hard to get working; custom hardware.", "est_tasks": 1, "source_agent": "github"}
+{"id": "roche-pipetting-performance-ot2", "title": "Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment", "doi": "10.1016/j.slast.2024.100180", "paper_url": "https://doi.org/10.1016/j.slast.2024.100180", "year": 2024, "venue": "SLAS Technology", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/arthur-theuer/pipetting-performance", "code_files": ["templates/opentrons/OT2_pipetting_performance_p20.py", "templates/opentrons/OT2_pipetting_performance_p300.py"], "code_license": "GPL-3.0", "stars": 2, "last_push": "2025-10-11", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "liquid-handler QC: photometric pipetting accuracy/precision (dye dilution)", "results_evidence": "SLAS Technology 2024 (Roche pRED) reports OT-2 integration into AutoLab and pipetting accuracy/precision benchmarks (CV, systematic error) per volume.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "GPL-3.0 apiv2 templates (p20/p300) filled by notebook; open SLAS paper; similar to existing pipetting-speed-ot2 so pairs well as hard variant.", "est_tasks": 2, "source_agent": "github", "note": "repo is the public adaptation by the Roche author; link to paper is inferred from topic/author, verify"}
+{"id": "ai4pd-flex-protein-purification", "title": "Opentrons Flex protein purification and molecular biology scripts (AI4PD Lab)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/AI4PDLab/Opentrons_Flex_Protocols", "code_files": ["protein_purification/NiNTA_Protein_Purification.py", "protein_purification/inoculation_protein_expression.py", "protein_purification/reverse_imac_tev_digestion.py", "cloning/golden_gate.py", "plasmid_purification/MiniPrep_ZippyKit_FerruzLab.py"], "code_license": "MIT", "stars": 0, "last_push": "2026-05-08", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "protein expression, Ni-NTA purification, TEV digestion, Golden Gate, miniprep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT Flex scripts, no linked paper (AI4PD / Ferruz lab protein design validation likely). Overlaps apex.", "est_tasks": 2, "source_agent": "github"}
+{"id": "rtwizard-antigen-ot2", "title": "rtWIZARD: OT-2 running 42 rapid antigen tests in parallel", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/BenHinnant/rtWIZARD", "code_files": ["final_labware_position_checks/run_labware_position_check_p300_ingezim_asf_crom_ag.py"], "code_license": "none", "stars": 0, "last_push": "2024-10-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "lateral-flow rapid antigen test loading (ASF, PPA)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper located, no license, custom LFA holder labware.", "est_tasks": 1, "source_agent": "github"}
+{"id": "evotron-evolver-ot2", "title": "evotron: OT-2 automated sampling for eVOLVER", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/santkumar/evotron", "code_files": ["ot2/protocol_code/main_protocol.py"], "code_license": "none", "stars": 5, "last_push": "2022-07-26", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "continuous culture sampling", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Heavy custom hardware (needle, pumps, Arduino), no paper/license.", "est_tasks": 0, "source_agent": "github"}
+{"id": "fastkris-crystallisation", "title": "fastKris: Opentrons crystallisation screen protocol builder", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/LucoDevro/fastKris", "code_files": ["protocol.py", "template.py"], "code_license": "MIT", "stars": 1, "last_push": "2022-12-17", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein crystallisation screen setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "protein-crystallization-ot2", "readiness": "partial", "readiness_reason": "MIT generator, no paper; topic overlaps existing protein-crystallization-ot2.", "est_tasks": 1, "source_agent": "github"}
+{"id": "hydrogel-crosslink-ot2", "title": "Semi-autonomous synthesis and modelling of chemically cross-linked hydrogels (OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-", "code_files": ["Liquid Handler Script.py"], "code_license": "none", "stars": 0, "last_push": "2025-10-30", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "materials: hydrogel formulation synthesis", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single script; paper not located; no license.", "est_tasks": 1, "source_agent": "github"}
+{"id": "pvlab-solubility-dropcast-ot2", "title": "PV-Lab Robotic_Liquid_Handling (MIT AMLS OT-2 solubility testing / drop casting)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/PV-Lab/Robotic_Liquid_Handling", "code_files": ["drop_casting.py", "DRY_VERSION_solubility_testing.py", "Opentrons_Unit_Tests/test_96_gradient.py"], "code_license": "MIT", "stars": 2, "last_push": "2025-05-21", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "materials: solubility testing, thin-film drop casting", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, UROP code; no paper linked.", "est_tasks": 1, "source_agent": "github"}
+{"id": "dup-copick-copick", "title": "sysbio-cnb/COPICK (already in corpus as copick)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/sysbio-cnb/COPICK", "code_files": [], "code_license": "MIT", "stars": 9, "last_push": "2023-03-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "colony picking", "results_evidence": "See existing corpus entry copick.", "wet_lab_validated": true, "duplicate_of_existing": "copick", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-proxy-viscometer-opentrons-proxyviscometer", "title": "Kedar-Materials-by-Design-Lab/Opentrons-ProxyViscometer (already in corpus as proxy-viscometer)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Kedar-Materials-by-Design-Lab/Opentrons-ProxyViscometer", "code_files": [], "code_license": "none", "stars": 3, "last_push": "2023-03-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscosity estimation", "results_evidence": "See existing corpus entry proxy-viscometer.", "wet_lab_validated": true, "duplicate_of_existing": "proxy-viscometer", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-opencell-automation-2024-accs-pub", "title": "czbiohub-sf/2024-accs-pub (already in corpus as opencell-automation)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/czbiohub-sf/2024-accs-pub", "code_files": [], "code_license": "none", "stars": 3, "last_push": "2026-01-22", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated cell culture splitting", "results_evidence": "See existing corpus entry opencell-automation.", "wet_lab_validated": true, "duplicate_of_existing": "opencell-automation", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-opencell-automation-accs-protocol-software-pu", "title": "czbiohub-sf/accs-protocol-software-pub (already in corpus as opencell-automation)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/czbiohub-sf/accs-protocol-software-pub", "code_files": [], "code_license": "BSD-3-Clause", "stars": 1, "last_push": "2025-01-13", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated cell culture splitting framework", "results_evidence": "See existing corpus entry opencell-automation.", "wet_lab_validated": true, "duplicate_of_existing": "opencell-automation", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-assemblytron-assemblytron", "title": "PlantSynBioLab/AssemblyTron (already in corpus as assemblytron)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/PlantSynBioLab/AssemblyTron", "code_files": [], "code_license": "NOASSERTION", "stars": 12, "last_push": "2024-12-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA assembly", "results_evidence": "See existing corpus entry assemblytron.", "wet_lab_validated": true, "duplicate_of_existing": "assemblytron", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-ot-mation-ot-mation-repo", "title": "tphoward/OT-Mation_Repo (already in corpus as ot-mation)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/tphoward/OT-Mation_Repo", "code_files": [], "code_license": "Apache-2.0", "stars": 2, "last_push": "2025-03-21", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "synbio automation", "results_evidence": "See existing corpus entry ot-mation.", "wet_lab_validated": true, "duplicate_of_existing": "ot-mation", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-chory-2021-hamilton-roboplaque", "title": "dgretton/roboplaque (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/roboplaque", "code_files": [], "code_license": "MIT", "stars": 4, "last_push": "2020-11-30", "robot_platform": "hamilton", "api": "other", "protocol_category": "phage plaque assay (pyhamilton)", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-chory-2021-hamilton-pyhamilton-population-dyn", "title": "dgretton/pyhamilton_population_dynamics (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/pyhamilton_population_dynamics", "code_files": [], "code_license": "MIT", "stars": 1, "last_push": "2020-11-23", "robot_platform": "hamilton", "api": "other", "protocol_category": "population dynamics (pyhamilton)", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-chory-2021-hamilton-pyhamilton", "title": "dgretton/pyhamilton (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/pyhamilton", "code_files": [], "code_license": "MIT", "stars": 192, "last_push": "2026-09-05", "robot_platform": "hamilton", "api": "other", "protocol_category": "PyHamilton library", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-slowpoke-slowpoke", "title": "Tom-Ellis-Lab/Slowpoke (already in corpus as slowpoke)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Tom-Ellis-Lab/Slowpoke", "code_files": [], "code_license": "MIT", "stars": 3, "last_push": "2026-02-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate + colony PCR", "results_evidence": "See existing corpus entry slowpoke.", "wet_lab_validated": true, "duplicate_of_existing": "slowpoke", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-hulp-rna-extraction-rna-extraction-ot2opentro", "title": "HULPopentrons/RNA_extraction_OT2opentrons (already in corpus as hulp-rna-extraction)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/HULPopentrons/RNA_extraction_OT2opentrons", "code_files": [], "code_license": "none", "stars": 2, "last_push": "2020-07-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viral RNA extraction", "results_evidence": "See existing corpus entry hulp-rna-extraction.", "wet_lab_validated": true, "duplicate_of_existing": "hulp-rna-extraction", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-covid19clinic-covid19clinic", "title": "CDB-coreBM/covid19clinic (already in corpus as covid19clinic)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/CDB-coreBM/covid19clinic", "code_files": [], "code_license": "GPL-3.0", "stars": 4, "last_push": "2021-04-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 RT-qPCR", "results_evidence": "See existing corpus entry covid19clinic.", "wet_lab_validated": true, "duplicate_of_existing": "covid19clinic", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-shotgun-proteomics-jove-standarddigestion-opentro", "title": "MaggieLam-Lab/StandardDigestion-Opentrons (already in corpus as shotgun-proteomics-jove)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/MaggieLam-Lab/StandardDigestion-Opentrons", "code_files": [], "code_license": "MIT", "stars": 4, "last_push": "2021-09-24", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics digestion", "results_evidence": "See existing corpus entry shotgun-proteomics-jove.", "wet_lab_validated": true, "duplicate_of_existing": "shotgun-proteomics-jove", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-botany-botany", "title": "cvoiniciuc/BOTany (already in corpus as botany)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/cvoiniciuc/BOTany", "code_files": [], "code_license": "none", "stars": 2, "last_push": "2026-03-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plant biology protocols", "results_evidence": "See existing corpus entry botany.", "wet_lab_validated": true, "duplicate_of_existing": "botany", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-moeller-hackflex-moeller-opentrons-protoco", "title": "tanaes/Moeller_Opentrons_protocol_library (already in corpus as moeller-hackflex)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/tanaes/Moeller_Opentrons_protocol_library", "code_files": [], "code_license": "MIT", "stars": 14, "last_push": "2022-07-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA extraction/library prep", "results_evidence": "See existing corpus entry moeller-hackflex.", "wet_lab_validated": true, "duplicate_of_existing": "moeller-hackflex", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-sidekick-liquid-handler", "title": "rodolfokeesey/Liquid-Handler (already in corpus as sidekick)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/rodolfokeesey/Liquid-Handler", "code_files": [], "code_license": "NOASSERTION", "stars": 32, "last_push": "2023-02-06", "robot_platform": "other", "api": "other", "protocol_category": "open-hardware liquid handler", "results_evidence": "See existing corpus entry sidekick.", "wet_lab_validated": true, "duplicate_of_existing": "sidekick", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "dup-transporter-screening-transporterscreening", "title": "ljm176/TransporterScreening (already in corpus as transporter-screening)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/ljm176/TransporterScreening", "code_files": [], "code_license": "none", "stars": 1, "last_push": "2024-01-05", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "transporter screening", "results_evidence": "See existing corpus entry transporter-screening.", "wet_lab_validated": true, "duplicate_of_existing": "transporter-screening", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github"}
+{"id": "sarscov2-hypercube-pooling-ot2", "title": "Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing", "doi": "10.1038/s41598-021-96934-z", "paper_url": "https://doi.org/10.1038/s41598-021-96934-z", "year": 2021, "venue": "Scientific Reports", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/CERI-KRISP/efficient-SARS-CoV-2-pooled-testing-strategy-code", "code_files": ["scripts/pooling27_300pip.py", "scripts/pooling27_50pip.py", "scripts/pooling81_300pip.py", "scripts/pooling81_50pip.py"], "code_license": "MIT", "stars": 1, "last_push": "2021-04-07", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "specimen pooling (hypercube design) for SARS-CoV-2 RT-PCR", "results_evidence": "Sci Rep 2021 reports hypercube pooling sensitivity/efficiency on clinical specimens with OT-2 pooling, identifying positives with fewer tests.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, open CC BY paper with results, but legacy APIv1 scripts and custom plate; needs port to v2 (good hard task).", "est_tasks": 2, "source_agent": "github"}
+{"id": "metclo-ot2", "title": "MetCloOT2: Automated MetClo assembly on Opentrons OT-2 (MSc project, based on Lin & O Callaghan 2018/2020)", "doi": "10.1007/978-1-0716-0908-8_9", "paper_url": "https://doi.org/10.1007/978-1-0716-0908-8_9", "year": 2020, "venue": "Methods in Molecular Biology (method chapter); OT-2 code is MSc project", "open_access_license": null, "code_url": "https://github.com/Edinburgh-Genome-Foundry/OT2Metclo", "code_files": ["ot2metclo.py"], "code_license": "none", "stars": 2, "last_push": "2022-08-16", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA assembly (MetClo methylation-based Golden Gate)", "results_evidence": "Underlying MetClo method papers (NAR 2018; Methods Mol Biol 2020) report manual assembly results; OT-2 implementation is an MSc project without published validation.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No license; method paper NAR 2018 is OA but the robot code is not validated in it.", "est_tasks": 1, "source_agent": "github"}
+{"id": "ecoli-protein-expr-purif-ot2", "title": "OT-2 assisted recombinant protein expression and purification in E. coli (Norton-Baker)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/nortonbakerbc/opentrons", "code_files": ["1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "2-Inoculation/Inoculation_platetoplate/Inoculation_1x96_to_4x24_OT2.py", "3-Lysis/Lysis_buffer_addition/Lysis_buffer_addition_OT2.py", "4-Transfer/Transfer_plate-to-plate/Transfer_plate-to-plate_4x24_to_1x96_OT2.py"], "code_license": "none", "stars": 0, "last_push": "2024-09-11", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein expression: transformation, inoculation, lysis, purification transfers", "results_evidence": "README says protocols are described in a paper (citation not resolved in README head); likely reports expression/purification yields.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Many apiv2 scripts with custom labware; paper citation needs manual resolution; no license.", "est_tasks": 4, "source_agent": "github"}
+{"id": "trypanosomatid-drug-combo-ot2", "title": "OT-2 protocols for drug combination screening (Trypanosomatics Lab, UNSAM)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/FranAguero07/OT2_protocols", "code_files": ["PROTOCOLS/Drugs_combination.py", "PROTOCOLS/Cell_lysis.py", "PROTOCOLS/Transfer_to_384_well_plate.py"], "code_license": "none", "stars": 0, "last_push": "2025-04-02", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "drug dilution/combination matrix, cell lysis, 384-well transfer (luciferase readout)", "results_evidence": "README states protocols are described in the lab paper (not cited by DOI).", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean apiv2 scripts with labware spec files; paper DOI needs resolution; no license.", "est_tasks": 3, "source_agent": "github"}
+{"id": "dup-proxy-viscometer-otproxy", "title": "beatricesoh/OTProxyViscometer (Opentrons for Automated and High-Throughput Viscometry)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/beatricesoh/OTProxyViscometer", "code_files": ["OT-2_80FR.py"], "code_license": "none", "stars": 0, "last_push": "2025-01-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscometry", "results_evidence": "See existing corpus entry proxy-viscometer.", "wet_lab_validated": true, "duplicate_of_existing": "proxy-viscometer", "readiness": "partial", "readiness_reason": "Second code repo for an existing corpus paper (includes raw mass-profile data).", "est_tasks": 0, "source_agent": "github"}
+{"id": "detectr-covid-ot2", "title": "Mammoth DETECTR COVID-19 assay on OT-2", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/tsdobbs/mammoth-COVID19-assay-OT2", "code_files": ["DETECTR_COVID-19_PART1.py", "DETECTR_COVID-19_PART2.py"], "code_license": "none", "stars": 1, "last_push": "2020-04-15", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CRISPR-Cas12 diagnostic (RNP prep + DETECTR reaction)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Implements a company white paper (Broughton et al. 2020 Nat Biotech is the DETECTR paper) but robot run not validated; no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "vadr-vacuum-miniprep-flex", "title": "An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2", "doi": "10.64898/2026.09.16.746974", "paper_url": "https://doi.org/10.64898/2026.09.16.746974", "year": 2026, "venue": "bioRxiv", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/JackATDalton/VADR", "code_files": ["Protocol Files/Miniprep_var_sample.py"], "code_license": "none", "stars": 0, "last_push": "2026-01-28", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "plasmid miniprep with 3D-printed vacuum manifold", "results_evidence": "bioRxiv 2026 reports improved DNA isolation yields with the open-source vacuum manifold on Opentrons Flex (link between repo and preprint inferred from content/date; verify).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single Flex script + STL/labware JSON; requires custom 3D-printed manifold; no license; repo-paper link unverified.", "est_tasks": 2, "source_agent": "github"}
+{"id": "exposomics-384-flex", "title": "An Ultra-High-Throughput 384-Well Sample Preparation Workflow for Nontargeted Exposomics Across Four LC-HRMS Assays (in prep)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols", "code_files": ["protocols/step1_solvent_addition_and_sample_aliquoting.py", "protocols/step2_dilution_and_supernatant_transfer.py"], "code_license": "MIT", "stars": 0, "last_push": "2026-10-02", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "metabolomics/exposomics: protein precipitation in 384-well", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, clean Flex protocols + labware; paper not yet published - watch list.", "est_tasks": 2, "source_agent": "github"}
+{"id": "ufdutton-16s-flex", "title": "UF Dutton Lab Opentrons 16S microbiome workflow (OT-2 + Flex)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/UFDuttonLab/lab_automation_opentrons", "code_files": ["protocols/Flex/Zymo_Magbead_DNA_Kit_48samples.py", "protocols/Flex/Zymo_LibraryPrep_TG_V2.py", "protocols/Flex/NEBNext_Ultra_II_FS_DNA_Library_Prep_FlexV18.py", "protocols/Flex/SelectaSize96.py"], "code_license": "none", "stars": 0, "last_push": "2026-09-29", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "microbiome DNA extraction + 16S/shotgun library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Production-style Flex protocols but no paper and no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "locost-covid-nanopore-ot2", "title": "Opentrons_LoCost_Covid19 (ARTIC LoCost nanopore library prep on OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/JDMirza/Opentrons_LoCost_Covid19", "code_files": ["1_dilution_pool_per_plate.py", "2_endrepair.py", "3_barcoding.py", "4_pooling_96_samples.py"], "code_license": "none", "stars": 0, "last_push": "2022-01-13", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 nanopore library prep (dilution, end-repair, barcode ligation, pooling)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Automates Quick 2019 LoCost protocol (protocols.io); no own paper, no license.", "est_tasks": 2, "source_agent": "github"}
+{"id": "angelovangel-ot2-ngs", "title": "angelovangel/opentrons (KAUST Bioscience core NGS/Sanger OT-2 + Flex protocols)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/angelovangel/opentrons", "code_files": ["protocols/01-sanger-setup-pcr.py", "protocols/02-ont-rapidlsk.py", "protocols/06-normalize-dna.py", "protocols/08-kinnex-pcr.py"], "code_license": "none", "stars": 1, "last_push": "2026-09-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Sanger PCR setup, ONT rapid library, DNA normalisation, PacBio Kinnex PCR", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Core-facility scripts; README notes not all tested on robot; no paper/license.", "est_tasks": 1, "source_agent": "github"}
+{"id": "nioz-ot2-database", "title": "MolLabNIOZ/OT2 protocol database (NIOZ molecular ecology)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/MolLabNIOZ/OT2", "code_files": ["Protocol_database/EVE/Qubit/Qubit_v1.py", "Protocol_database/EVE/Adding_sample_to_barcoded_PCR-plate/Adding_sample_to_barcoded_PCR-plate_V3.py"], "code_license": "none", "stars": 2, "last_push": "2026-06-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "amplicon PCR setup, Qubit quantification, dilution, pooling", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Large (222 .py) lab library, no paper, no license.", "est_tasks": 1, "source_agent": "github"}
diff --git a/research/expansion/github_notes.md b/research/expansion/github_notes.md
new file mode 100644
index 0000000..8c850ae
--- /dev/null
+++ b/research/expansion/github_notes.md
@@ -0,0 +1,116 @@
+# GitHub code-first sweep: PyLabRobot + Opentrons (paper, code, results) triples
+
+Agent: `github` · run 2026-10-11/12 · output: `github_candidates.jsonl` (77 records, one per candidate repo)
+
+## What was run
+
+**GitHub code search** (`gh search code`, ~8 s between calls, 92 queries logged):
+- PyLabRobot: `"import pylabrobot"`, `"from pylabrobot.liquid_handling import LiquidHandler"`, `pylabrobot.liquid_handling.backends`, `ChatterboxBackend`, `LiquidHandlerChatterboxBackend` (py and ipynb), `pylabrobot` + `LiquidHandler` / `STAR` / `OTDeck` / `STARLetDeck` / `TIP_CAR_480_A00` / `Cor_96_wellplate_360ul_Fb` / `HTF_L` / `plate_reader` / `aspirate dispense` / `pick_up_tips`, `pylabrobot` in `requirements.txt` / `pyproject.toml` / `.ipynb`, `pylabrobot doi` / `biorxiv` in README.
+  - Note: exact dotted-phrase queries such as `"from pylabrobot"` return 0 on the legacy code-search API. Bare-token queries work.
+- Opentrons: `"from opentrons import protocol_api"` + doi/biorxiv/paper/publication (all 0 hits on the legacy API), `apiLevel` + doi / biorxiv / "et al" / Nature / PLOS / Supplementary / doi.org / Cell / Science, `"protocol_api" "doi"`, `opentrons|OT-2|OT2` + doi / biorxiv / medRxiv / chemRxiv / "please cite" / Journal / published / Citation / "Nature Communications" / "ACS Synthetic Biology" / PLOS / "Scientific Reports" / SLAS / HardwareX / protocols.io / "Digital Discovery" / zenodo in README.md, `opentrons` in CITATION.cff, and pyhamilton / Hamilton STAR / Tecan EVO + doi.
+  - `apiLevel` queries are very noisy: they match CPython `locale.py`, `twisted adbapi`, androguard and similar. Real protocol hits were separated by importing-file verification.
+
+**Repo search** (`gh search repos`, 79 result files): `pylabrobot`, `opentrons`, `opentrons protocol(s)`, `OT-2`, `OT2 protocol`, `opentrons flex`, `pyhamilton`, `liquid handler`, `liquid-handling`, `self-driving lab`, topics (`opentrons`, `ot-2`, `opentrons-ot2`, `pylabrobot`, `liquid-handling`, `lab-automation`, `laboratory-automation`, `self-driving-lab`, `hamilton`), README-match variants, plus **date-partitioned** `opentrons` / `ot2` / `pylabrobot` searches over 11 creation windows from 2016 to 2026. These got past the 100-result cap and found 1,041 repos, 729 of them not seen before.
+
+**Other sources**
+- Opentrons/Protocols library (833 protocol folders, shallow clone): grepped every README for DOI, bioRxiv, PubMed, protocols.io, "et al." and journal names. **None cite a research paper.** The only "publication" hits are kit-vendor boilerplate and a thermocycler white paper. The library is not a source of triples.
+- PyLabRobot `docs/img/used_by` showcase: Adaptyv, Bio-Techne, Cheshire Labs, Constructive, Duke (Chory lab), MIT, Pioneer Labs, RetroBio, Sanofi, TTx, UKM, X. These are mostly companies with no public protocol code.
+- GitHub "Used by" page for pylabrobot: 13 repos and 6 packages.
+- WebSearch + Crossref (`api.crossref.org`) were used to resolve paper titles, DOIs and licences. bioRxiv full text was read for the OLH and LabscriptAI preprints.
+
+**Verification:** for each shortlisted repo I listed the tree via the GitHub API, fetched up to 40 `.py` files from raw.githubusercontent, and confirmed real imports or metadata (`from opentrons` / `apiLevel` / `protocol_api`, `from pylabrobot`, `pyhamilton`). I also scanned the README for citations.
+
+Two GitHub REST rate-limit lockouts interrupted the run (core 5,000/h). Rate-limited repos were re-screened afterwards.
+
+## Counts
+
+| | n |
+|---|---|
+| Repos screened (metadata + README + tree via API) | 1,542 |
+| Extra repos README-screened (date-partitioned enumeration) | 729 |
+| **Total distinct repos screened** | **2,271** |
+| Opentrons-related repos among them (name/desc/README) | ~880 (363 + 515) |
+| Repos hit by PyLabRobot code queries | 227 (≈170 are TTS "Chatterbox" noise, PLR forks or agent-skill mirrors) |
+| **Genuine public repos using PyLabRobot (outside the PLR org)** | **~50** |
+| Opentrons protocol library folders checked | 833 |
+| Candidates recorded in `github_candidates.jsonl` | 77 |
+| … duplicates of the existing 48-paper corpus (marked, not dropped) | 22 |
+| … new candidates | 55 |
+| New candidates with a resolvable paper or preprint DOI (excl. protocols.io-only) | 25 |
+| Readiness, all 77 records: ready / partial / no | 10 / 65 / 2 |
+| Readiness, new candidates only: ready / partial / no | 10 / 43 / 2 |
+| API split, all 77 records: opentrons_v2 / opentrons_v1 / pylabrobot / other (pyhamilton, HTTP API) | 63 / 2 / 5 / 7 |
+| Estimated tasks: all new candidates / "ready" only | ~124 / ~36 |
+
+## PyLabRobot ecosystem
+
+- **Size:** about 50 public non-fork repos actually use PyLabRobot. GitHub's dependents page lists only 13 repos and 6 packages. Most are teaching or demo material, tooling, agent/MCP wrappers or vendor drivers:
+  - Teaching/demo: Chory lab BME590 courses, `stefangolas/PyLabRobot_Tutorials_BME590`, `rickwierenga/plr-game-of-life`, `tic-tac-tobot`, T-Rex game.
+  - Tooling: Cheshire-Labs orca, `Koeng101/pylabrobot-protobuf`, `maraxen/praxis`, `norle/plr-gui`.
+  - Agent/MCP wrappers: `Infera-Bio/plr-mcp`, IvoryOS-PLR, `nygmeta/OpenLabAI`, Biomni's `lab_automation.py`, many "scientific-skills" mirrors.
+  - Vendor drivers: `SLKS99/PyFluent` for Tecan Fluent.
+- **Paper-linked PLR code is nearly absent.** Only two triples were found:
+  1. **OLH: A Purpose-Built Open Source Liquid Handler** (Golas, …, Chory; bioRxiv 2026, 10.64898/2026.03.02.709168). PLR turbidostat code is at `chory-lab/plr-turbidostat`, with an MIT PLR fork at `chory-lab/olh-pylabrobot`. Results: pipetting MAE 4.1 vs 7.2 µL manual, and about 200 turbidostat cultures held at setpoint. *Partial*: custom hardware, and the turbidostat repo has no licence.
+  2. **LabscriptAI** (bioRxiv 2025.09.30.679666; `KRATSZ/LabScript-AI`, 131★). This is an LLM protocol-generation system with a PLR simulator. Experiments ran on OT-2, Flex, Hamilton Vantage and Tecan Fluent: 318 GFP variants characterised, and enzyme mutants with more than 3× activity. *Partial*: the repo holds the agent, not the executed scripts. It is also **directly related work / a competitor for Text2WetLab**.
+- Real PLR wet-lab scripts without a paper: `har1eyk/hamilton-starlet-scripts` (STARlet protein extraction, Orange G volume QC) and `Pioneer-Research-Labs/ngs_library_prep` (already in the corpus as `pioneer-ngs`).
+- PyHamilton (the PLR predecessor) has more paper-linked code: `finyl/parseq-pyhamilton` (parSEQ, bioRxiv 2023), `stefangolas/iPSC-Robot` (bioRxiv 2020) and the dgretton repos (already in the corpus as `chory-2021-hamilton`). These could be ported to the PLR STAR simulator.
+- **Conclusion:** PLR is not yet a source of published triples. If PLR tasks are needed, port Opentrons or PyHamilton triples into PLR (for example parSEQ, MSD Bradford/PicoGreen, GFP burden) rather than waiting for native PLR papers.
+
+## Top 15 new candidates
+
+| # | id | paper (venue, year) | code | why |
+|---|---|---|---|---|
+| 1 | `gfp-codon-burden-ot2` | Codon usage modulates burden vs yield (J Biol Eng 2025, CC BY) | alexismhill3/gfp_deoptimization_burden (MIT) | apiLevel 2.18 growth/induction protocols per day; raw + processed plate-reader data in repo; ready |
+| 2 | `msd-biochem-assays-ot2` | Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler (SLAS Tech 2024) | MSDLLCpapers/Opentrons-OT2-BioChemical-Assays (Apache-2.0) | Bradford + PicoGreen standard curves, self-contained; ready |
+| 3 | `massspecpreppy-ot2` | MassSpecPreppy (Proteomics 2023) | stemicha/MassSpecPreppy (GPL-3.0) | BCA + red/alk + SP3 digestion templates; ready (needs parameter fill) |
+| 4 | `arcadia-his-elisa-ot2` | Automated Cayman His-tag ELISA (Arcadia pub, CC BY) | Arcadia-Science/cayman-his-elisa-opentrons-workflow (MIT) | 2-protocol ELISA with plate-map CSV + analysis notebook; ready |
+| 5 | `flat-agar-celegans-ot2` | Flat agar and optimized media for C. elegans imaging (Arcadia pub, CC BY) | Arcadia-Science/menisquish-flat-agar (MIT) | bleach sync, OP50 spotting, worm plating; ready |
+| 6 | `roboctab-dna-extraction` | RoboCTAB high-throughput plant DNA extraction (Plants 2025, CC BY) | tomstamour/RoboCTAB (no licence) | OT-2 + Flex versions; ready (licence flag) |
+| 7 | `lysostaphin-turbidity-ot2` | Turbid but accurate: lysostaphin quantification (Microb Cell Fact 2026, CC BY) | JuBiotech/Supplement-to-Prigolovkin-et-al.-2025 (AGPL) | enzyme turbidity assay, raw data; ready (link only, AGPL) |
+| 8 | `halogenation-pharma-ot2` | Automated late-stage halogenation of pharmaceuticals (ChemRxiv 2026) | GreenawayLab/automated_halogenation_of_pharmaceuticals (BSD-3) | chemistry reaction-setup and NMR-prep protocols; ready |
+| 9 | `roche-pipetting-performance-ot2` | Deep integration of low-cost LH robots in pharma (SLAS Tech 2024) | arthur-theuer/pipetting-performance (GPL-3.0) | photometric accuracy/precision QC (p20/p300); ready; repo-paper link inferred, verify |
+| 10 | `shampoo-formulations-ot2` | High-throughput shampoo formulations dataset (Sci Data 2024, CC BY) | AniketChitre/formulations-prep (no licence) | viscous formulation prep + dataset; ready |
+| 11 | `ant-cloning-ot2` | Automating Cloning by Natural Transformation (ACS Synth Biol 2020) | ljm176/ANTCloning | 5-step PCR → DpnI → OE-PCR → transformation → plating pipeline; partial (licence, OA) |
+| 12 | `moc-screening-ot2` | Automated workflow for metal-organic cage screening (Angew Chem 2025, CC BY) | GreenawayLab/development-automated-workflow-mocs | 5 apiv2 scripts + Zenodo data; partial (no licence) |
+| 13 | `tobis-cytof-barcoding-ot2` | Multiplexed single-cell analysis of organoid signalling (Nat Protoc 2021) | TAPE-Lab/OT-2_Code | 35/126-plex barcode production/aliquoting; partial (paywall, licence) |
+| 14 | `sarscov2-hypercube-pooling-ot2` | Efficient SARS-CoV-2 specimen pooling (Sci Rep 2021, CC BY) | CERI-KRISP/... (MIT) | APIv1 pooling scripts: good v1→v2 "hard" task |
+| 15 | `parseq-pyhamilton` | parSEQ (bioRxiv 2023) | finyl/parseq-pyhamilton | Hamilton barcoding PCR / cherry-pick / Illumina + nanopore library prep; best PLR-port candidate |
+
+Honourable mentions:
+- `pasta-spatial-ot2` (Nat Methods 2026; repo has no licence)
+- `robotic-titration-cv-ot2` and `viscous-liquid-bo-ot2` (Digital Discovery; robot driven by a camera/HTTP loop)
+- `olh-turbidostat-plr` (the only native PLR triple)
+- `pac832-galr1-ot2` (rich data; paper DOI not yet found)
+- `ecoli-protein-expr-purif-ot2` and `trypanosomatid-drug-combo-ot2` (READMEs say "our paper" but give no DOI)
+
+Related work worth citing, not as tasks: `labscriptai-protein-eng`, `prism-protocol-gen` (Digital Discovery 2026) and `ot2-cherrypick`. These are LLM- or GUI-driven protocol generators evaluated on real robots.
+
+## Duplicates of the existing corpus (marked `duplicate_of_existing`)
+
+| Repo(s) | Existing corpus entry |
+|---|---|
+| COPICK | copick |
+| Opentrons-ProxyViscometer, beatricesoh/OTProxyViscometer | proxy-viscometer |
+| czbiohub 2024-accs-pub, accs-protocol-software-pub | opencell-automation |
+| AssemblyTron | assemblytron |
+| OT-Mation | ot-mation |
+| dgretton pyhamilton, roboplaque, population_dynamics | chory-2021-hamilton |
+| Slowpoke | slowpoke |
+| HULP RNA extraction | hulp-rna-extraction |
+| covid19clinic | covid19clinic |
+| StandardDigestion-Opentrons | shotgun-proteomics-jove |
+| BOTany | botany |
+| Moeller library | moeller-hackflex |
+| SideKick Liquid-Handler | sidekick |
+| TransporterScreening | transporter-screening |
+| Pioneer ngs_library_prep | pioneer-ngs |
+| Biocomputation-CBGP/OT2 | lap-transposon-genotyping (same group/workflow) |
+| BU-ISCIII opentrons_covid19 | possibly covid-diagnostic-capacity-2021 (needs checking) |
+| fastKris | protein-crystallization-ot2 (topic overlap only) |
+
+## Caveats
+
+- `est_tasks` is a rough count: an easy+hard pair counts as 2, and distinct experiments are counted separately.
+- Open-access status comes from Crossref licence metadata; bioRxiv entries show bioRxiv's generic licence URL. Check each paper before vendoring a PDF.
+- No `.py` was run through `opentrons_simulate` or the PLR simulator. "Ready" is judged from code inspection: self-contained apiv2, standard or bundled labware, and no external hardware loops.
+- Repo-to-paper links marked "inferred" (`roche-pipetting-performance-ot2`, `vadr-vacuum-miniprep-flex`) need a manual check.
diff --git a/research/expansion/merged_candidates.jsonl b/research/expansion/merged_candidates.jsonl
new file mode 100644
index 0000000..18e3c51
--- /dev/null
+++ b/research/expansion/merged_candidates.jsonl
@@ -0,0 +1,263 @@
+{"id": "alabos-alab", "title": "AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories (A-Lab)", "doi": "10.1039/d4dd00129j", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/dd/d4dd00129j", "year": 2024, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/CederGroupHub/alab_management", "code_files": ["alab_management/builders/experimentbuilder.py", "examples/alab_example/alab_example/devices/box_furnace.py", "examples/alab_example/alab_example/tasks/", "tests/fake_lab/"], "code_license": "MIT", "language": "Python", "hardware": ["A-Lab: UR5e arms", "box/tube furnaces", "powder dosing (Labman)", "XRD", "ball mill", "capping grippers"], "domain": "materials", "task_type": "scheduling", "results_evidence": "AlabOS ran A-Lab for months (>3500 samples) of solid-state synthesis; A-Lab Nature 2023 reported 41 synthesized targets (later disputed).", "wet_lab_validated": true, "simulatable": "true: fake_lab devices + example device classes run without hardware (needs MongoDB)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT, fake devices, experiment builder API; tasks: 'synthesis recipe text -> ExperimentBuilder task graph (heating profile, dosing, XRD)'.", "est_tasks": 5, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ant-cloning", "title": "Automated cloning by natural transformation (ANT) OT-2 workflow", "doi": "10.1021/acssynbio.0c00240", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.0c00240", "year": 2020, "venue": "ACS Synthetic Biology", "open_access_license": "unclear (journal)", "code_url": "https://github.com/ljm176/ANTCloning", "code_files": ["Step 1_PCRSetup.py", "Step 2_Dilution and Digestion.py", "Step 3_OEPCR.py", "Step 4_Transformation.py", "Step 5_Plating.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "PCR, digestion, overlap-extension PCR, natural transformation, plating", "results_evidence": "Cloning efficiency and correct-assembly rates for automated natural transformation reported in the paper.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Five numbered end-to-end scripts explicitly tied to a named publication; repo unlicensed and the ACS text may need an author copy.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "autoprotocol-dnada", "title": "Automated Platform for the Plasmid Construction Process (DNAda -> Autoprotocol)", "doi": "10.1021/acssynbio.3c00292", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.3c00292", "year": 2023, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY", "code_url": "https://github.com/JBEI/dnada", "code_files": ["backend/app/app/core/autoprotocols.py", "backend/app/app/api/utils/pcrrun_helper.py", "backend/app/app/api/utils/assemblyrun_helper.py"], "code_license": "Apache-2.0", "language": "Python", "hardware": ["Strateos-style Autoprotocol targets", "thermocyclers", "plate sealers", "liquid handlers"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Hundreds of plasmid constructions executed with reported success rates.", "wet_lab_validated": true, "simulatable": "true: Autoprotocol JSON is generated offline (autoprotocol-python)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Autoprotocol JSON (seal/thermocycle/spin/incubate instructions) is an inspectable non-LH target; Apache-2.0.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "beckham-enzyme-pipeline", "title": "Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline", "doi": "10.1038/s41598-024-64938-0", "paper_url": "https://www.nature.com/articles/s41598-024-64938-0", "year": 2024, "venue": "Scientific Reports", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/beckham-lab/opentrons", "code_files": ["1-Transformation/Transformation_cherrypicking/2024-03-18_Transformation_cherrypicking_OT2.py", "1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "2-Inoculation/*.py", "(21 OT-2 scripts total)"], "code_license": "none (no LICENSE file)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "E. coli transformation, inoculation, expression, lysis, enzyme assay", "results_evidence": "Robot-assisted pipeline screened enzyme variant libraries; activity/expression measured and compared with manual handling.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper plus modular per-step OT-2 v2 scripts; only blocker is the unlicensed repo (cannot vendor, can still reference).", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "blots-ot2", "title": "Bacterial Lysis Observation Over Time Assay (BLOTS) for High-Throughput Isolation and Screening", "doi": "10.1002/cpz1.70454", "paper_url": "https://doi.org/10.1002/cpz1.70454", "year": 2026, "venue": "Current Protocols", "open_access_license": "CC BY-NC 4.0", "code_url": "https://github.com/eyaplab/BLOTS-OT2", "code_files": ["BLOTS-OT2_code.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "384-well assay plate assembly / lysis kinetics screening", "results_evidence": "Assay plates assembled by the robot yielded time-resolved lysis curves used to recover and sequence isolates.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Current Protocols article is a step-by-step protocol (ideal NL input) with a single matching OT-2 script; licence of code unstated.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "cayman-his-elisa", "title": "An Opentrons OT-2 workflow for the Cayman His-tag detection ELISA kit", "doi": "10.17504/protocols.io.n92ld4x3nl5b", "paper_url": "https://dx.doi.org/10.17504/protocols.io.n92ld4x3nl5b", "year": 2026, "venue": "protocols.io (Arcadia Science)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow", "code_files": ["scripts/ot2_p1000single_elisa_sample_loading_final.py", "scripts/ot2_p300multi_elisa_wash_substrate.py", "scripts/ot2_p1000single_elisa_sample_loading_waste_chute.py", "tests/ot2_tip_drop_waste_chute_test.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "ELISA sample/standard loading, plate washing, substrate addition", "results_evidence": "Standard curves and His-tag quantification generated from the automated ELISA runs in the Arcadia protocol record.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY protocols.io text, MIT scripts including a hardware test; a clean easy/hard pair (loading vs wash+substrate).", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "chemputer-acra", "title": "Verification and execution of the scientific literature via chemputation augmented by large language models", "doi": "10.1038/s42004-026-01993-w", "paper_url": "https://www.nature.com/articles/s42004-026-01993-w", "year": 2026, "venue": "Communications Chemistry", "open_access_license": "CC BY", "code_url": "https://github.com/croningp/acra", "code_files": ["acra/agents/agents/xdl_generator.py", "acra/agents/prompts/xdl_prompt.py", "acra/data/xdls/CHEMIFY-*.xdl"], "code_license": "(LICENSE present, unrecognised text)", "language": "Python / XDL", "hardware": ["Chemputer"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "LLM-generated XDL from literature procedures executed on the Chemputer with yields reported; >100 reference XDLs released.", "wet_lab_validated": true, "simulatable": "true: chemputer XDL compiles/simulates against a graph (xdl dry-run)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Ready-made literature->XDL pairs with executed results; check licence text before vendoring.", "est_tasks": 15, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chemputer-blueprints", "title": "Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer", "doi": "10.1038/s41467-024-54238-6", "paper_url": "https://www.nature.com/articles/s41467-024-54238-6", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://gitlab.com/croningroup/chemputer/xdl", "code_files": ["xdl v2.0.0 (blueprints)", "SI XDL files"], "code_license": "see GitLab (unverified)", "language": "Python / XDL", "hardware": ["Chemputer"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Parallel chiral syntheses executed with reported yields/ee using XDL blueprints.", "wet_lab_validated": true, "simulatable": "true: XDL 2.0 compile + simulate mode", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "XDL procedures in SI map to methods text; xdl package supports simulation without hardware.", "est_tasks": 4, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chemputer-peptide", "title": "Universal peptide synthesis via solid-phase methods fused with chemputation", "doi": "10.1038/s41467-025-62344-2", "paper_url": "https://www.nature.com/articles/s41467-025-62344-2", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.15948769", "code_files": ["Zenodo XDL archive"], "code_license": "Zenodo (check)", "language": "XDL", "hardware": ["Chemputer", "SPPS module"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Synthesised multiple peptides (incl. semaglutide-type) with purity/yield reported.", "wet_lab_validated": true, "simulatable": "true: XDL simulation", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "XDL in Zenodo + methods text; good protocol_language tasks.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "clairify-xdl", "title": "Large language models for chemistry robotics (CLAIRify: NL -> XDL)", "doi": "10.1007/s10514-023-10136-2", "paper_url": "https://link.springer.com/article/10.1007/s10514-023-10136-2", "year": 2023, "venue": "Autonomous Robots", "open_access_license": "CC BY", "code_url": "https://github.com/ac-rad/xdl-generation", "code_files": ["xdlgenerator/nlp2xdl.py", "web-interface/verify.py", "dataset/ (chem-eval .txt protocols)"], "code_license": "MIT", "language": "Python", "hardware": ["Franka Panda", "Chemputer (via XDL)"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Generated XDL executed on a Franka robot for solubility/recrystallisation; expert-evaluated XDL validity on 108 protocols.", "wet_lab_validated": true, "simulatable": "true: XDL verifier (syntax/static checks) runs offline; robot execution via simulation", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Directly a 'methods text -> XDL' task with a bundled verifier and ~100 protocol texts; MIT.", "est_tasks": 10, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "culturomics-isolation", "title": "Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex communities", "doi": "10.1002/imo2.70037", "paper_url": "https://doi.org/10.1002/imo2.70037", "year": 2025, "venue": "iMetaOmics", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/microenvgen/Culturomics", "code_files": ["Library preparation/First_PCR.py", "Library preparation/Second_PCR.py", "Library preparation/MicrovolumeDNAextraction.py", "Library preparation/OmegaMagBindPCRpurificationMultichannel.py", "Library preparation/pool_plate_to_screw_cap_by_volume.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "microvolume DNA extraction, two-step amplicon PCR, bead purification, pooling", "results_evidence": "Isolates recovered and phylogenetically identified from automated plates; sequencing success rates reported vs manual pipeline.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper with 11 modular OT-2 scripts, each a clean single-step task; repo has no licence.", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "damplab-moclo-transformation", "title": "A linear programming-based strategy to save pipette tips in automated DNA assembly (with DAMP Lab MoClo/transformation workflow)", "doi": "10.1093/synbio/ysac004", "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac004/6542944", "year": 2022, "venue": "Synthetic Biology (OUP)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/DAMPLAB/OT2-MoClo-Transformation-Ecoli", "code_files": ["moclo_transformation/data/moclo_template.py", "moclo_transformation/data/moclo_transform_template.py", "moclo_transformation/data/transform_template.py"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "MoClo Golden Gate assembly + E. coli transformation + plating", "results_evidence": "Tip-saving assembly strategy evaluated on OT-2 runs; assembly/transformation success measured against standard tip usage.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "BSD-3 templates, open paper; templates are parameterised so labware/volume filling is needed before simulation.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "eda-event-driven", "title": "Event-driven acquisition for content-enriched microscopy", "doi": "10.1038/s41592-022-01589-x", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613693/", "year": 2022, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC, CC BY)", "code_url": "https://github.com/wl-stepp/eda_plugin", "code_files": ["eda_plugin/examples/main.py", "eda_plugin/examples/actuators.py", "eda_plugin/examples/interpreters.py", "(LEB-EPFL/EDA) analysis"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["iSIM microscope", "Micro-Manager"], "domain": "biology", "task_type": "imaging", "results_evidence": "Adaptive frame-rate imaging of mitochondrial and bacterial division events with reported photobleaching reduction.", "wet_lab_validated": true, "simulatable": "true: Micro-Manager demo config + recorded data replay", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Feedback rule (interpreter thresholds -> frame rate) is checkable by replaying image streams.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ester-library-synthesis", "title": "Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction", "doi": "10.1039/d2cc05670d", "paper_url": "https://doi.org/10.1039/d2cc05670d", "year": 2023, "venue": "Chemical Communications", "open_access_license": "unclear (preprint CC BY-NC-ND on ChemRxiv 10.26434/chemrxiv-2022-9grb8)", "code_url": "https://github.com/rz-flask/concise-ester-library-synthesis", "code_files": ["substrate_screen_acids.py", "substrate_screen_quench.py", "substrate_screen_solvent_katsalt_KI.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "96-well library synthesis, quench, solvent/salt screen", "results_evidence": "96-well esterification library synthesised on OT-2 with yields/conversions measured by LC-MS.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "MIT code with custom labware JSON included; journal text may be paywalled but the ChemRxiv version is open.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "etsted", "title": "Event-triggered STED imaging", "doi": "10.1038/s41592-022-01588-y", "paper_url": "https://www.nature.com/articles/s41592-022-01588-y", "year": 2022, "venue": "Nature Methods", "open_access_license": "CC BY", "code_url": "https://github.com/jonatanalvelid/etSTED-widget", "code_files": ["EtSTEDController.py", "mockcamera.py", "analysis_pipelines/pipeline_fake.py"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["STED microscope", "ImSwitch"], "domain": "biology", "task_type": "imaging", "results_evidence": "Event-triggered STED of vesicle/synaptic events with reported detection rates.", "wet_lab_validated": true, "simulatable": "true: mockcamera + fake pipeline included", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Mock camera bundled; GPL limits vendoring but can be referenced.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "evolver-2018", "title": "Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER", "doi": "10.1038/nbt.4151", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035058/", "year": 2018, "venue": "Nature Biotechnology", "open_access_license": "author manuscript (PMC); journal paywalled", "code_url": "https://github.com/FYNCH-BIO/dpu", "code_files": ["experiment/template/eVOLVER.py", "experiment/template/custom_script.py", "(FYNCH-BIO/evolver) evolver/evolver.py server"], "code_license": "MIT", "language": "Python", "hardware": ["eVOLVER continuous-culture array (16 vials)", "OD/temp sensors", "peristaltic pumps"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Turbidostat/chemostat growth curves and selection experiments across 16 vials reported with fitness measurements.", "wet_lab_validated": true, "simulatable": "partial: custom_script.py control loop is pure Python over OD arrays; can be driven by a fake socket server/replayed OD logs", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT; turbidostat/chemostat control functions are small and gradeable by replaying OD traces to check pump commands; paper PDF is PMC author manuscript.", "est_tasks": 5, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "exfab-qiaseq-flex", "title": "Automated QIAseq FX DNA Library Preparation on the Opentrons Flex", "doi": "10.17504/protocols.io.n2bvjer3pgk5", "paper_url": "https://dx.doi.org/10.17504/protocols.io.n2bvjer3pgk5", "year": 2025, "venue": "protocols.io (ExFAB Biofoundry)", "open_access_license": "CC BY 4.0 (protocols.io)", "code_url": "https://github.com/exfab/Opentrons_Flex_ExFAB", "code_files": ["QIASeq FX 48x 6_24_25.py"], "code_license": "GPL-3.0", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "NGS library preparation (fragmentation, adapter ligation, bead cleanup, PCR)", "results_evidence": "Protocol entry reports libraries prepared for Illumina short-read sequencing of bee gut samples (sequencing-ready yields).", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "A protocols.io DOI with CC BY text is an ideal NL input, GPL-3.0 Flex script matches it one-to-one; Flex coverage is thin in the corpus.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "flat-agar-celegans-ot2", "title": "Flat agar and optimized media enable high-throughput C. elegans imaging in 96-well plates", "doi": "10.57844/arcadia-h01v-2nxt", "paper_url": "https://doi.org/10.57844/arcadia-h01v-2nxt", "year": 2026, "venue": "Arcadia Science (The Stacks pub)", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/Arcadia-Science/menisquish-flat-agar", "code_files": ["opentrons/bowie_celegans_bleach_sync_var-col_v1.py", "opentrons/hopsy_p20multi_op50_agar_spotting_centrifuge_v4.py", "opentrons/hopsy_p20multi_worm_plating_centrifuge_v4.py"], "code_license": "MIT", "stars": 0, "last_push": "2026-09-25", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "C. elegans bleach synchronisation, OP50 agar spotting, worm plating for imaging", "results_evidence": "Pub reports flat-agar 96-well imaging quality (focus/worm detection) enabled by robot-prepared plates.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT, three apiv2 protocols, open CC BY pub; may need custom plate labware defs.", "est_tasks": 4, "source_agent": "github", "found_by": ["github"]}
+{"id": "formulations-prep-shampoo", "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset", "doi": "10.1038/s41597-024-03573-w", "paper_url": "https://www.nature.com/articles/s41597-024-03573-w", "year": 2024, "venue": "Scientific Data", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/sustainable-processes/formulations-prep", "code_files": ["OpentronsProtocol_FormulationSamples.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscous liquid formulation preparation with gravimetric verification", "results_evidence": "Gravimetric analysis of robot-prepared formulations and downstream property measurements form the published dataset.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY data descriptor plus one OT-2 script; viscous-liquid handling parameters make a good hard variant. Repo unlicensed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "github", "web"]}
+{"id": "gfp-codon-burden-ot2", "title": "Codon usage modulates the relationship between the burden and yield of protein overexpression", "doi": "10.1186/s13036-025-00521-z", "paper_url": "https://doi.org/10.1186/s13036-025-00521-z", "year": 2025, "venue": "Journal of Biological Engineering", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/alexismhill3/gfp_deoptimization_burden", "code_files": ["wet_scripting/low_temp_day_1/generate_protocol.py", "wet_scripting/low_temp_day_1/base_protocol_multichannel.py", "wet_scripting/low_temp_day_1/complete_protocol.py", "wet_scripting/low_temp_day_2/complete_protocol.py", "wet_scripting/low_temp_day_3/complete_protocol.py"], "code_license": "MIT", "stars": 0, "last_push": "2025-04-30", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "bacterial growth/induction burden assay (IPTG titration, GFP + OD plate-reader)", "results_evidence": "J Biol Eng 2025 (preprint 10.1101/2024.11.28.625058) reports growth-rate burden vs GFP yield across codon-deoptimised strains; raw plate-reader data and processed data are in the repo.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT repo with apiLevel 2.18 protocols generated from plate-reader CSV, raw+processed data included, CC BY paper; generator needs input CSV but complete_protocol.py is concrete.", "est_tasks": 4, "source_agent": "github", "found_by": ["github"]}
+{"id": "greenaway-halogenation", "title": "An automated platform for tailored late-stage halogenation of pharmaceuticals", "doi": "10.26434/chemrxiv.15000393", "paper_url": "https://chemrxiv.org/engage/chemrxiv/article-details/15000393", "year": 2025, "venue": "ChemRxiv (preprint)", "open_access_license": "ChemRxiv CC BY (per posting)", "code_url": "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals", "code_files": ["opentrons_dispense_code/reaction_setup/protocol_1(stage1_screening).py", "opentrons_dispense_code/reaction_setup/protocol_2(stage2_0to6_chlor).py", "opentrons_dispense_code/nmr_sample_prep/nmr_sample_preparation.py", "(9 OT-2 scripts total)"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "reaction array setup, quench, NMR/LC-MS sample prep", "results_evidence": "Screening arrays dispensed by OT-2 gave halogenation conversions/selectivities measured by NMR and LC-MS across substrate panels.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "BSD-3 code, several independent stage scripts, chemistry (non-bio) diversity for the benchmark; must confirm final journal version.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "greenaway-mocs", "title": "Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages", "doi": "10.1002/anie.202424270", "paper_url": "https://doi.org/10.1002/anie.202424270", "year": 2025, "venue": "Angewandte Chemie Int. Ed.", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/GreenawayLab/development-automated-workflow-mocs", "code_files": ["Opentrons_Protocols/automated_synthesis_opentron_script.py", "Opentrons_Protocols/automated_screen_refined_opentron_script.py", "Opentrons_Protocols/automated_host_guest_assay_opentron_script.py", "Opentrons_Protocols/Solvent_benchmark_acetonitrile_automated_screen.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "solution-phase screening array + host-guest assay", "results_evidence": "Automated screen identified assembled cages confirmed by MS/NMR and host-guest binding measured across the array.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper, five discrete OT-2 scripts; repo carries no licence so reference-only.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "greenaway-pocs", "title": "Streamlining the automated discovery of porous organic cages", "doi": "10.1039/d3sc06133g", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc06133g", "year": 2024, "venue": "Chemical Science", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/GreenawayLab/Streamlining-Automated-Discovery-POCs", "code_files": ["Opentrons_Protocols/Plate_example/opentron_script.py", "Opentrons_Protocols/NMR_transfer/opentron_script.py", "Opentrons_Protocols/HRMS_transfer/opentron_script.py", "Opentrons_Protocols/simulate.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cage synthesis plate + analytical transfer protocols", "results_evidence": "Automated workflow produced porous organic cages characterised by HRMS/NMR, with hit rates reported vs manual discovery.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper and a repo that even ships simulate.py (so scripts are known to run in opentrons_simulate); unlicensed repo.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "hyrad-adna-capture", "title": "Performance and automation of ancient DNA capture with RNA hyRAD probes", "doi": "10.1111/1755-0998.13518", "paper_url": "https://doi.org/10.1111/1755-0998.13518", "year": 2022, "venue": "Molecular Ecology Resources", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/TomaszSuchan/opentrons-hyRAD", "code_files": ["hyRAD.ot2.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "hybridization capture + magnetic bead washes (magnetic module, thermocycler)", "results_evidence": "Capture efficiency and on-target read fractions for automated vs manual hybridization reported for ancient DNA libraries.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Single self-contained module-driven script; good hard task (magnetic module + temperature steps). Paper is ND-licensed so text can be linked not redistributed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "jubiotech-ot2-autoclone", "title": "Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation", "doi": "10.1007/s00253-022-12017-7", "paper_url": "https://doi.org/10.1007/s00253-022-12017-7", "year": 2022, "venue": "Applied Microbiology and Biotechnology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/JuBiotech/OT-2-autoclone", "code_files": ["scripts/golden_gate_assembly.py", "scripts/heat-shock_transformation.py", "scripts/restriction_digestion.py", "scripts/plasmid_purification.py", "scripts/distributing_cells_on_agar_plates.py"], "code_license": "AGPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate assembly, heat-shock transformation, plasmid prep, plating", "results_evidence": "Automated strain construction produced verified C. glutamicum secretion strains characterised in microbioreactor cultivations.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Open paper, one script per protocol step, each self-contained; AGPL-3.0 means reference-only (same constraint as APEX).", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "labop", "title": "LabOP (Laboratory Open Protocol language, formerly PAML) - iGEM interlab growth-curve/calibration protocols", "doi": null, "paper_url": "https://bioprotocols.github.io/labop/", "year": 2023, "venue": "software + iGEM Interlab use (journal paper not verified)", "open_access_license": null, "code_url": "https://github.com/Bioprotocols/labop", "code_files": ["examples/protocols/growth-curve/growth_curve.py", "examples/protocols/iGEM/interlab-endpoint.py", "examples/protocols/calibration/", "labop_convert/ (to Opentrons/Autoprotocol/markdown)"], "code_license": "MIT", "language": "Python", "hardware": ["plate reader", "incubator", "liquid handlers (via converters)"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Protocols used in the iGEM Interlab study (results published separately); executable via converters.", "wet_lab_validated": true, "simulatable": "true: execution engine runs protocols abstractly and emits markdown/Autoprotocol without hardware", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Protocol DSL with a hardware-free execution engine; 'methods text -> LabOP protocol' graded by executed trace.", "est_tasks": 5, "source_agent": "nonlh", "found_by": ["github", "nonlh"]}
+{"id": "lucks-cellfree-biosensor", "title": "Semi-automated production of cell-free biosensors", "doi": "10.1101/2024.10.13.618078", "paper_url": "https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1", "year": 2024, "venue": "bioRxiv", "open_access_license": "bioRxiv (CC licence per preprint page)", "code_url": "https://github.com/LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024", "code_files": ["Opentrons_Code/Figure_2_Sensor_Build.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free reaction assembly (384-well biosensor build)", "results_evidence": "A full 384-well plate of fluoride-sensing cell-free reactions assembled robotically matched expected colorimetric/fluorescent detection performance.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "One script maps to one figure, open preprint text, viscous cell-free liquid class makes it a good hard task; repo unlicensed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "lysostaphin-turbidity", "title": "Turbid but accurate: automating lysostaphin quantification including uncertainty quantification", "doi": "10.1186/s12934-025-02911-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12836826/", "year": 2026, "venue": "Microbial cell factories", "open_access_license": "cc-by", "code_url": "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025", "code_files": ["code/Turbidity_assay_OT_8samples.py"], "code_license": "AGPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "antibacterial activity turbidity assay (serial dilution + OD lysis kinetics)", "results_evidence": "Turbidity assay quantified lysostaphin over a 0.63-10 mg/L dynamic range with Bayesian uncertainty quantification using autoclaved S. carnosus indicator cells.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Single self-contained OT-2 apiLevel script (Turbidity_assay_OT_8samples.py) matching the paper; OA paper; licence AGPL-3.0 (clear, but like APEX cannot be vendored).", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Fuaep5GZ3DJGlqCuFCqpNgo1dwp"], "found_by": ["amass", "github"]}
+{"id": "mantis-shrimpy", "title": "Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells", "doi": "10.1093/pnasnexus/pgae323", "paper_url": "https://academic.oup.com/pnasnexus/article/3/9/pgae323/7742297", "year": 2024, "venue": "PNAS Nexus", "open_access_license": "CC BY-NC", "code_url": "https://github.com/czbiohub-sf/shrimPy", "code_files": ["archive/pycromanager/acquisition_settings/*.yaml", "archive/pycromanager/cli/run_acquisition.py", "mantis acquisition engine"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["custom light-sheet + label-free microscope", "Micro-Manager stages/cameras"], "domain": "biology", "task_type": "imaging", "results_evidence": "Multi-well 4D imaging of cell lines acquired and analysed with reported throughput.", "wet_lab_validated": true, "simulatable": "true: demo acquisition settings YAML + Micro-Manager demo config", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Acquisition settings YAMLs map directly to methods text; demo config enables dry-run.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "massspecpreppy", "title": "MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics", "doi": "10.1002/pmic.202300294", "paper_url": "https://doi.org/10.1002/pmic.202300294", "year": 2023, "venue": "PROTEOMICS", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/stemicha/MassSpecPreppy", "code_files": ["OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_mix.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_Ev*.py"], "code_license": "GPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "BCA assay, reduction/alkylation, SP3 digestion, Evotip loading", "results_evidence": "BCA recovery 101.3% (SD 7.8) for the automated workflow vs 96.3% manual; 94.5% of protein groups passed thresholds for OT-2 digestion.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "GPL-3.0 templates, one file per workflow stage, quantitative wet-lab comparison in the paper; templates are parameterised by the Shiny app so some placeholder filling is needed.", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "github", "web"]}
+{"id": "msd-biochem-assays-ot2", "title": "Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler", "doi": "10.1016/j.slast.2024.100205", "paper_url": "https://doi.org/10.1016/j.slast.2024.100205", "year": 2024, "venue": "SLAS Technology", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays", "code_files": ["Bradford_standard_curve.py", "PicoGreen_standard_curve_YW_validated.py"], "code_license": "Apache-2.0", "stars": 1, "last_push": "2024-08-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Bradford and PicoGreen standard curves / quantitation assays", "results_evidence": "SLAS Technology 2024 paper compares OT-2 Bradford/PicoGreen standard curves and sample quantitation to manual (linearity, CV, accuracy).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Two self-contained apiv2 scripts, Apache-2.0, open-access SLAS paper with validated assay results; standard labware.", "est_tasks": 4, "source_agent": "github", "found_by": ["amass", "github", "web"]}
+{"id": "navigate-2024", "title": "Navigate: an open-source platform for smart light-sheet microscopy", "doi": "10.1038/s41592-024-02413-4", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540721/", "year": 2024, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/TheDeanLab/navigate", "code_files": ["src/navigate/controller/controller.py", "src/navigate/model/features/ (feature lists = smart acquisition programs)", "config/configuration.yaml (synthetic hardware)"], "code_license": "BSD-style (LICENSE.md)", "language": "Python", "hardware": ["light-sheet microscopes (ASLM, OPM)", "stages", "cameras", "galvos"], "domain": "biology", "task_type": "imaging", "results_evidence": "Smart acquisition (autofocus, tiling, decision-based imaging) demonstrated on multiple microscopes with images.", "wet_lab_validated": true, "simulatable": "true: ships 'synthetic' hardware devices for every device class", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Feature-list programs are a compact DSL; synthetic hardware enables execution-based grading.", "est_tasks": 4, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "openflexure-autofocus", "title": "Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope", "doi": "10.1111/jmi.13064", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13064", "year": 2022, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://gitlab.com/openflexure/openflexure-microscope-server", "code_files": ["openflexure_microscope/api/default_extensions/autofocus.py", "scan extension"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["OpenFlexure Microscope", "Raspberry Pi camera", "Sangaboard stage"], "domain": "biology", "task_type": "imaging", "results_evidence": "Automated malaria blood-smear tiling scans with autofocus success rates reported.", "wet_lab_validated": true, "simulatable": "true: server has a simulation/mock camera+stage mode (dev)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "GitLab server includes mock hardware; scan/autofocus parameters gradeable.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "openworkstation", "title": "OpenWorkstation: A modular open-source technology for automated in vitro workflows", "doi": "10.1016/j.ohx.2020.e00152", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067220300468", "year": 2020, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "https://github.com/SebastianEggert/OpenWorkstation", "code_files": ["api/openworkstation/robot/robot.py", "api/openworkstation/drivers/smoothie_drivers/v2_0_0/virtual_smoothie.py", "examples/microphysiometry-setup/camera.py"], "code_license": "CC BY-SA (repo)", "language": "Python", "hardware": ["modular gantry", "plate handling modules", "camera", "incubation"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Automated microphysiometry/cell-culture workflow demonstrated with measurements.", "wet_lab_validated": true, "simulatable": "true: virtual_smoothie driver (Opentrons-derived simulator)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Virtual driver bundled; scripts are short and gradeable.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["amass", "nonlh"]}
+{"id": "panda-bear", "title": "PANDA: a self-driving lab for studying electrodeposited polymer films", "doi": "10.1039/d4mh00797b", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/mh/d4mh00797b", "year": 2024, "venue": "Materials Horizons", "open_access_license": "CC BY", "code_url": "https://github.com/BU-KABlab/PANDA-BEAR", "code_files": ["examples/run_experiment.py", "src/panda_lib/hardware/grbl_cnc_mill/mock.py", "src/panda_lib/hardware/gamry_potentiostat/gamry_control_mock.py", "src/panda_lib/hardware/emstat_potentiostat/emstat_control_mock.py"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["CNC gantry (GRBL)", "syringe pump", "Gamry/EmStat potentiostat", "telecentric camera"], "domain": "materials", "task_type": "characterisation", "results_evidence": "BO campaign optimised PEDOT:PSS electrochromic switching; data reported.", "wet_lab_validated": true, "simulatable": "true: mock CNC, mock potentiostats, path simulation shipped", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Mocks for every instrument; experiment definitions translate from methods (deposition potential/time, CV params).", "est_tasks": 4, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "plant-phenotyping-ot2", "title": "Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience", "doi": "10.1002/aisy.202500624", "paper_url": "https://doi.org/10.1002/aisy.202500624", "year": 2026, "venue": "Advanced Intelligent Systems", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Synthetic-Automated-Systems/automated_phenotyping_system", "code_files": ["Code/OT2Code.py", "Code/OT2Code-FillPlates.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plate filling and treatment dosing for plant phenotyping", "results_evidence": "Automated phenotyping screen measured growth responses used to select stress-resilient conditions.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper and MIT scripts; two scripts give an easy (fill plates) and harder (full protocol) pair.", "est_tasks": 3, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "pycromanager-2021", "title": "Pycro-Manager: open-source software for customized and reproducible microscope control", "doi": "10.1038/s41592-021-01087-6", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532176/", "year": 2021, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/micro-manager/pycro-manager", "code_files": ["pycromanager/acquisition/", "misc/examples/", "docs/source/*.ipynb (application notebooks)"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["Micro-Manager-controlled microscopes (cameras, stages, light sources)"], "domain": "biology", "task_type": "imaging", "results_evidence": "Applications in paper (adaptive illumination, light-sheet, high-throughput imaging) with acquired data.", "wet_lab_validated": true, "simulatable": "true: Micro-Manager Demo config (DemoCamera/DemoStage) via pymmcore / Java backend", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Demo hardware lets acquisition events be executed and checked (axes, positions, exposures, hooks).", "est_tasks": 5, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "pymmcore-plus-mda", "title": "pymmcore-plus + useq-schema (multi-dimensional acquisition engine)", "doi": null, "paper_url": "https://pymmcore-plus.github.io/pymmcore-plus/", "year": 2024, "venue": "software (used by Mantis/shrimPy and others)", "open_access_license": null, "code_url": "https://github.com/pymmcore-plus/pymmcore-plus", "code_files": ["examples/run_mda.py", "examples/event_driven_acquisition.py", "(useq-schema) src/useq/_mda_sequence.py"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["Micro-Manager devices"], "domain": "biology", "task_type": "imaging", "results_evidence": "Software; validated through downstream papers (e.g., Mantis PNAS Nexus 2024).", "wet_lab_validated": false, "simulatable": "true: loadSystemConfiguration() demo config, fully headless", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Best grading substrate for imaging tasks: MDASequence is declarative and comparable; pair with papers' imaging methods.", "est_tasks": 4, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "roboctab", "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping", "doi": "10.3390/plants14152263", "paper_url": "https://www.mdpi.com/2223-7747/14/15/2263", "year": 2025, "venue": "Plants (MDPI)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/tomstamour/RoboCTAB", "code_files": ["RoboCTAB_OT2.py", "RoboCTAB_Flex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CTAB plant DNA extraction", "results_evidence": "DNA yield/purity and genotyping call rates from robot-extracted samples compared with manual CTAB extraction.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper; two complete protocols (OT-2 and Flex variants) give a natural easy/hard pair; repo unlicensed.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "github", "web"]}
+{"id": "roche-pipetting-performance-ot2", "title": "Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment", "doi": "10.1016/j.slast.2024.100180", "paper_url": "https://doi.org/10.1016/j.slast.2024.100180", "year": 2024, "venue": "SLAS Technology", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/arthur-theuer/pipetting-performance", "code_files": ["templates/opentrons/OT2_pipetting_performance_p20.py", "templates/opentrons/OT2_pipetting_performance_p300.py"], "code_license": "GPL-3.0", "stars": 2, "last_push": "2025-10-11", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "liquid-handler QC: photometric pipetting accuracy/precision (dye dilution)", "results_evidence": "SLAS Technology 2024 (Roche pRED) reports OT-2 integration into AutoLab and pipetting accuracy/precision benchmarks (CV, systematic error) per volume.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "GPL-3.0 apiv2 templates (p20/p300) filled by notebook; open SLAS paper; similar to existing pipetting-speed-ot2 so pairs well as hard variant.", "est_tasks": 2, "source_agent": "github", "note": "repo is the public adaptation by the Roche author; link to paper is inferred from topic/author, verify", "found_by": ["amass", "github"]}
+{"id": "sapp-dmx-protein-design", "title": "Accelerating protein design by scaling experimental characterization", "doi": "10.1038/s41467-026-76740-9", "paper_url": "https://doi.org/10.1038/s41467-026-76740-9", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/bwicky/SAPP_DMX", "code_files": ["SAPP/SEC_pool_and_norm_v3.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SEC fraction pooling and normalisation for protein characterisation", "results_evidence": "High-throughput expression/characterisation of designed proteins; thousands of designs assayed with the automated pipeline.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper, MIT single-purpose script (pool and normalise) \u2014 a clean medium task.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "sdl-demo-clslab", "title": "What is a minimal working example for a self-driving laboratory? (SDL-Demo / CLSLab:Light)", "doi": "10.1016/j.matt.2022.11.007", "paper_url": "https://www.cell.com/matter/fulltext/S2590-2385(22)00651-1", "year": 2022, "venue": "Matter", "open_access_license": "author accepted (NSF PAR)", "code_url": "https://github.com/sparks-baird/self-driving-lab-demo", "code_files": ["src/self_driving_lab_demo/", "notebooks/2.2-sensor-simulator.ipynb", "scripts/bayesian_optimization_basic.py"], "code_license": "MIT", "language": "Python/MicroPython", "hardware": ["Raspberry Pi Pico W", "RGB LEDs", "AS7341 spectral sensor"], "domain": "other", "task_type": "characterisation", "results_evidence": "Optimisation of LED mixing to match target spectra; simulator vs hardware comparison reported.", "wet_lab_validated": true, "simulatable": "true: SensorSimulator class mirrors hardware", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Built-in simulator; tasks like 'set up BO campaign / MQTT commands per methods'; low biology relevance.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "slab-scheduling", "title": "Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints", "doi": "10.1177/24726303211021790", "paper_url": "https://journals.sagepub.com/doi/10.1177/24726303211021790", "year": 2021, "venue": "SLAS Technology", "open_access_license": "CC BY-NC", "code_url": "https://github.com/labauto/SLab.jl", "code_files": ["src/*.jl (MIP scheduler)", "tsv job/instrument definitions"], "code_license": "MIT", "language": "Julia", "hardware": ["LabDroid Maholo robot", "incubators", "centrifuges"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Schedules for cell-culture protocols computed and compared to baseline; executed on Maholo.", "wet_lab_validated": true, "simulatable": "true: pure scheduler", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Scheduling-as-code: methods text with time constraints -> job/time-constraint spec; makespan verifiable.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "tidytron", "title": "TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 robots", "doi": "10.1016/j.slast.2023.08.007", "paper_url": "https://doi.org/10.1016/j.slast.2023.08.007", "year": 2024, "venue": "SLAS Technology", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/PlantSynBioLab/TidyTron", "code_files": ["scripts/optimization_scripts/DNAcleaning.py", "scripts/optimization_scripts/fig1C_10ul_tip_cleaning_optimization.py", "scripts/*.py (37 OT-2 scripts total)"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plasticware wash-and-reuse / tip and plate cleaning", "results_evidence": "Carryover after wash validated by qPCR/transformation and fluorescence assays showing no detectable cross-contamination vs fresh plasticware.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Open paper text (CC BY-NC-ND), Apache-2.0 repo with 37 standalone OT-2 API v2 scripts that should simulate as-is; wash/reuse figures give measured outcomes.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "a-lab-2023", "title": "An autonomous laboratory for the accelerated synthesis of novel materials (A-Lab)", "doi": "10.1038/s41586-023-06734-w", "paper_url": "https://www.nature.com/articles/s41586-023-06734-w", "year": 2023, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://github.com/njszym/ARROWS", "code_files": ["ARROWS (active-learning synthesis planner)", "XRD-AutoAnalyzer"], "code_license": "none (ARROWS); see repos", "language": "Python", "hardware": ["UR5e", "furnaces", "XRD", "powder dosing"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Claimed 41/58 novel compounds synthesized in 17 days (phase claims later contested).", "wet_lab_validated": true, "simulatable": "partial: planning/XRD analysis code runs offline; robot control via AlabOS", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Robot code is AlabOS (separate entry); contested results lower ground-truth reliability.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ac-training-lab", "title": "Acceleration Consortium Training Lab (remote-access SDL modules incl. Hello-World, sample transfer)", "doi": null, "paper_url": "https://github.com/AccelerationConsortium/ac-training-lab", "year": 2025, "venue": "software (several Digital Discovery / ChemRxiv tutorials)", "open_access_license": null, "code_url": "https://github.com/AccelerationConsortium/ac-training-lab", "code_files": ["scripts/prefect_scripts/my_gh_sample_transfer_workflow.py", "src/ac_training_lab/"], "code_license": "MIT", "language": "Python", "hardware": ["xArm/MyCobot arms", "Cobra sample transfer", "Raspberry Pi devices", "3D-printer gantries"], "domain": "other", "task_type": "plate_transport", "results_evidence": "Educational SDL modules; no single results paper verified.", "wet_lab_validated": false, "simulatable": "partial: Prefect workflows run with MQTT mocks", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No canonical results paper.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ada-thin-films", "title": "Self-driving laboratory for accelerated discovery of thin-film materials (Ada)", "doi": "10.1126/sciadv.aaz8867", "paper_url": "https://www.science.org/doi/10.1126/sciadv.aaz8867", "year": 2020, "venue": "Science Advances", "open_access_license": "CC BY-NC", "code_url": "https://github.com/berlinguette/ada", "code_files": ["per-paper folders: campaign data, user_config.py, transformations_config.py, analysis scripts"], "code_license": "MIT", "language": "Python", "hardware": ["N9 robot arm (North Robotics)", "spin coater", "annealing", "UV-Vis-NIR", "4-point probe", "camera"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Optimised hole-transport-layer pseudomobility via closed-loop BO; data released per campaign.", "wet_lab_validated": true, "simulatable": "false: robot orchestration (ChemOS/N9) not released; only configs/data", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Campaign configs + data released but not hardware control code.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "afion-plasmonic", "title": "Self-driving lab for the photochemical synthesis of plasmonic nanoparticles (AFION)", "doi": "10.1038/s41467-025-56788-9", "paper_url": "https://www.nature.com/articles/s41467-025-56788-9", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/Taylorwutianyi/AFION-LAB", "code_files": ["General_AFION_Platform_Control_Software_Code/PythonLab/microreactor_v12.py", "pylab/instruments/pumps/hamilton_pump.py", "pylab/instruments/thorlabs_spectrometer/ccs.py"], "code_license": "none", "language": "Python", "hardware": ["flow microreactors", "syringe pumps", "UV LEDs (Arduino stepper)", "Thorlabs spectrometer"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Targeted Ag nanoparticle morphologies/spectra achieved autonomously with reported spectra.", "wet_lab_validated": true, "simulatable": "partial: instrument classes need serial stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; instrument-level Python is clear; flow chemistry rig.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "agentex-genetic-codes", "title": "Automated prototyping of genetic codes", "doi": "10.1038/s41586-026-10949-y", "paper_url": "https://doi.org/10.1038/s41586-026-10949-y", "year": 2026, "venue": "Nature", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/FelixRadford/AGENTEX", "code_files": ["AGENTEX reactions/Reactions/mixing.py", "Nucleic_acid_purifications/RNA/Step 1/Purification.py", "Nucleic_acid_purifications/RNA/Step 2/mixing.py", "Nucleic_acid_purifications/RNA/Step 3/Purification.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "in vitro translation reaction assembly, RNA purification", "results_evidence": "Automated prototyping produced and characterised reassigned genetic codes with mass-spec/translation readouts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Repo states Opentrons API 2.13 and has stage scripts, but the paper is ND-licensed and the repo unlicensed; scripts are tied to bespoke labware.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "ahtech-electrochem", "title": "A high-throughput experimentation platform for data-driven discovery in electrochemistry (AHTech)", "doi": "10.1126/sciadv.adu4391", "paper_url": "https://www.science.org/doi/10.1126/sciadv.adu4391", "year": 2025, "venue": "Science Advances", "open_access_license": "CC BY-NC", "code_url": "https://github.com/Liu-Lab-JHU/AHTech", "code_files": ["Code/AHTech Operation/AHTech_run.py", "Code/AHTech Operation/OpentronsClient.py", "easy-biologic potentiostat driver"], "code_license": "MIT", "language": "Python", "hardware": ["Opentrons OT-2 (electrode carrier)", "BioLogic multichannel potentiostat"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Thousands of CVs on redox mediators with discovered reactivity trends reported.", "wet_lab_validated": true, "simulatable": "partial: OT-2 HTTP client mockable; potentiostat via easy-biologic needs stub", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Electrochemistry is non-LH but OT-2 used as robot; MIT.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ai4pd-flex-protein-purification", "title": "Opentrons Flex protein purification and molecular biology scripts (AI4PD Lab)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/AI4PDLab/Opentrons_Flex_Protocols", "code_files": ["protein_purification/NiNTA_Protein_Purification.py", "protein_purification/inoculation_protein_expression.py", "protein_purification/reverse_imac_tev_digestion.py", "cloning/golden_gate.py", "plasmid_purification/MiniPrep_ZippyKit_FerruzLab.py"], "code_license": "MIT", "stars": 0, "last_push": "2026-05-08", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "protein expression, Ni-NTA purification, TEV digestion, Golden Gate, miniprep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT Flex scripts, no linked paper (AI4PD / Ferruz lab protein design validation likely). Overlaps apex.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "aliquot-niaid", "title": "ALIQUOT: Automated Liquid handling Infection Quantification Using OpenTrons (NIH/NIAID QVEU)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/QVEU/ALIQUOT", "code_files": ["OT-2/Serial Dilution/1 Plate/Serial_Dilution_1plate.py", "OT-2/Fix/1 Plate/Fix_1_plate.py", "OT-2/Full Protocol/1 Plate/Fix_and_Stain_1_plate.py"], "code_license": "none", "stars": 1, "last_push": "2026-03-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "virus infection quantification: serial dilution, fix, immunostain (OT-2 + Flex)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Well-organised apiv2 scripts + R analysis; paper not linked yet; no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "aml-drug-synergy-pyhamilton", "title": "High-throughput approaches to uncover synergistic drug combinations in leukemia", "doi": "10.1016/j.slasd.2023.04.004", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10449086/", "year": 2023, "venue": "SLAS discovery : advancing life sciences R & D", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/stefangolas/drug_dilutions", "code_files": ["robot_method.py"], "code_license": "none", "robot_platform": "hamilton", "api": "other", "protocol_category": "drug combination dilution matrix and dosing for synergy screening (leukemia cells)", "results_evidence": "Multidimensional drug-combination screens identified synergistic combinations in leukemia (H3K27 modification-related), with viability readouts and synergy scores.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "pyhamilton script (needs Hamilton VENUS layout/.lay file, Windows); no license; could be ported to PLR/OT-2 as a serial-dilution matrix task.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_2wDq20Fozm18kEnjSpNC6xxLKdO"], "found_by": ["amass"]}
+{"id": "amplicon-seq-bisanz", "title": "AmpliconSeq (16S amplicon library OT-2 scripts, Bisanz lab)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/jbisanz/AmpliconSeq", "code_files": ["ot2_scripts/1_ZymoMagWash.py", "ot2_scripts/2_PrimaryPCR.py", "ot2_scripts/3_CheryPickAndIndex_template.py", "ot2_scripts/4_PoolEquimolar_template.py", "ot2_scripts/O4_AmpureXPWash.py"], "code_license": "none", "stars": 8, "last_push": "2021-10-04", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "16S amplicon library prep (extraction wash, PCR, indexing, pooling, AMPure)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean pipeline with wet-lab markdown protocols but no paper/results, no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "angelovangel-ot2-ngs", "title": "angelovangel/opentrons (KAUST Bioscience core NGS/Sanger OT-2 + Flex protocols)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/angelovangel/opentrons", "code_files": ["protocols/01-sanger-setup-pcr.py", "protocols/02-ont-rapidlsk.py", "protocols/06-normalize-dna.py", "protocols/08-kinnex-pcr.py"], "code_license": "none", "stars": 1, "last_push": "2026-09-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Sanger PCR setup, ONT rapid library, DNA normalisation, PacBio Kinnex PCR", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Core-facility scripts; README notes not all tested on robot; no paper/license.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "aquarium", "title": "Aquarium laboratory operating system (UW BIOFAB) - used in SD2 robustness studies", "doi": "10.1093/synbio/ysad005", "paper_url": "https://academic.oup.com/synbio/article/8/1/ysad005/7069301", "year": 2023, "venue": "Synthetic Biology (usage paper)", "open_access_license": "CC BY-NC", "code_url": "https://github.com/aquariumbio/aquarium", "code_files": ["Ruby operation types (protocols run by technicians)"], "code_license": "MIT", "language": "Ruby", "hardware": ["human-executed bench protocols", "plate readers", "cytometers"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Aquarium-run yeast logic circuit experiments with cytometry outcomes reported.", "wet_lab_validated": true, "simulatable": "partial: Aquarium docker runs protocols with simulated technician", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Ruby, heavy docker; mostly human-in-loop protocols.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "artic-normalisation-esr", "title": "ESR-NZ ARTIC normalisation/end-repair/barcoding (OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/ESR-NZ/opentrons_protocols", "code_files": ["normalisation_artic.py", "normalisation_artic_multi.py", "NGS_normalisation.py"], "code_license": "none", "stars": 0, "last_push": "2020-06-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 ARTIC DNA normalisation + nanopore end-repair/barcoding", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper/license; reads plate-reader xlsx at runtime.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "auto-sp-proteomics", "title": "AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications", "doi": "10.1021/acs.analchem.5c00886", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12355475/", "year": 2025, "venue": "Analytical chemistry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics BCA, digestion and PTM enrichment", "results_evidence": "AUTO-SP automated BCA, digestion and PTM enrichment on PDX breast tumour tissue, with protein/PTM IDs comparable to manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocols provided in Supporting Information (not a repo); need SI retrieval to confirm .py.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_MxqtygMHV1Ej6q6nLxjWToWK6jk"], "found_by": ["amass"]}
+{"id": "autoprotocol-python", "title": "Autoprotocol-python (Strateos/Transcriptic protocol IR)", "doi": null, "paper_url": "https://autoprotocol.org", "year": 2016, "venue": "specification/software", "open_access_license": null, "code_url": "https://github.com/autoprotocol/autoprotocol-python", "code_files": ["autoprotocol/protocol.py", "autoprotocol/instruction.py", "autoprotocol/harness.py"], "code_license": "BSD-3-Clause (LICENSE.rst)", "language": "Python", "hardware": ["Strateos cloud lab: thermocycler, plate reader, sealer, centrifuge, incubator"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Specification; experimental results come from cloud-lab papers (e.g., SD2 replication papers).", "wet_lab_validated": false, "simulatable": "true: emits JSON without hardware", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Substrate rather than paper; pair with DNAda/SD2 papers.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "bean-kasp-anthracnose", "title": "Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR", "doi": "10.1186/s13007-023-01071-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10546687/", "year": 2023, "venue": "Plant methods", "open_access_license": "cc-by", "code_url": "https://github.com/McGillHaricots/peas-andlove", "code_files": ["protocols/Extraction & PACE Assay Part 2 (thermocycling_Co-42(1)).json", "protocols/PACE Assay (dual marker no dna).json", "protocols/... (Opentrons JSON protocols)"], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "plant DNA extraction + KASP/PACE allele-specific PCR genotyping", "results_evidence": "Automated DNA extraction and KASP assays genotyped common bean lines at four anthracnose resistance markers with clear allele clustering, matching expected genotypes.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocols are Opentrons Protocol Designer JSON files inside a large mixed lab repo, not Python; no license.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_RvNHz2cHbnDsOx9V5pABxjs3t2d"], "found_by": ["amass"]}
+{"id": "bear-mechanics", "title": "Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership (BEAR)", "doi": "10.1038/s41467-024-48534-4", "paper_url": "https://www.nature.com/articles/s41467-024-48534-4", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/KelseyEng/BEAR_ADTS", "code_files": ["*.m MATLAB orchestration", "*.py printer control", "gcode"], "code_license": "(LICENSE present, unrecognised)", "language": "MATLAB/Python", "hardware": ["FDM 3D printers", "UR5e arm", "Instron compression tester", "scale"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Record 75% energy-absorbing efficiency structures discovered; >25,000 experiments.", "wet_lab_validated": true, "simulatable": "partial: MATLAB orchestration with hardware calls; geometry generation simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MATLAB; arm/printer sequencing could be stubbed.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "biomationscripter", "title": "BiomationScripter: Python library for scripting bio-automation protocols", "doi": null, "paper_url": "https://biomationscripterlib.readthedocs.io", "year": 2022, "venue": "software (associated paper not located)", "open_access_license": null, "code_url": "https://github.com/intbio-ncl/BiomationScripterLib", "code_files": ["BiomationScripter/OTProto/*.py (20 Opentrons-aware files incl. labware test protocols)"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protocol-generation library (templates for PCR, dilution, transformation)", "results_evidence": "No wet-lab results tied to a publication found.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT library whose OTProto templates could seed tasks, but no paper and protocols are generated rather than literal scripts.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "brightfield-biofilm", "title": "Label-free microscopy enables high-throughput identification of genes controlling biofilm development", "doi": "10.1128/mbio.00448-26", "paper_url": "https://journals.asm.org/doi/10.1128/mbio.00448-26", "year": 2026, "venue": "mBio", "open_access_license": "CC BY", "code_url": "https://github.com/BridgesLabCMU/Brightfield-biofilm-assay", "code_files": ["*.jl analysis", "acquisition settings"], "code_license": "none", "language": "Julia", "hardware": ["automated widefield microscope", "plate handling"], "domain": "biology", "task_type": "imaging", "results_evidence": "Genome-wide biofilm screen with hit genes reported.", "wet_lab_validated": true, "simulatable": "partial: analysis only", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; mostly analysis.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "cfrna-pipeline", "title": "An inexpensive semi-automated sample processing pipeline for cell-free RNA (extraction)", "doi": "10.1038/s41596-023-00855-2", "paper_url": "https://doi.org/10.1038/s41596-023-00855-2", "year": 2023, "venue": "Nature Protocols (preprint: 10.1101/2020.08.18.256545)", "open_access_license": "preprint CC BY-NC-ND 4.0; journal version subscription", "code_url": "https://github.com/miramou/cfRNA_pipeline_automation", "code_files": ["Opentrons/scripts/48_format/1_add_slurry_lysis_to_plate.py", "Opentrons/scripts/48_format/3_transfer_etoh_centrifuge_remove_sup_add_etoh.py", "Opentrons/scripts/48_format/5_norgen_add_wash_buffer_elute.py", "Opentrons/scripts/48_format/6_zymo_clean_conc.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free RNA extraction and cleanup", "results_evidence": "RNA yields and sequencing library quality from the semi-automated pipeline compared with manual extraction.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Six numbered OT-2 steps (good task series) but code is unlicensed and the open text is the earlier preprint, not the Nature Protocols version.", "est_tasks": 5, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "chemcrow", "title": "Augmenting large language models with chemistry tools (ChemCrow)", "doi": "10.1038/s42256-024-00832-8", "paper_url": "https://www.nature.com/articles/s42256-024-00832-8", "year": 2024, "venue": "Nature Machine Intelligence", "open_access_license": "CC BY", "code_url": "https://github.com/ur-whitelab/chemcrow-public", "code_files": ["chemcrow/agents/", "chemcrow/tools/rxn4chem.py", "(chemcrow-runs) notebooks"], "code_license": "MIT", "language": "Python", "hardware": ["IBM RoboRXN cloud synthesis platform"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Executed syntheses of DEET and three thioureas plus a chromophore on RoboRXN, with characterisation.", "wet_lab_validated": true, "simulatable": "false: RoboRXN cloud API required (no simulator)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Execution is via proprietary cloud API; could grade generated RXN action sequences offline.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chemos-2020", "title": "ChemOS: An orchestration software to democratize autonomous discovery", "doi": "10.1371/journal.pone.0229862", "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229862", "year": 2020, "venue": "PLoS ONE", "open_access_license": "CC BY", "code_url": "https://github.com/aspuru-guzik-group/ChemOS", "code_files": ["Experiments/_dummy_dump/", "DatabaseManager/interfaces.py", "Communicator/"], "code_license": "Apache-2.0", "language": "Python", "hardware": ["robotic bartender (barmixvah)", "HPLC (in demos)"], "domain": "chemistry", "task_type": "scheduling", "results_evidence": "Demonstrates closed-loop optimisation on a cocktail-mixing robot and HPLC calibration, with reported optimisation traces.", "wet_lab_validated": true, "simulatable": "partial: dummy experiment folders; py2-era code, needs revival", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Old code (pyc, Python2-era); grading via dummy instrument possible but setup heavy.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chemos2-atlas", "title": "Atlas: a brain for self-driving laboratories (BO library used in ChemOS 2.0 campaigns)", "doi": "10.1039/D4DD00115J", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d4dd00115j", "year": 2025, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/aspuru-guzik-group/atlas", "code_files": ["src/atlas/planners/", "examples/"], "code_license": "MIT", "language": "Python", "hardware": [], "domain": "chemistry", "task_type": "other", "results_evidence": "BO planners benchmarked on emulators and deployed on SDL campaigns (e.g., electrochemistry with ChemOS 2.0).", "wet_lab_validated": true, "simulatable": "true: pure software, Olympus emulators", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Planner library only; hardware-free but task would be optimisation config, not lab-automation code.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chemputer-modules-acscs", "title": "Robotic Modules for the Programmable Chemputation of Molecules and Materials", "doi": "10.1021/acscentsci.3c00304", "paper_url": "https://pubs.acs.org/doi/10.1021/acscentsci.3c00304", "year": 2023, "venue": "ACS Central Science", "open_access_license": "CC BY", "code_url": "https://gitlab.com/croningroup/chemputer", "code_files": ["SI XDL/graph files"], "code_license": "unverified", "language": "XDL", "hardware": ["Chemputer modules"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Several syntheses executed on new modules with yields reported.", "wet_lab_validated": true, "simulatable": "true: XDL simulation", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Code link not in full text; relies on SI.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "chibio-2020", "title": "In situ characterisation and manipulation of biological systems with Chi.Bio", "doi": "10.1371/journal.pbio.3000794", "paper_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000794", "year": 2020, "venue": "PLoS Biology", "open_access_license": "CC BY", "code_url": "https://github.com/HarrisonSteel/ChiBio", "code_files": ["app.py (single-file Flask controller incl. turbidostat, optogenetics, custom programs)"], "code_license": "none (no LICENSE file)", "language": "Python", "hardware": ["Chi.Bio reactors (BeagleBone)", "LEDs", "spectrometer", "pumps"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Turbidostat growth, optogenetic feedback control and fluorescence measurements demonstrated with reported traces.", "wet_lab_validated": true, "simulatable": "partial: hardware I2C calls must be stubbed; control functions (Turbidostat, CustomProgram) are pure logic", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence on code; single large app.py; otherwise excellent methods->control-program tasks.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "clio-electrolytes", "title": "Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation (Clio)", "doi": "10.1038/s41467-022-32938-1", "paper_url": "https://www.nature.com/articles/s41467-022-32938-1", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/BattModels/Clio-PythonAPI", "code_files": ["Experiment.py", "demo_electrolytecomp.py", "(Clio-LabViewControl) LabVIEW VIs"], "code_license": "none", "language": "Python/LabVIEW", "hardware": ["Clio: pumps, mixing, conductivity cell", "pouch cells"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Found electrolyte with 13% higher conductivity in 42 experiments; pouch-cell validation.", "wet_lab_validated": true, "simulatable": "partial: Python API sends to LabVIEW; demo script mockable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; LabVIEW backend.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "coscientist", "title": "Autonomous chemical research with large language models (Coscientist)", "doi": "10.1038/s41586-023-06792-0", "paper_url": "https://www.nature.com/articles/s41586-023-06792-0", "year": 2023, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://github.com/gomesgroup/coscientist", "code_files": ["simple_implementation/coscientist.py", "simple_implementation/tools.py", "simple_implementation/run.py"], "code_license": "(LICENSE present, unrecognised text)", "language": "Python", "hardware": ["Opentrons OT-2", "Emerald Cloud Lab", "UV-Vis plate reader (via OT-2/heater-shaker)", "Heater-shaker"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Suzuki/Sonogashira couplings executed and confirmed by GC-MS; plate-reader colour tasks executed.", "wet_lab_validated": true, "simulatable": "partial: OT-2 simulate for LH parts; ECL SLL steps not simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Heavily overlaps LH (OT-2); non-LH element is ECL cloud-lab and plate-reader calls; released code is a reduced implementation.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["amass", "nonlh"]}
+{"id": "covid-mastermix-omix", "title": "Development and validation of automated methods for COVID-19 PCR Master Mix preparation", "doi": "10.1016/j.slast.2024.100195", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11639134/", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by", "code_url": "https://github.com/Donald-OMIX/Liquid_Handler_Methods", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "PCR master mix preparation (diagnostic COVID-19)", "results_evidence": "Automated PCR master mix preparation matched manual pipetting accuracy in a diagnostic lab (Ct value comparisons, gravimetric checks).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Methods are proprietary binary .pkg/.dfx liquid-handler method packages (non-Python); useful as paper-only reference task.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_F2lqGDVrkmw72Y3hIXeAkI354m8"], "found_by": ["amass"]}
+{"id": "culturomics-colony-picking", "title": "High-throughput microbial culturomics using automation and machine learning (CAMII colony picker)", "doi": "10.1038/s41587-023-01674-2", "paper_url": "https://www.nature.com/articles/s41587-023-01674-2", "year": 2023, "venue": "Nature Biotechnology", "open_access_license": "CC BY", "code_url": "see paper code availability (not verified)", "code_files": ["colony imaging + morphology-guided picking code"], "code_license": "unverified", "language": "Python", "hardware": ["custom imaging + colony-picking robot"], "domain": "biology", "task_type": "imaging", "results_evidence": "Isolated >26,000 gut isolates with morphology-guided picking efficiency reported.", "wet_lab_validated": true, "simulatable": "partial: picking selection runs on images", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Code link not verified; strong colony-picking triple if code available.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "damplab-taqpath-ot2", "title": "Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex RT-PCR (BU DAMP Lab)", "doi": "10.17504/protocols.io.brhvm366", "paper_url": "https://doi.org/10.17504/protocols.io.brhvm366", "year": 2021, "venue": "protocols.io", "open_access_license": null, "code_url": "https://github.com/DAMPLAB/OT2-SARS-CoV2", "code_files": ["rna_extraction_magmax/rna_extraction_magmax.py", "qPCR_taqpath_multiplex/qPCR_taqpath_multiplex.py"], "code_license": "none", "stars": 2, "last_push": "2021-03-29", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "MagMAX RNA extraction + TaqPath RT-qPCR setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean apiv2 + simulation notebooks; protocols.io only; no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github", "web"]}
+{"id": "daxi-lightsheet", "title": "DaXi: high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy", "doi": "10.1038/s41592-022-01417-2", "paper_url": "https://www.nature.com/articles/s41592-022-01417-2", "year": 2022, "venue": "Nature Methods", "open_access_license": "CC BY", "code_url": "https://github.com/royerlab/daxi", "code_files": ["Micro-Manager beanshell (.bsh) acquisition scripts", "python control"], "code_license": "CC BY (repo)", "language": "Python/BeanShell", "hardware": ["custom light-sheet", "Micro-Manager"], "domain": "biology", "task_type": "imaging", "results_evidence": "Zebrafish/drosophila volumetric imaging reported.", "wet_lab_validated": true, "simulatable": "partial: Micro-Manager demo for scripts", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Small scripts; mostly hardware-specific.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "detectr-covid-ot2", "title": "Mammoth DETECTR COVID-19 assay on OT-2", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/tsdobbs/mammoth-COVID19-assay-OT2", "code_files": ["DETECTR_COVID-19_PART1.py", "DETECTR_COVID-19_PART2.py"], "code_license": "none", "stars": 1, "last_push": "2020-04-15", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CRISPR-Cas12 diagnostic (RNP prep + DETECTR reaction)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Implements a company white paper (Broughton et al. 2020 Nat Biotech is the DETECTR paper) but robot run not validated; no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "dtu-synbio-automation", "title": "DTU Synbio lab automation protocol collection", "doi": null, "paper_url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation", "code_files": ["protocols/opentrons/library_examples/*.py", "protocols/opentrons/Course_Introduction_to_automation/*.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "teaching/library protocols (agar plating, liquid-class optimisation, parameterised transfers)", "results_evidence": "No published results; teaching and internal-use repository.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT and clean enough to simulate, and useful as extra solution exemplars, but no paper so it is not a triple.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "duckbot-jubilee", "title": "The Duckbot: A system for automated imaging and manipulation of duckweed", "doi": "10.1371/journal.pone.0296717", "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0296717", "year": 2024, "venue": "PLOS ONE", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/machineagency/duckbot", "code_files": ["(Jupyter notebooks driving science_jubilee; no Opentrons .py)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "duckweed plate manipulation, media exchange, imaging", "results_evidence": "Automated growth assays measured duckweed area/growth across treatments.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the Jubilee/science_jubilee API is a third platform; valuable for platform breadth, needs a new runner.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "ecoli-protein-expr-purif-ot2", "title": "OT-2 assisted recombinant protein expression and purification in E. coli (Norton-Baker)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/nortonbakerbc/opentrons", "code_files": ["1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "2-Inoculation/Inoculation_platetoplate/Inoculation_1x96_to_4x24_OT2.py", "3-Lysis/Lysis_buffer_addition/Lysis_buffer_addition_OT2.py", "4-Transfer/Transfer_plate-to-plate/Transfer_plate-to-plate_4x24_to_1x96_OT2.py"], "code_license": "none", "stars": 0, "last_push": "2024-09-11", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein expression: transformation, inoculation, lysis, purification transfers", "results_evidence": "README says protocols are described in a paper (citation not resolved in README head); likely reports expression/purification yields.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Many apiv2 scripts with custom labware; paper citation needs manual resolution; no license.", "est_tasks": 4, "source_agent": "github", "found_by": ["github"]}
+{"id": "evogen-ot-library", "title": "EvoGenOT (UCPH EvoGenomics Opentrons protocol library)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/anttonalberdi/EvoGenOT", "code_files": ["Extractions/D-Rex/1_D-Rex_initial_v2.py", "Extractions/D-Rex/2_D-Rex_RNA_v2_part1.py", "Extractions/D-Rex/3_D-Rex_DNA_v2.py", "BEST_purification_14102020.py", "Library_Build/BEST/1_BEST_ER.v2.py"], "code_license": "none", "stars": 3, "last_push": "2023-03-10", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA/RNA co-extraction (D-Rex), BEST library build, bead purification", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Mixed v1/v2 scripts, no license; BEST library protocol is published (Car\u00f8e et al. 2018 MEE) but not linked from repo \u2014 would need tracing.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "evolver-ddr-elife", "title": "Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community (eVOLVER)", "doi": "10.7554/eLife.67175", "paper_url": "https://elifesciences.org/articles/67175", "year": 2021, "venue": "eLife", "open_access_license": "CC BY", "code_url": "https://github.com/khalillab/DDR-eVOLVER-model", "code_files": ["*.ipynb (model)", "DPU custom_script variants in SI (unverified)"], "code_license": "MIT", "language": "Python", "hardware": ["eVOLVER"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Fluctuating dilution regimes run on eVOLVER with community composition measured by sequencing.", "wet_lab_validated": true, "simulatable": "partial: eVOLVER custom_script logic replayable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Released repo is the model, not the eVOLVER control script; would need reconstructing the dilution program from methods.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "evotron-evolver-sampling", "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback", "doi": "10.1038/s41467-022-32392-z", "paper_url": "https://www.nature.com/articles/s41467-022-32392-z", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/santkumar/evotron", "code_files": ["ot2/protocol_code/main_protocol.py", "ot2/calibration/get_xyz_location.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated sampling from eVOLVER bioreactors into plates", "results_evidence": "Closed-loop optogenetic control held co-culture ratios at setpoints, measured by cytometry/OD from robot-sampled timepoints.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "CC BY paper and a real sampling protocol, but hardware-coupled (custom needle, eVOLVER) and unlicensed, so simulation needs labware stubs.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "github", "nonlh", "web"]}
+{"id": "exposomics-384-flex", "title": "Opentrons Flex 384-well protein-precipitation sample preparation for nontargeted exposomics", "doi": null, "paper_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols", "year": 2025, "venue": "repository only (associated manuscript not located)", "open_access_license": null, "code_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols", "code_files": ["protocols/step1_solvent_addition_and_sample_aliquoting.py", "protocols/step2_dilution_and_supernatant_transfer.py"], "code_license": "MIT", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "protein precipitation / dilution in 384-well format for LC-HRMS", "results_evidence": "README reports up to 288 biological samples plus QC per plate feeding multiple LC-HRMS assays, but no peer-reviewed results found.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT Flex protocols with custom labware (rare and valuable), but no paper located yet, so the paper->code triple is incomplete.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "fish-fluidics", "title": "An open source 16-channel fluidics system for automating sequential FISH-based imaging", "doi": "10.1016/j.ohx.2022.e00343", "paper_url": "https://www.sciencedirect.com/science/article/pii/S246806722200088X", "year": 2022, "venue": "HardwareX", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/dzhaojie/Fluidics-system-for-FISH", "code_files": ["fluidics control + imaging sync scripts"], "code_license": "unverified", "language": "Python", "hardware": ["valves", "pumps", "microscope"], "domain": "biology", "task_type": "imaging", "results_evidence": "seqFISH rounds automated with imaging results.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Fluidics overlaps LH; licence unverified.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "flex-genomics-di-omics", "title": "Opentrons Flex whole-genome / methylation / TIP-seq workflows (di-omics)", "doi": null, "paper_url": "https://github.com/di-omics/ot-flex-automation", "year": 2026, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/di-omics/ot-flex-automation", "code_files": ["protocols/whole_genome_seq_flex.py", "protocols/methylation_sequencing_flex.py", "protocols/tipseq_epigenome_flex.py", "bench/wgs_preparation_water_test_flex.py"], "code_license": "none", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "NGS library prep on Flex with off-deck handoffs", "results_evidence": "README tracks validation status per protocol but no publication.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Rich Flex protocol set with explicit validation status, but unlicensed and unpublished.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "har1eyk-starlet-protein-extraction", "title": "hamilton-starlet-scripts (PyLabRobot STARlet protein extraction / Orange G volume tests)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/har1eyk/hamilton-starlet-scripts", "code_files": ["Exp1021-Automated_Protein_Extraction/ape_96w_protocol.py", "Exp1021-Automated_Protein_Extraction/bpq_protocol.py"], "code_license": "none", "stars": 0, "last_push": "2026-07-03", "robot_platform": "hamilton", "api": "pylabrobot", "protocol_category": "protein extraction; volume QC (Orange G)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Genuine PLR STARlet protocols but no paper/results and no license.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "helao-async", "title": "HELAO-async: autonomous electrochemistry/high-throughput experimentation orchestration (Caltech/TRI)", "doi": "10.1039/d3dd00193h", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00193h", "year": 2023, "venue": "Digital Discovery (DOI unverified)", "open_access_license": "CC BY", "code_url": "https://github.com/High-Throughput-Experimentation/helao-async", "code_files": ["helao/deploy/hexagon/servers/action/ws_simulator.py", "helao/deploy/hexagon/servers/action/sim_db_server.py", "sequences/ & experiments/ libraries"], "code_license": "MIT", "language": "Python", "hardware": ["scanning droplet cell", "potentiostats", "PAL autosampler", "XY stages"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Used for autonomous electrocatalyst/OER composition screening with reported datasets.", "wet_lab_validated": true, "simulatable": "true: simulator action servers in repo", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "DOI not verified here; complex multi-server deployment; experiment/sequence functions are gradeable.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ht-hcr-sea-urchin", "title": "Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos", "doi": "10.1242/dev.204814", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12516323/", "year": 2025, "venue": "Development (Cambridge, England)", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/ylee-sio/HL_HTHCR", "code_files": ["HL_HTHCRv16.json"], "code_license": "none", "robot_platform": "flex", "api": "other", "protocol_category": "whole-mount in situ HCR on embryos in 96-well plates", "results_evidence": "Processed 192 probe sets in 32 h; produced localisation data for 101 genes across three developmental stages.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Protocol is an Opentrons Flex Protocol Designer JSON (schema v8), not Python; could be exported/converted; no license.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Wz78wSUCdhU6RWyec7626bqjRZZ"], "found_by": ["amass"]}
+{"id": "hydrogel-crosslink-ot2", "title": "Semi-autonomous synthesis and modelling of chemically cross-linked hydrogels (OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-", "code_files": ["Liquid Handler Script.py"], "code_license": "none", "stars": 0, "last_push": "2025-10-30", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "materials: hydrogel formulation synthesis", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single script; paper not located; no license.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "icfree-cfps", "title": "An AI-driven workflow for the accelerated optimization of cell-free protein synthesis", "doi": "10.1016/j.isci.2025.113599", "paper_url": "https://doi.org/10.1016/j.isci.2025.113599", "year": 2025, "venue": "iScience", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/brsynth/icfree-ml", "code_files": ["(no Opentrons protocol .py; generates Echo/liquid-handler instruction CSVs)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "cell-free reaction composition DoE and instruction generation", "results_evidence": "Iterative ML rounds improved cell-free protein yields measured on plate reader across generated compositions.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the output is an instruction CSV for an acoustic dispenser, so a task would need a translation layer rather than an Opentrons script.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "imperial-colony-picker", "title": "Automated colony picker add-on for the OT-2 (Imperial SSB MRes; cited by Slowpoke)", "doi": null, "paper_url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker", "year": 2022, "venue": "project report / cited in ACS Synth Biol 2026", "open_access_license": null, "code_url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker", "code_files": ["Client/colony_pcr_reagent_prep_protocol.py", "Client/colony_pcr_resuspension_protocol.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "colony PCR reagent prep and colony resuspension", "results_evidence": "Vision-guided colony picking demonstrated on OT-2; results reported only in the project write-up and via the Slowpoke citation.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Two clean OT-2 scripts closely related to the existing colony-PCR tasks, but no standalone peer-reviewed paper and no licence.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "imswitch", "title": "ImSwitch: generalizing microscope control in Python", "doi": "10.21105/joss.03394", "paper_url": "https://joss.theoj.org/papers/10.21105/joss.03394", "year": 2021, "venue": "JOSS", "open_access_license": "CC BY", "code_url": "https://github.com/ImSwitch/ImSwitch", "code_files": ["imswitch/imcontrol/", "imswitch/_data/user_defaults/imcontrol_setups/example_virtual_microscope.json"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["many microscope devices"], "domain": "biology", "task_type": "imaging", "results_evidence": "Software paper; underpins etSTED and UC2 experiments.", "wet_lab_validated": false, "simulatable": "true: virtual microscope setup", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Software paper; results via downstream papers.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ipsc-robot-pyhamilton", "title": "Automated hiPSC culture and sample preparation for 3D live cell microscopy", "doi": "10.1101/2020.12.18.423371", "paper_url": "https://doi.org/10.1101/2020.12.18.423371", "year": 2020, "venue": "bioRxiv", "open_access_license": "publisher TDM/other: https://www.biorxiv.org/about/FAQ#license", "code_url": "https://github.com/stefangolas/iPSC-Robot", "code_files": ["Feed.py", "96w_Seed.py", "96w_Scan.py", "ipsc_utils.py"], "code_license": "none", "stars": 1, "last_push": "2022-12-16", "robot_platform": "hamilton", "api": "other", "protocol_category": "iPSC culture: media exchange, seeding, imaging scan", "results_evidence": "Code implements Allen Institute iPSC culture protocols (bioRxiv 2020.12.18.423371); robot-specific results not in repo.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyHamilton by PLR co-author S. Golas; linked preprint is the source protocol, not a validation of this code; no license; Celigo integration.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "krisp-sars2-pooling", "title": "Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing", "doi": "10.1038/s41598-021-96934-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8423848/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/krisp-kwazulu-natal/efficient-SARS-CoV-2-pooled-testing-strategy-code", "code_files": ["scripts/pooling27_300pip.py", "scripts/pooling27_50pip.py", "scripts/pooling81_50pip.py", "scripts/pooling81_300pip.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "SARS-CoV-2 hypercube sample pooling", "results_evidence": "Infected samples reliably detected in pools of 27 and 81 with minimal sensitivity loss for individual Ct up to 32.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "4 pooling scripts use the deprecated Opentrons v1 API (from opentrons import robot); would need porting to v2; MIT.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Kt4JG1AeKTTljzD16AIh1saLcLf"], "found_by": ["amass", "github"]}
+{"id": "labdroid-cell-culture", "title": "Robotic search for optimal cell culture in regenerative medicine (LabDroid Maholo, iPSC-RPE)", "doi": "10.7554/eLife.77007", "paper_url": "https://elifesciences.org/articles/77007", "year": 2022, "venue": "eLife", "open_access_license": "CC BY", "code_url": "https://github.com/labauto/LabDroid_optimizer", "code_files": ["src/ (GPyOpt-based BO driver)", "parameter csvs"], "code_license": "none", "language": "Python", "hardware": ["LabDroid Maholo dual-arm robot", "incubator", "microscope"], "domain": "biology", "task_type": "other", "results_evidence": "BO over 7 culture parameters improved iPSC-RPE differentiation scores (pigmentation) in 111 days.", "wet_lab_validated": true, "simulatable": "partial: optimizer only; robot protocols proprietary (Maholo)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; robot program not released.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "labscriptai-protein-eng", "title": "Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows", "doi": "10.1101/2025.09.30.679666", "paper_url": "https://www.biorxiv.org/content/10.1101/2025.09.30.679666v1.full", "year": 2025, "venue": "bioRxiv", "open_access_license": "cc-by-nc-nd/4.0", "code_url": "https://github.com/KRATSZ/LabScript-AI", "code_files": ["labscriptai/planir/plr_sim.py", "labscriptai/webdemo/python/compile_hamilton.py", "labscriptai/plugins/mcp/opentrons-mcp/examples/flex_noop_protocol.py"], "code_license": "none", "stars": 131, "last_push": "2026-10-10", "robot_platform": "other", "api": "pylabrobot", "protocol_category": "LLM protocol generation; cell-free GFP variant characterisation; enzyme screening; fluorescence calibration", "results_evidence": "Fluorescence standard curves CV<5%, R2>0.999; 318 GFP variants characterised (best 5.0x avGFP); enzyme double mutants >3x catalytic efficiency.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Repo is an LLM agent/tooling, not the executed protocol scripts; no license; experiments span OT-2, Flex, Hamilton Vantage, Tecan Fluent; executed scripts would need extraction. Also a competitor system to Text2WetLab (useful as related work).", "est_tasks": 2, "source_agent": "github", "also_code": ["https://github.com/KRATSZ/labscriptai-ot (curated OT protocol library)"], "found_by": ["github"]}
+{"id": "llm-rdf-synthesis", "title": "An automatic end-to-end chemical synthesis development platform powered by large language models", "doi": "10.1038/s41467-024-54457-x", "paper_url": "https://www.nature.com/articles/s41467-024-54457-x", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/Ruan-Yixiang/LLM-RDF", "code_files": ["Backend Files/backend/input_screen.py"], "code_license": "MIT (per README badge)", "robot_platform": "other", "api": "other", "protocol_category": "LLM-driven reaction development and robotic execution", "results_evidence": "End-to-end synthesis campaigns executed with reported yields and optimised conditions.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Strong paper+code pairing but the robot layer is not Opentrons/PLR, so it is more a comparison system than a task source.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["nonlh", "web"]}
+{"id": "locost-covid-nanopore-ot2", "title": "Opentrons_LoCost_Covid19 (ARTIC LoCost nanopore library prep on OT-2)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/JDMirza/Opentrons_LoCost_Covid19", "code_files": ["1_dilution_pool_per_plate.py", "2_endrepair.py", "3_barcoding.py", "4_pooling_96_samples.py"], "code_license": "none", "stars": 0, "last_push": "2022-01-13", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 nanopore library prep (dilution, end-repair, barcode ligation, pooling)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Automates Quick 2019 LoCost protocol (protocols.io); no own paper, no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "madsci-ad-sdl", "title": "MADSci: A modular Python-based framework to enable autonomous science", "doi": "10.21105/joss.09416", "paper_url": "https://doi.org/10.21105/joss.09416", "year": 2026, "venue": "Journal of Open Source Software", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/AD-SDL/MADSci", "code_files": ["examples/example_experiment.py", "examples/example_lab/compose.yaml", "examples/example_lab/example_modules/liquidhandler.py"], "code_license": "MIT", "language": "Python", "hardware": ["Brooks PF400", "OT-2/Flex", "plate readers", "sealers", "thermocyclers"], "domain": "other", "task_type": "scheduling", "results_evidence": "Framework; experiments reported via ANL RPL deployments but no single peer-reviewed results paper verified.", "wet_lab_validated": false, "simulatable": "true: example_lab ships virtual example modules via docker compose", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "JOSS software paper (no wet-lab results paper of its own); simulatable example lab makes it a good execution substrate for WEI/RPL-derived tasks.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "memplex-printing", "title": "Designer artificial environments for membrane protein synthesis", "doi": "10.1038/s41467-025-59471-1", "paper_url": "https://www.nature.com/articles/s41467-025-59471-1", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/ccmeyer/printing-platform", "code_files": ["Scripts/control_platform.py", "Scripts/Dobot/DobotControl.py", "Scripts/Precigenome/PGMFC/control_c.py"], "code_license": "MIT", "language": "Python", "hardware": ["Dobot arm", "piezo droplet printer", "pressure controller", "plate reader"], "domain": "biology", "task_type": "other", "results_evidence": "Thousands of cell-free membrane-protein reactions printed and measured; formulations identified.", "wet_lab_validated": true, "simulatable": "partial: Dobot/pressure DLL calls need stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Nanolitre droplet printing = liquid dispensing (overlap); arm control is non-LH.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "metclo-ot2", "title": "MetCloOT2: Automated MetClo assembly on Opentrons OT-2 (MSc project, based on Lin & O Callaghan 2018/2020)", "doi": "10.1007/978-1-0716-0908-8_9", "paper_url": "https://doi.org/10.1007/978-1-0716-0908-8_9", "year": 2020, "venue": "Methods in Molecular Biology (method chapter); OT-2 code is MSc project", "open_access_license": null, "code_url": "https://github.com/Edinburgh-Genome-Foundry/OT2Metclo", "code_files": ["ot2metclo.py"], "code_license": "none", "stars": 2, "last_push": "2022-08-16", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA assembly (MetClo methylation-based Golden Gate)", "results_evidence": "Underlying MetClo method papers (NAR 2018; Methods Mol Biol 2020) report manual assembly results; OT-2 implementation is an MSc project without published validation.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No license; method paper NAR 2018 is OA but the robot code is not validated in it.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "mobile-robots-dai-2024", "title": "Autonomous mobile robots for exploratory synthetic chemistry", "doi": "10.1038/s41586-024-08173-7", "paper_url": "https://www.nature.com/articles/s41586-024-08173-7", "year": 2024, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.11174257", "code_files": ["Zenodo: workflow + decision-maker code, Chemspeed scripts, robot ROS code (several records)"], "code_license": "Zenodo (check per record)", "language": "Python", "hardware": ["KUKA KMR iiwa mobile robots", "Chemspeed ISynth", "UPLC-MS", "benchtop NMR"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "Supramolecular/structural diversification chemistry run autonomously with UPLC-MS/NMR-based decisions; hits reported.", "wet_lab_validated": true, "simulatable": "partial: decision-maker runs on released data; robot/ROS code needs hardware or Gazebo stub", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Strong triple; Zenodo code bundle sizeable; grading via decision logic or workflow script structure.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "myra-cfe-platform", "title": "A liquid handling platform for standardized quantification of cell-free enzymatic activity", "doi": "10.1093/synbio/ysag010", "paper_url": "https://academic.oup.com/synbio/article/doi/10.1093/synbio/ysag010", "year": 2026, "venue": "Synthetic Biology (OUP)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Mo42-mb/Myra_automation", "code_files": ["(R script generates python for BMS Myra; no Opentrons protocol)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "cell-free enzymatic activity assay setup", "results_evidence": "Standardised enzymatic activity quantification reproducible across operators/platforms reported in the paper.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "CC BY paper with generated-protocol code for a BMS Myra; useful for cross-platform generalisation tasks but not directly simulatable.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "myrplate-flex-casting", "title": "myrPlate engineered connective tissue casting on Opentrons Flex", "doi": null, "paper_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15", "code_files": ["myrPlate_tissue_casting_8Ch1ml_Fast_V15-ECTsFinal.py", "myrPlate-V15(aspiration).py", "myrPlate-V15(dispensing).py"], "code_license": "MIT", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "collagen/cell suspension casting into 48-well tissue plates", "results_evidence": "README describes casting engineered connective tissues; no publication located.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT Flex scripts with viscous cell-laden gel handling (valuable hard task) but no paper yet.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "nioz-ot2-database", "title": "MolLabNIOZ/OT2 protocol database (NIOZ molecular ecology)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/MolLabNIOZ/OT2", "code_files": ["Protocol_database/EVE/Qubit/Qubit_v1.py", "Protocol_database/EVE/Adding_sample_to_barcoded_PCR-plate/Adding_sample_to_barcoded_PCR-plate_V3.py"], "code_license": "none", "stars": 2, "last_push": "2026-06-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "amplicon PCR setup, Qubit quantification, dilution, pooling", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Large (222 .py) lab library, no paper, no license.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "olh-turbidostat-plr", "title": "A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments", "doi": "10.64898/2026.03.02.709168", "paper_url": "https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full", "year": 2026, "venue": "bioRxiv", "open_access_license": "publisher TDM/other: https://www.biorxiv.org/about/FAQ#license", "code_url": "https://github.com/chory-lab/plr-turbidostat", "code_files": ["turbidostat.py", "simple_transfer.py", "tests/test_dilute_200ul.py", "tests/test_dilute_single_column.py", "tests/calibration.py"], "code_license": "none", "stars": 2, "last_push": "2026-05-07", "robot_platform": "pylabrobot", "api": "pylabrobot", "protocol_category": "turbidostat / continuous culture; pipetting accuracy calibration", "results_evidence": "OLH pipetting MAE 4.1 vs 7.2 uL manual (p<0.005); closed-loop turbidostat held ~200 cultures at OD setpoints.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyLabRobot code for a custom open liquid handler (OLH) + Byonoy reader; no license on turbidostat repo; full build package promised on publication; simulation needs custom backend.", "est_tasks": 4, "source_agent": "github", "also_code": ["https://github.com/chory-lab/olh-pylabrobot (MIT PLR fork with OLH backend)"], "found_by": ["github"]}
+{"id": "openblend-media", "title": "Modular development enables rapid design of media for alternative hosts", "doi": "10.1002/bit.27947", "paper_url": "https://doi.org/10.1002/bit.27947", "year": 2022, "venue": "Biotechnology and Bioengineering", "open_access_license": "unclear (likely subscription)", "code_url": "https://github.com/abiedermann/openblend_public", "code_files": ["run_plate_prep.py", "openblend_plates.py", "plate_builder.py", "cal_protocol.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "combinatorial media blending into microplates", "results_evidence": "Blended media designs were tested in growth experiments for alternative microbial hosts, with growth rates reported per formulation.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "MIT code with a calibration protocol and plate-prep generator, but the paper text is probably not open, and the protocol is generated from an Excel template.", "est_tasks": 3, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "openframe-openaf", "title": "openFrame: modular open microscopy platform with single-shot optical autofocus", "doi": "10.1111/jmi.13219", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13219", "year": 2023, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://github.com/ImperialCollegeLondon/openAF", "code_files": ["Java Micro-Manager plugin + Python scripts"], "code_license": "BSD", "language": "Java/Python", "hardware": ["openFrame microscope", "autofocus module"], "domain": "biology", "task_type": "imaging", "results_evidence": "Autofocus accuracy/stability characterised and used in HCA imaging.", "wet_lab_validated": true, "simulatable": "partial: Micro-Manager demo for plugin shell only", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Autofocus algorithm checkable on images; Java plugin.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "opentrons-covid19-dev", "title": "Opentrons/covid19 (OT-2 COVID-19 RT-qPCR station development repo, Opentrons + Open Medicine Institute)", "doi": null, "paper_url": "https://www.protocols.io/groups/opentrons-covid19-testing/publications", "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Opentrons/covid19", "code_files": ["experiments/20200324-lod-study-1/station-C-qpcr-map.py", "experiments/20200319-end-to-end-qpcr-1/station-C-qpcr-map.py"], "code_license": "Apache-2.0", "stars": 12, "last_push": "2020-06-07", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 RNA extraction + RT-qPCR setup stations A/B/C", "results_evidence": "Experiment folders contain LOD/contamination study notes; formal results only on protocols.io, no peer-reviewed paper.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Apache-2.0, many dated experiment scripts; no paper; overlaps covid19clinic/hulp-rna-extraction topics.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "organa", "title": "ORGANA: a robotic assistant for automated chemistry experimentation and characterization", "doi": "10.1016/j.matt.2024.10.015", "paper_url": "https://arxiv.org/abs/2401.06949", "year": 2025, "venue": "Matter (arXiv 2401.06949)", "open_access_license": "arXiv non-exclusive / journal TBD", "code_url": "https://github.com/ac-rad/organa", "code_files": ["clairify/xdlgenerator/nlp2xdl.py", "moveit_pddlstream/xdl_parse.py", "output/plan_*.xdl"], "code_license": "none", "language": "Python", "hardware": ["Franka Panda", "pH meter", "electrochemistry potentiostat", "camera", "Isaac Sim digital twin"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Solubility, pH, recrystallisation and electrochemistry (quinone) experiments executed with reported user-study times and measured values.", "wet_lab_validated": true, "simulatable": "partial: XDL plans + PDDLStream/MoveIt planning simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence on repo; XDL plans gradeable, robot layer needs ROS/MoveIt.", "est_tasks": 4, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ot2-cherrypick", "title": "OT2-CherryPick: A Zero-Install Web Platform for Orchestrating Complex Liquid Handling on the Opentrons OT-2", "doi": "10.26434/chemrxiv.15000637", "paper_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15000637/v1", "year": 2026, "venue": "ChemRxiv", "open_access_license": "unknown (ChemRxiv; check)", "code_url": "https://github.com/HiteSit/OT2_CherryPick", "code_files": ["CherryPick_OT2.py"], "code_license": "GPL-3.0", "stars": 2, "last_push": "2026-06-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CSV-driven cherry-picking / liquid transfer generator", "results_evidence": "ChemRxiv preprint describing a GUI/CSV cherry-picking platform; validation is mainly simulation/operational, check for gravimetric data.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "GPL-3.0 protocol generator rather than a fixed experiment; results evidence unclear.", "est_tasks": 1, "source_agent": "github", "crossref_error": "HTTP Error 404: Not Found", "found_by": ["github"]}
+{"id": "ot2-moclo-jove", "title": "Modular Cloning with the OT2 (OT2_MoClo_JoVE)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/emernic/OT2_MoClo_JoVE", "code_files": ["ot2_moclo_jove/moclo_transform/data/moclo_transform_template.py", "ot2_moclo_jove/colony_picking/data/colony_pick_template.py", "ot2_moclo_jove/miniprep/data/miniprep_template.py"], "code_license": "MIT", "stars": 7, "last_push": "2019-05-07", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "MoClo Golden Gate, heat-shock transformation, plating, colony picking, bead miniprep", "results_evidence": "Repo targets a JoVE article (not resolved in Crossref); JoVE articles typically include representative results.", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT but legacy APIv1 templates; JoVE likely paywalled; overlaps apex/slowpoke/assemblytron tasks.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "ot2-proteomics-thesis", "title": "Automated Versus Manual Proteomics Sample Preparation: A Comparative Evaluation of Liquid Handling Workflows (MSc thesis)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/martineingolfsrud/Opentrons-OT-2-performance-assessment", "code_files": ["BCA/bca_multichannel.py", "BCA/bca_singlechannel_v2.py", "SP3/sp3_multi.py", "SP3/sp3_version7_1.py"], "code_license": "none", "stars": 0, "last_push": "2026-06-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics: BCA assay + SP3 digestion", "results_evidence": "Thesis raw data in repo comparing OT-2 vs human BCA/SP3 performance; not peer reviewed.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Thesis (no DOI), no license; good raw data though.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "ot2-yeast-spot-assay", "title": "Automation of yeast spot assays using an affordable liquid handling robot", "doi": "10.1016/j.slast.2022.12.001", "paper_url": "https://doi.org/10.1016/j.slast.2022.12.001", "year": 2022, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": "https://github.com/bioinfo-tsukuba/ot2_spot_assay", "code_files": ["ot2_execute/compiler/compile_after_plate_reader_for_paper.py", "ot2_execute/compiler/compile_predispense.py", "ot2_execute/compiler/compile_after_plate_reader.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "yeast serial dilution spot assay on agar (3D-printed Petri mount, z-adjust)", "results_evidence": "Automated spot assays of budding yeast reproduced manual growth phenotypes, imaged with a flatbed scanner (spot intensity quantified).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Compiler scripts generate OT-2 apiLevel protocols from plate-reader data; needs custom Petri-dish labware definition; no license.", "est_tasks": 3, "source_agent": "amass", "amass_ids": ["AMBC_Z44qoWuOtzrQkgx2l6lRuw0NcNX"], "found_by": ["amass", "web"]}
+{"id": "pac832-galr1-ot2", "title": "PAC-832: A selective small-molecule antagonist of galanin receptor 1 (GalR1) - supplementary data and OT-2 protocols", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/douglasyao/pac-832-supplementary-data", "code_files": ["ot2_protocols/ach_assay/GalR1-SY5Y_PAC-832_only_ACh_part1.py", "ot2_protocols/ach_assay/GalR1-SY5Y_PAC-832_plus_galanin_ACh_plate1.py", "ot2_protocols/ach_assay/PTX_controls_ACh.py"], "code_license": "none", "stars": 1, "last_push": "2026-04-07", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-based GPCR pharmacology assays (cAMP, acetylcholine release) dose-response plating", "results_evidence": "Repo includes raw and processed cAMP/ACh assay data for PAC-832 vs galanin; paper DOI not yet resolved (likely preprint).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Many apiv2 scripts + raw data, but no license and paper not located; strong candidate once paper DOI found.", "est_tasks": 4, "source_agent": "github", "found_by": ["github"]}
+{"id": "parseq-pyhamilton", "title": "parSEQ:  Probe and Rescue Sequencing for Advanced Variant Retrieval from DNA Pool", "doi": "10.1101/2023.12.12.571337", "paper_url": "https://doi.org/10.1101/2023.12.12.571337", "year": 2023, "venue": "bioRxiv", "open_access_license": "unknown", "code_url": "https://github.com/finyl/parseq-pyhamilton", "code_files": ["parseqpyhamilton/methods/bpcr.py", "parseqpyhamilton/methods/cherry_picking.py", "parseqpyhamilton/methods/lib_illumina.py", "parseqpyhamilton/methods/lib_nanopore.py", "parseqpyhamilton/methods/plate_filling.py"], "code_license": "none", "stars": 2, "last_push": "2023-12-13", "robot_platform": "hamilton", "api": "other", "protocol_category": "variant library sequencing pipeline: barcoding PCR, cherry picking, Illumina/nanopore library prep", "results_evidence": "bioRxiv 2023 parSEQ preprint reports retrieval of sequence-verified variants from pooled DNA libraries using the Hamilton pipeline.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "PyHamilton (not PLR) code needs Hamilton VENUS; no license; could be ported to PLR STAR simulator with work.", "est_tasks": 3, "source_agent": "github", "found_by": ["github"]}
+{"id": "pasta-spatial", "title": "PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology", "doi": "10.1038/s41592-026-03200-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13539481/", "year": 2026, "venue": "Nature methods", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/SizunJiangLab/PASTA", "code_files": ["automation/PASTA_oligoHRP_automation.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "spatial proteomics staining (tyramide-oligo amplification cycles on slides)", "results_evidence": "High-plex protein and RNA codetection on FFPE tissue via cyclical tyramide-oligonucleotide amplification and imaging (Nature Methods figures).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single OT-2 apiLevel 2.7 script for oligo-HRP staining cycles; no LICENSE; custom slide labware likely needed.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_8AMU8xpBC4bYAOyoUy4ljNomnML"], "found_by": ["amass", "github"]}
+{"id": "peg-solubility-assay", "title": "An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement", "doi": "10.1038/s41598-021-01126-4", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8578320/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://gitlab.developers.cam.ac.uk/ch/sormanni/peg-solubility-assay", "code_files": ["PEG_Assay_Step1.py", "PEG_Assay_Step2.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein solubility assay (PEG titration, plate prep and transfer)", "results_evidence": "Relative solubility of proteins/antibodies quantified from PEG-precipitation midpoints using ~200 ug material; accuracy compared against established methods.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Two OT-2 API v2 scripts (step1 PEG gradient setup, step2 transfer after centrifugation) with clear paper protocol; no LICENSE; may need aluminium-block labware definitions.", "est_tasks": 4, "source_agent": "amass", "amass_ids": ["AMBC_J9kXwo9tekw77p29y6R0RRYa3n"], "found_by": ["amass"]}
+{"id": "phage-cocktails-robotics", "title": "High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails", "doi": "10.1038/s41467-026-68684-x", "paper_url": "https://www.nature.com/articles/s41467-026-68684-x", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.17594564", "code_files": ["Zenodo: robot scripts + CV pipeline"], "code_license": "check Zenodo", "language": "Python", "hardware": ["robotic arm", "plate reader", "imaging"], "domain": "biology", "task_type": "imaging", "results_evidence": "Phage cocktails designed and validated with plaque/plate-reader data.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Zenodo contents unverified.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "photobioreactor-fluorescence", "title": "Integration of Fluorescence Spectroscopy into a Photobioreactor for the Monitoring of Cyanobacteria", "doi": "10.3390/bios15030128", "paper_url": "https://www.mdpi.com/2079-6374/15/3/128", "year": 2025, "venue": "Biosensors", "open_access_license": "CC BY", "code_url": "https://github.com/borjaggarcia/fluorescence-monitoring", "code_files": ["(not probed)"], "code_license": "unverified", "language": "Python", "hardware": ["Pioreactor-based photobioreactor", "spectrometer"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Cyanobacterial growth monitored by fluorescence with reported correlation to OD.", "wet_lab_validated": true, "simulatable": "partial: Pioreactor plugin runs in testing mode", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Small repo; licence unverified.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "pioreactor", "title": "Pioreactor open-source bioreactor software (used in published studies)", "doi": null, "paper_url": "https://docs.pioreactor.com", "year": 2025, "venue": "software (no primary paper; cited in e.g. Microb Cell Fact 2025, Nature 2026)", "open_access_license": null, "code_url": "https://github.com/pioreactor/pioreactor", "code_files": ["core/pioreactor/automations/dosing/turbidostat.py", "core/pioreactor/actions/leader/experiment_profile.py", "experiment profile YAMLs"], "code_license": "MIT", "language": "Python", "hardware": ["Pioreactor 20/40 mL bioreactor (Raspberry Pi)"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "No first-party results paper; third-party papers (e.g., 10.1186/s12934-025-02670-8) use it for culture experiments.", "wet_lab_validated": false, "simulatable": "true: built-in testing/fake hardware mode (TESTING env var) runs automations without hardware", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Highly simulatable experiment-profile YAMLs, but no paper with its own released profile + results; could pair with a citing paper's methods.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "polar-sarscov2-ot2", "title": "POLAR: Pathogen-Oriented Low-cost Assembly & Re-sequencing SARS-CoV-2 (OT-2 automation)", "doi": "10.17504/protocols.io.bearjad6", "paper_url": "https://doi.org/10.17504/protocols.io.bearjad6", "year": 2020, "venue": "protocols.io", "open_access_license": null, "code_url": "https://github.com/Zanecrc1/POLAR-SARS-CoV-2-Automation-for-OT-2", "code_files": ["Protocols/POLAR/POLAR_48_Samples.py", "Protocols/Zymo extraction/Zymo_extraction_48_sample_V1i.py"], "code_license": "MIT", "stars": 2, "last_push": "2020-08-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viral RNA magbead extraction + SARS-CoV-2 amplicon library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT apiv2 scripts but only protocols.io, no paper with automation results; overlaps existing magbead extraction papers.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "polybot-pedot", "title": "Autonomous platform for solution processing of electronic polymers (Polybot)", "doi": "10.1038/s41467-024-55655-3", "paper_url": "https://www.nature.com/articles/s41467-024-55655-3", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/polybot-nexus/PEDOT_PSS_supporting_data", "code_files": ["*.ipynb (analysis only)"], "code_license": "MIT", "language": "Python", "hardware": ["Chemspeed", "UR5e", "N9 robot", "film coater", "annealing", "probe station", "camera"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Autonomously optimised PEDOT:PSS film conductivity/defects over closed-loop campaigns; conductivities reported.", "wet_lab_validated": true, "simulatable": "false: only analysis notebooks released; orchestration code not public", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Results + data public but robot orchestration (Polybot/WEI) not released for this paper.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "polymerization-planner", "title": "Automation-Assisted Photoinduced Atom Transfer Radical Polymerization", "doi": "10.1021/acspolymersau.5c00067", "paper_url": "https://doi.org/10.1021/acspolymersau.5c00067", "year": 2026, "venue": "ACS Polymers Au", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/GormleyLab/polymerization_planner", "code_files": ["polymerization_planner/runner.py", "polymerization_planner/atrp/calculator.py", "polymerization_planner/pet_raft/calculator.py"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "polymerisation recipe planning for automated dispensing", "results_evidence": "Polymerisations run from planner recipes characterised by GPC (conversion, dispersity).", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the package only computes recipes; the dispensing layer (custom handler) is separate.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "pozzo-ot2-doe", "title": "Pozzo group OT-2 design-of-experiments protocols", "doi": null, "paper_url": "https://github.com/pozzo-research-group/OT2Protocols", "year": 2021, "venue": "repository only (group has related SDL papers)", "open_access_license": null, "code_url": "https://github.com/pozzo-research-group/OT2Protocols", "code_files": ["ot2protocol/app_protocols/DES_combined_protocol.py", "PlanPrepareProcess_OT2/Modules/OT2Commands.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "formulation DoE sample preparation", "results_evidence": "Results appear in separate group publications, not this repo.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT and simulatable, but the paper pairing must be established before it is a triple.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "prism-protocol-gen", "title": "PRISM: Protocol Refinement through Intelligent Simulation Modeling", "doi": "10.1039/d6dd00004e", "paper_url": "https://doi.org/10.1039/d6dd00004e", "year": 2026, "venue": "Digital Discovery", "open_access_license": "cc-by-nc/3.0", "code_url": "https://github.com/ramanathanlab/PRISM", "code_files": ["ProtocolGenerator/Code/projects/prism/pcr_master_mix_and_sample_prep.py"], "code_license": "MIT", "stars": 5, "last_push": "2026-04-26", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "LLM protocol generation + simulation validation; PCR master mix/sample prep", "results_evidence": "Digital Discovery 2026: LLM-generated, simulation-refined protocols executed on OT-2 (PCR prep).", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Competitor/related-work system (LLM->robot protocols); one concrete generated PCR protocol; MIT.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "pudu-synbio-ot2", "title": "PUDU (Protocol Unified Design Unit) - OT-2 synthetic biology workflows", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/RudgeLab/PUDU", "code_files": ["scripts/automated_ot2/Automated_Golden_Gate.py", "scripts/automated_ot2/run_Loop_assembly.py", "scripts/automated_ot2/run_Bacterial_Transformation.py", "scripts/automated_ot2/run_Plating.py", "scripts/automated_ot2/run_iGEM_gfp_od.py", "scripts/automated_ot2/run_iGEM_rgb_od.py"], "code_license": "MIT", "stars": 6, "last_push": "2026-07-14", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate / Loop assembly, transformation, plating, iGEM GFP/OD calibration", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, many apiv2 scripts (Rudge/Myers labs); no linked paper with results found in README.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "pvlab-solubility-dropcast-ot2", "title": "PV-Lab Robotic_Liquid_Handling (MIT AMLS OT-2 solubility testing / drop casting)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/PV-Lab/Robotic_Liquid_Handling", "code_files": ["drop_casting.py", "DRY_VERSION_solubility_testing.py", "Opentrons_Unit_Tests/test_96_gradient.py"], "code_license": "MIT", "stars": 2, "last_push": "2025-05-21", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "materials: solubility testing, thin-film drop casting", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, UROP code; no paper linked.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "pysted", "title": "Development of AI-assisted microscopy frameworks through realistic simulation with pySTED", "doi": "10.1038/s42256-024-00903-w", "paper_url": "https://www.nature.com/articles/s42256-024-00903-w", "year": 2024, "venue": "Nature Machine Intelligence", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/FLClab/pySTED", "code_files": ["pysted/base.py", "(gym-sted) gym_sted/envs/"], "code_license": "CC (Attribution, check NC)", "language": "Python", "hardware": ["STED microscope (real validation)", "simulator"], "domain": "biology", "task_type": "imaging", "results_evidence": "RL policies trained in simulation were deployed on a real STED microscope with image quality reported.", "wet_lab_validated": true, "simulatable": "true: the code is a simulator (gym environment)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Simulator itself rather than lab-automation code; good as a grader for imaging-parameter tasks; NC licences.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "raft-polymerization-platform", "title": "A fully automated platform for photoinitiated RAFT polymerization", "doi": "10.1039/d2dd00100d", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d2dd00100d", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.7379060", "code_files": ["Zenodo: Chemspeed/robot scripts + data"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Chemspeed SWING", "UV photoreactor", "GPC/NMR"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Automated photo-RAFT polymerisations with Mn/\u0110 characterisation reported.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Zenodo contents unverified.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "reacsight", "title": "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight", "doi": "10.1038/s41467-022-31033-9", "paper_url": "https://www.nature.com/articles/s41467-022-31033-9", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.4776009", "code_files": ["Zenodo: ReacSight orchestration (Flask instrument servers, OT-2 sampling, cytometer driving)"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Chi.Bio/eVOLVER bioreactors", "Opentrons OT-2 (sampling robot)", "Guava flow cytometer"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Automated cytometry-based optogenetic control of yeast populations and co-cultures with reported dynamics.", "wet_lab_validated": true, "simulatable": "partial: instrument servers are HTTP; mockable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Combines bioreactor + cytometer scheduling; partial LH overlap (OT-2 sampler).", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["amass", "nonlh"]}
+{"id": "retro-10x-ot2", "title": "OT-2 10x scRNA-seq library prep (Retro Biosciences)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/retrobiosciences/opentrons-10x", "code_files": ["multi_8sample.py"], "code_license": "none", "stars": 13, "last_push": "2023-03-25", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "10x Genomics single-cell library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper/license; README warns protocol is hard to get working; custom hardware.", "est_tasks": 1, "source_agent": "github", "found_by": ["github", "web"]}
+{"id": "robochem", "title": "Automated self-optimization, intensification, and scale-up of photocatalysis in flow (RoboChem)", "doi": "10.1126/science.adj1817", "paper_url": "https://www.science.org/doi/10.1126/science.adj1817", "year": 2024, "venue": "Science", "open_access_license": "paywalled (UvA repository copy)", "code_url": "https://github.com/Noel-Research-Group/Robochem_v1.0", "code_files": ["ML_GUI/run_optimization.py", "ML_GUI/Dragonfly_BO.py", "Platform_/Eagle_Reactor/Eagle_control.py", "Platform_/Liquid_Handler/GX_241_Liquid_Handler.py"], "code_license": "MIT", "language": "Python", "hardware": ["Gilson GX-241 liquid handler", "Vapourtec/Eagle flow photoreactor", "benchtop NMR", "pumps"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "19 photocatalytic transformations self-optimised; yields often exceeded literature.", "wet_lab_validated": true, "simulatable": "partial: BO loop runnable; instrument classes need serial stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Paper paywalled; code MIT; flow chemistry rig with no built-in mocks.", "est_tasks": 3, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "roborna-nirvana", "title": "An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing", "doi": "10.1038/s41598-023-47190-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10663496/", "year": 2023, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/strubelab/roboRNA", "code_files": ["EvoScripts/roboRNA_everything.exd"], "code_license": "none", "robot_platform": "tecan", "api": "other", "protocol_category": "SARS-CoV-2 magnetic-bead RNA extraction + RT-qPCR + nanopore variant sequencing", "results_evidence": "Automated extraction showed high reproducibility with no cross-contamination; limit of detection, sensitivity and specificity comparable to commercial assays; NIRVANA identified circulating variants.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Tecan Freedom EVOware .exd scripts (non-Python) with deck images and protocol summary; no license; good paper-only task for porting to OT-2/PLR.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_Vnwuovs621rAfxFbZZ7xtkq9lKj"], "found_by": ["amass"]}
+{"id": "robotic-titration-cv-ot2", "title": "High-throughput robotic colourimetric titrations using computer vision", "doi": "10.1039/d4dd00334a", "paper_url": "https://doi.org/10.1039/d4dd00334a", "year": 2025, "venue": "Digital Discovery", "open_access_license": "cc-by/3.0", "code_url": "https://github.com/yuanlee0325/HTE-robotic-titration-using-computer-vision", "code_files": ["folder4ot2/utils/titration_general.py"], "code_license": "MIT", "stars": 2, "last_push": "2025-03-31", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "chemistry: colourimetric acid-base titration with webcam endpoint detection", "results_evidence": "Digital Discovery paper reports titration accuracy vs manual/reference concentrations using OT-2 + webcam colour analysis.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, open RSC paper, but protocol is driven with camera loop/HTTP; needs refactor for opentrons_simulate.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "rtwizard-antigen-ot2", "title": "rtWIZARD: OT-2 running 42 rapid antigen tests in parallel", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/BenHinnant/rtWIZARD", "code_files": ["final_labware_position_checks/run_labware_position_check_p300_ingezim_asf_crom_ag.py"], "code_license": "none", "stars": 0, "last_push": "2024-10-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "lateral-flow rapid antigen test loading (ASF, PPA)", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No paper located, no license, custom LFA holder labware.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "sample-protein-sdl", "title": "Self-driving laboratories to autonomously navigate the protein fitness landscape (SAMPLE)", "doi": "10.1038/s44286-023-00002-4", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926838/", "year": 2024, "venue": "Nature Chemical Engineering", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.10048592", "code_files": ["Zenodo: agent code + Strateos protocols/data"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Strateos cloud lab (Golden Gate, PCR, cell-free expression, thermostability assays on plate readers/thermocyclers)"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Four agents converged on glycoside hydrolases >12 C more thermostable.", "wet_lab_validated": true, "simulatable": "partial: Autoprotocol JSON generation offline", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Cloud-lab program; Zenodo contents need inspection.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "sd2-yeast-replication", "title": "Highly-automated, high-throughput replication of yeast-based logic circuit design assessments (SD2/Strateos/Aquarium)", "doi": "10.1093/synbio/ysac018", "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac018/6703309", "year": 2022, "venue": "Synthetic Biology", "open_access_license": "CC BY", "code_url": "https://github.com/rpgoldman/replication-paper-data-analysis", "code_files": ["analysis notebooks", "(SD2E/pysd2cat, jvrana/Terrarium for Aquarium planning)"], "code_license": "none", "language": "Python", "hardware": ["Strateos cloud lab", "Aquarium (UW BIOFAB)", "flow cytometer", "plate reader"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Logic-circuit assays replicated across labs with cytometry results compared.", "wet_lab_validated": true, "simulatable": "partial: protocol plans not released as executable code", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Released code is analysis; cloud-lab protocols not public.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "sdl-enzyme-flex", "title": "Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab", "doi": "10.1002/bit.70038", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12503018/", "year": 2025, "venue": "Biotechnology and bioengineering", "open_access_license": "cc-by", "code_url": "https://github.com/putzsebastian/sdl-enzymes-optimization", "code_files": [], "code_license": "MIT", "robot_platform": "flex", "api": "other", "protocol_category": "self-driving enzymatic reaction optimisation (pH, temperature, cosubstrate)", "results_evidence": "ML-driven Opentrons Flex platform optimised enzymatic reaction conditions after >10,000 simulated campaigns selected the best algorithm; experimental campaigns improved activity.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Repo has optimisation scripts only (no Flex protocol). Same author's KAISA-LSE_SDL-Platform and automation-isotherms-complexes repos contain Opentrons apiLevel protocols, incl. an LLM protocol-generation replication study (MIT) worth a look.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_UlURib8c7yzycxPTXEqd9KsArMa"], "found_by": ["amass", "nonlh"]}
+{"id": "sdl-guide-gormley", "title": "A user's guide to your first self-driving liquid handling lab", "doi": "10.1039/d5dd00525f", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2026/dd/d5dd00525f", "year": 2026, "venue": "Digital Discovery", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/GormleyLab/SDLGuide", "code_files": ["(GUI/driver python for ACRO + Integra pipette; no Opentrons protocol)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "self-driving lab enzyme assay optimisation", "results_evidence": "Closed-loop campaign optimised enzyme assay conditions with plate-reader readouts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Great tutorial-style open text and MIT code, but a bespoke handler API; useful as a non-Opentrons generalisation target.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["amass", "web"]}
+{"id": "solubility-hein", "title": "Automated solubility screening platform using computer vision", "doi": "10.1016/j.isci.2021.102176", "paper_url": "https://www.cell.com/iscience/fulltext/S2589-0042(21)00144-0", "year": 2021, "venue": "iScience", "open_access_license": "CC BY-NC-ND", "code_url": "https://gitlab.com/heingroup/automated_solubility_h1", "code_files": ["N9 robot scripts", "HeinSight turbidity CV"], "code_license": "unverified", "language": "Python", "hardware": ["North Robotics N9 arm", "camera", "dosing", "hotplate"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Solubility of compounds determined by CV turbidity with comparison to HPLC.", "wet_lab_validated": true, "simulatable": "partial: N9 'north' package has a simulation mode (unverified)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "GitLab licence unverified.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "spatial-tx-bravo", "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues", "doi": "10.1186/s12864-020-6631-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7158132/", "year": 2020, "venue": "BMC genomics", "open_access_license": "cc-by", "code_url": "https://github.com/jemten/Bravo_ST", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "Spatial Transcriptomics library prep (Agilent Bravo)", "results_evidence": "Automated ST library prep cut prep time by 35%, increased samples per run and showed near-zero technical variability between preparations.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Agilent VWorks Bravo protocol files (non-Python); no license; good paper-only porting target (bead cleanups, many steps).", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_7iUsjz95kTSaVU3lS34UgJNbiDH"], "found_by": ["amass"]}
+{"id": "star-hardwarex", "title": "Sequential Treatment Application Robot (STAR) for high-replication marine experimentation", "doi": "10.1016/j.ohx.2024.e00524", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067224000178", "year": 2024, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.10048123", "code_files": ["Zenodo: xArm control scripts"], "code_license": "check Zenodo", "language": "Python", "hardware": ["UFACTORY xArm", "dosing"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Marine organism treatment experiments with high replication reported.", "wet_lab_validated": true, "simulatable": "partial: xArm SDK has no official sim; stub required", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "xArm script readable; Zenodo licence unverified.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "tape-organoid-barcoding", "title": "Cell-type-specific signaling networks in heterocellular organoids (TOBis barcoding / robotic organoid extraction)", "doi": "10.1038/s41592-020-0737-8", "paper_url": "https://doi.org/10.1038/s41592-020-0737-8", "year": 2020, "venue": "Nature Methods", "open_access_license": "unclear (subscription)", "code_url": "https://github.com/TAPE-Lab/OT-2_Code", "code_files": ["TOBis_Barcoding/Barcode_Production/126_Plex_Production_Protocol.py", "TOBis_Barcoding/Barcode_Aliquoting/126_Plex_Aliquoting/126_Plex_Aliquoting_Barcodes_1_to_96_using_PCR_plates.py", "REPO/REPO_126_plex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "mass-cytometry barcode production/aliquoting, organoid extraction", "results_evidence": "TOBis barcoded organoids profiled by mass cytometry; signalling networks resolved per cell type.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Seven complete OT-2 protocols, but the paper is subscription-only and the repo has no licence, so paper text must be sourced elsewhere.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "teemi", "title": "teemi: open-source literate programming for iterative DBTL cycles", "doi": "10.1371/journal.pcbi.1011929", "paper_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011929", "year": 2024, "venue": "PLoS Computational Biology", "open_access_license": "CC0", "code_url": "https://github.com/hiyama341/teemi", "code_files": ["teemi/build/", "teemi/lims/", "notebooks for G8H/CPR yeast library"], "code_license": "MIT", "language": "Python", "hardware": ["Flowbot/OT-2 (LH)", "plate reader", "colony picking (manual/robot)"], "domain": "biology", "task_type": "other", "results_evidence": "Yeast strain library built and screened with titres reported.", "wet_lab_validated": true, "simulatable": "true: pure Python", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Mostly design/LIMS; minor non-LH content.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "tmt-bead-platform-ot2", "title": "A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation", "doi": "10.1021/jasms.1c00077", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8210952/", "year": 2021, "venue": "Journal of the American Society for Mass Spectrometry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "TMTpro isobaric-tag proteomics sample prep", "results_evidence": "Robot-prepared TMTpro16-plex triplicates quantified similar numbers of proteins/peptides with good reproducibility vs manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Paper states open-source OT-2 templates are provided (likely SI), but no repository URL extracted; needs manual SI retrieval.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_E2Bo8H8BA9wM9XBVa6wJnkVtnJF"], "found_by": ["amass"]}
+{"id": "trypanosomatid-drug-combo-ot2", "title": "OT-2 protocols for drug combination screening (Trypanosomatics Lab, UNSAM)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/FranAguero07/OT2_protocols", "code_files": ["PROTOCOLS/Drugs_combination.py", "PROTOCOLS/Cell_lysis.py", "PROTOCOLS/Transfer_to_384_well_plate.py"], "code_license": "none", "stars": 0, "last_push": "2025-04-02", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "drug dilution/combination matrix, cell lysis, 384-well transfer (luciferase readout)", "results_evidence": "README states protocols are described in the lab paper (not cited by DOI).", "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Clean apiv2 scripts with labware spec files; paper DOI needs resolution; no license.", "est_tasks": 3, "source_agent": "github", "found_by": ["github"]}
+{"id": "ufdutton-16s-flex", "title": "UF Dutton Lab Opentrons 16S microbiome workflow (OT-2 + Flex)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/UFDuttonLab/lab_automation_opentrons", "code_files": ["protocols/Flex/Zymo_Magbead_DNA_Kit_48samples.py", "protocols/Flex/Zymo_LibraryPrep_TG_V2.py", "protocols/Flex/NEBNext_Ultra_II_FS_DNA_Library_Prep_FlexV18.py", "protocols/Flex/SelectaSize96.py"], "code_license": "none", "stars": 0, "last_push": "2026-09-29", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "microbiome DNA extraction + 16S/shotgun library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Production-style Flex protocols but no paper and no license.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "vadr-vacuum-miniprep-flex", "title": "An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2", "doi": "10.64898/2026.09.16.746974", "paper_url": "https://doi.org/10.64898/2026.09.16.746974", "year": 2026, "venue": "bioRxiv", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/JackATDalton/VADR", "code_files": ["Protocol Files/Miniprep_var_sample.py"], "code_license": "none", "stars": 0, "last_push": "2026-01-28", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "plasmid miniprep with 3D-printed vacuum manifold", "results_evidence": "bioRxiv 2026 reports improved DNA isolation yields with the open-source vacuum manifold on Opentrons Flex (link between repo and preprint inferred from content/date; verify).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Single Flex script + STL/labware JSON; requires custom 3D-printed manifold; no license; repo-paper link unverified.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "viscous-liquid-bo-ot2", "title": "Optimization of liquid handling parameters for viscous liquid transfers with pipetting robots, a sticky situation", "doi": "10.1039/d3dd00255a", "paper_url": "https://doi.org/10.1039/d3dd00255a", "year": 2024, "venue": "Digital Discovery", "open_access_license": "cc-by-nc/3.0", "code_url": "https://github.com/Quijanove/LiqTransferOptimizer", "code_files": ["BO_liquid_transfer.py", "Old scripts/Semi_automated_MOBO_OT2.py", "Old scripts/opentrons.py"], "code_license": "MIT", "stars": 3, "last_push": "2025-09-29", "robot_platform": "ot2", "api": "other", "protocol_category": "liquid-class optimisation (viscous liquids, gravimetric, Bayesian optimisation)", "results_evidence": "Digital Discovery 2024 reports gravimetric transfer error and speed after multi-objective BO for viscous liquids on OT-2 and Sartorius rLine.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MIT, open paper; OT-2 controlled via HTTP/closed loop with balance, not a standalone apiv2 protocol.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "worm-food-preference", "title": "C. elegans food preference protocol (bacteria and worm spotting on OT-2)", "doi": "10.1242/jeb.01955", "paper_url": "https://github.com/slhogle/c_elegans_food_preference_protocol", "year": 2023, "venue": "repository (protocol adapted from J Exp Biol 2006)", "open_access_license": "source paper subscription", "code_url": "https://github.com/slhogle/c_elegans_food_preference_protocol", "code_files": ["02_spot_bacteria.py", "03_spot_worms.py"], "code_license": "GPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "spotting bacteria and worms onto agar plates", "results_evidence": "Protocol reproduces a published behavioural assay; no new results in the repo.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "GPL-3.0 and two tidy scripts; the referenced paper predates the automation, so the triple is weak.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["github", "web"]}
+{"id": "zhao-autonomous-enzyme", "title": "A generalized platform for artificial intelligence-powered autonomous enzyme engineering (iBioFAB)", "doi": "10.1038/s41467-025-61209-y", "paper_url": "https://www.nature.com/articles/s41467-025-61209-y", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/Zhao-Group/closed-loop", "code_files": ["demo.py", "src/utils/experiment_utils.py", "(Primer_Design_and_Worklists) worklist generators"], "code_license": "MIT", "language": "Python", "hardware": ["iBioFAB: Thermo F5 arm", "thermocyclers", "incubators", "plate readers", "liquid handlers"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Engineered AtHMT and YmPhytase variants with 16-26x improvements in 4 rounds.", "wet_lab_validated": true, "simulatable": "partial: ML + worklist generation offline; iBioFAB scheduling proprietary (Thermo Momentum)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Robot-scheduler code not public; worklists are LH-centric.", "est_tasks": 2, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "adept-framework", "title": "The ADePT framework for assessing autonomous laboratory robotics", "doi": "10.1038/s42004-026-01932-9", "paper_url": "https://www.nature.com/articles/s42004-026-01932-9", "year": 2026, "venue": "Communications Chemistry", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": [], "domain": "other", "task_type": "other", "results_evidence": "Assessment framework; useful for rubric design, not tasks.", "wet_lab_validated": false, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Framework paper, no code.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "ai-chemist-ustc", "title": "An all-round AI-Chemist with a scientific mind", "doi": "10.1093/nsr/nwac190", "paper_url": "https://academic.oup.com/nsr/article/9/10/nwac190/6694179", "year": 2022, "venue": "National Science Review", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["mobile robot", "workstations"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "OER catalysts discovered autonomously.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "archemist", "title": "ARChemist: Autonomous Robotic Chemistry System Architecture (Fakhruldeen et al.)", "doi": "10.1109/ICRA46639.2022.9811996", "paper_url": "https://arxiv.org/abs/2204.13571", "year": 2022, "venue": "ICRA 2022", "open_access_license": "arXiv", "code_url": "https://github.com/ARChemist (unverified)", "code_files": [], "code_license": "unverified", "language": "Python/ROS", "hardware": ["KUKA KMR", "Franka", "solubility/crystallisation stations"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "Solubility screening and crystallisation workflows demonstrated.", "wet_lab_validated": true, "simulatable": "partial: ROS", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "aurora-materials", "title": "AURORA - An Automatic Robotic Platform for Materials Discovery", "doi": "10.1021/acsami.5c02605", "paper_url": "https://pubs.acs.org/doi/10.1021/acsami.5c02605", "year": 2025, "venue": "ACS Applied Materials & Interfaces", "open_access_license": "CC BY", "code_url": "https://github.com/PalmSens/MethodSCRIPT_Examples", "code_files": ["(vendor MethodSCRIPT examples only)"], "code_license": "vendor", "language": "Python", "hardware": ["xArm", "potentiostat (PalmSens)"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Electrochemical materials screening reported.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Platform code not released.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "autopots-proteome", "title": "Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling", "doi": "10.1021/acs.analchem.0c04240", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8140400/", "year": 2020, "venue": "Analytical chemistry", "open_access_license": "author manuscript (PMC)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "low-input one-pot proteomics prep in 384-well plates", "results_evidence": "autoPOTS quantified proteomes from low-input/single-cell-scale samples using an unmodified low-cost pipetting robot.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code; robot is OT-2 per full text but protocol not released.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_9SKC53Uk2sKzNuvdXAm8dqYRnks"], "found_by": ["amass"]}
+{"id": "autorelacs", "title": "AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq", "doi": "10.1038/s41598-020-69443-8", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7381599/", "year": 2020, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/FrancescoFerrari88/AutoRELACS", "code_files": [], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "ChIP-seq barcoding library prep (Biomek i7)", "results_evidence": "AutoRELACS generated ChIP-seq data comparable to the manual RELACS protocol across many samples.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo holds analysis notebooks only; Biomek i7 methods not released as code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_SYmOf482v5ytfvMV1Xbdpqc2FV1"], "found_by": ["amass"]}
+{"id": "baybe", "title": "BayBE: Bayesian Back End for design of experiments", "doi": "10.1039/D5DD00050E", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d5dd00050e", "year": 2025, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/emdgroup/baybe", "code_files": ["baybe/campaign.py", "examples/"], "code_license": "Apache-2.0", "language": "Python", "hardware": [], "domain": "chemistry", "task_type": "other", "results_evidence": "Campaign API with benchmarks; industrial case studies reported, few with released wet-lab data.", "wet_lab_validated": false, "simulatable": "true: pure software", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Not hardware-automation code; only adjunct planner.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "bead-digestion-ann", "title": "Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network", "doi": "10.1016/j.talanta.2024.125988", "paper_url": "https://doi.org/10.1016/j.talanta.2024.125988", "year": 2024, "venue": "Talanta", "open_access_license": "paywalled (Talanta)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics paramagnetic bead digestion", "results_evidence": "ANN-optimised OT-2 bead digestion showed high reproducibility across plasma, Arabidopsis, E. coli and mouse cortex; identified 385 unique rat bile proteins.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code found; paywalled.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_F15HwF4NineYWeVZrQQDYlLOWJW"], "found_by": ["amass"]}
+{"id": "bio-spec-hardwarex", "title": "BIO-SPEC: An open-source bench-top parallel bioreactor system", "doi": "10.1016/j.ohx.2025.e00670", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067225000690", "year": 2025, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "see paper repository (OSF/Zenodo, not verified)", "code_files": [], "code_license": "CC BY (hardware, per HardwareX)", "language": "Python/Arduino", "hardware": ["parallel bioreactors", "OD sensor"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Validation growth experiments reported in HardwareX.", "wet_lab_validated": true, "simulatable": "false: firmware", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified; hardware-centric.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "bioclonebot", "title": "BioCloneBot: A versatile, low-cost, and open-source automated liquid handler", "doi": "10.1016/j.ohx.2024.e00516", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10955647/", "year": 2024, "venue": "HardwareX", "open_access_license": "cc-by", "code_url": "https://osf.io/qdp7v", "code_files": [], "code_license": "see OSF (HardwareX requires open licence)", "robot_platform": "other", "api": "other", "protocol_category": "DIY low-cost liquid handler", "results_evidence": "Validated accuracy and repeatability across liquid handling tasks.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom hardware/Arduino code (GitHub KoaCWells/BioCloneBot has no .py).", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_AwknKbU7IM88dQ9ywOSIu4JiHte"], "found_by": ["amass"]}
+{"id": "catib-screening", "title": "\"High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization\"", "doi": "10.1186/s12934-024-02319-y", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10894497/", "year": 2024, "venue": "Microbial cell factories", "open_access_license": "cc-by", "code_url": "https://github.com/JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "semi-automated cloning of 63 CatIB variants and automated inclusion-body activity screening", "results_evidence": "Generated 63 BsGDH CatIB variants; automated screening workflow validated and used to rank variant activities in parallel.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Supplement repo has modelling notebooks only (GPL-3.0); robot methods (Tecan/OT-2 mix) not released as code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_6dJEL33HqVFIFPopNLW6tccMbse"], "found_by": ["amass", "web"]}
+{"id": "cellfree-biosensor-ot2", "title": "Semiautomated Production of Cell-Free Biosensors", "doi": "10.1021/acssynbio.4c00703", "paper_url": "https://doi.org/10.1021/acssynbio.4c00703", "year": 2025, "venue": "ACS synthetic biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free biosensor reaction assembly (LacZ colorimetric / fluorescent)", "results_evidence": "Compared manual vs semi-automated OT-2 assembly of cell-free reactions; robotic assembly reduced variability in colorimetric and fluorescent outputs.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code repository located.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_2gr7aV8pMyf5se5ktlfFCQkZdNX"], "found_by": ["amass"]}
+{"id": "cloudlab-chiral-perovskite", "title": "Autonomous discovery of optically active chiral inorganic perovskite nanocrystals through an intelligent cloud lab", "doi": "10.1038/s41467-020-15728-5", "paper_url": "https://www.nature.com/articles/s41467-020-15728-5", "year": 2020, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["cloud lab robotic synthesis + CD spectroscopy"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Chiral perovskite NCs with CD responses discovered.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "combinatorial-barcode-dna", "title": "Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications", "doi": "10.3390/ijms24032549", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9917336/", "year": 2023, "venue": "International journal of molecular sciences", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.7415652", "code_files": [], "code_license": "CC-BY-4.0", "robot_platform": "ot2", "api": "other", "protocol_category": "oligo mixing for combinatorial DNA barcode library assembly", "results_evidence": "Built 256- and 512-member modular barcode libraries from <50 oligos; OT-2 used for oligo mixing in Gen_2 library.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Zenodo scripts are NUPACK/BLAST design scripts; zip download failed to verify any OT-2 code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_ELVDy0e7Q2jFGAgyKxmb8hYtJNp"], "found_by": ["amass"]}
+{"id": "covid-fosh-review", "title": "High-throughput and automated screening for COVID-19", "doi": "10.3389/fmedt.2022.969203", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9521367/", "year": 2022, "venue": "Frontiers in medical technology", "open_access_license": "cc-by", "code_url": "https://www.protocols.io/groups/opentrons-covid19-testing", "code_files": [], "code_license": "unknown", "robot_platform": "ot2", "api": "other", "protocol_category": "review of open-source automated COVID-19 testing", "results_evidence": "Review of case studies (China, Spain, UK); no new wet-lab data.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Review article; points to Opentrons COVID protocols.io group.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_OaJc5wIMCiLR2rqrnf5sLmZb73s"], "found_by": ["amass"]}
+{"id": "curcumin-formulation-sdl", "title": "Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator", "doi": "10.1039/d5dd00171d", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13576497/", "year": 2025, "venue": "Digital discovery", "open_access_license": "cc-by", "code_url": "https://github.com/shorthouse-lab/Ros_SDformulation", "code_files": [], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "drug formulation solubility screening (excipient mixing)", "results_evidence": "Found 7 curcumin formulations with solubility >10 mg/mL after sampling 256 of 7776 candidates.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo has Bayesian-optimisation notebooks only; OT-2 protocol not released; no license (Zenodo CC-BY).", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_PnLa1CsDtEMYEsgnfmLycDR2B5o"], "found_by": ["amass"]}
+{"id": "diy-ot-linear-motion-qpcr", "title": "Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting", "doi": "10.1038/s41598-020-70465-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7424513/", "year": 2020, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "open-source DIY liquid handler for qPCR setup", "results_evidence": "Benchmarking showed micropipetting speed/positional accuracy adequate for qPCR setup reproducibility.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom hardware; no Opentrons/PLR code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_HoIJvKsIF5yFoutGHfRw4kxr5Dk"], "found_by": ["amass"]}
+{"id": "diy-stem-lhr", "title": "DIY liquid handling robots for integrated STEM education and life science research", "doi": "10.1371/journal.pone.0275688", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9645590/", "year": 2022, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "educational DIY liquid handling robot (Snap4Arduino)", "results_evidence": "Qualitative teacher study plus demonstration experiments.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Block-based Arduino programming; not relevant API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_JOobtuYcydkFfO4xTZ7mNKDzWv4"], "found_by": ["amass"]}
+{"id": "duckweed-hte", "title": "Accelerated high-throughput imaging and phenotyping system for small organisms", "doi": "10.1371/journal.pone.0287739", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10361482/", "year": 2023, "venue": "PloS one", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.8060938", "code_files": [], "code_license": "MIT", "robot_platform": "ot2", "api": "other", "protocol_category": "modified OT-2 loading duckweed into well plates for plant-microbe growth phenotyping", "results_evidence": "Study of 6,000 experimental units across 2,000 treatments with time-resolved growth data; system scales to 11,520 units.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Zenodo holds R analysis only; OT-2 loading protocol not found.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_1B9FNKPNZU8nO23095KgwBAzbKL"], "found_by": ["amass"]}
+{"id": "egf-sequeduct", "title": "Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing", "doi": "10.1021/acssynbio.3c00589", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10877595/", "year": 2024, "venue": "ACS synthetic biology", "open_access_license": "cc-by", "code_url": "https://github.com/Edinburgh-Genome-Foundry/Sequeduct", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "nanopore plasmid assembly QC (analysis pipeline)", "results_evidence": "Biofoundry-scale validation of assembled plasmids via nanopore long-read sequencing with automated reports.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Analysis pipeline only; no robot code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Orw4zCCJAZKmeiuONAxiZlV2SA1"], "found_by": ["amass"]}
+{"id": "endylab-opentrons", "title": "Endy Lab Opentrons protocol collection", "doi": null, "paper_url": "https://github.com/EndyLab/opentrons", "year": 2018, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/EndyLab/opentrons", "code_files": ["protocols/OT2/pcr.py", "protocols/OT2/primer-dilute.py", "protocols/dilution-series.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "PCR setup, dilution series, calibration", "results_evidence": "No linked publication.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "Mostly legacy API v1, no paper, no licence.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "evobot", "title": "New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot", "doi": "10.1177/2472630316689285", "paper_url": "https://doi.org/10.1177/2472630316689285", "year": 2017, "venue": "SLAS technology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "modular open-source liquid handling robot (droplet/artificial life experiments)", "results_evidence": "New capabilities demonstrated for long-running artificial-life experiments.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom robot software; code not verified.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_TYMC8o5BkU3fl3B2gzqtDi6PWI0"], "found_by": ["amass"]}
+{"id": "findus", "title": "FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences", "doi": "10.1177/2472630319877374", "paper_url": "https://doi.org/10.1177/2472630319877374", "year": 2019, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology, verify)", "code_url": "https://github.com/FBarthels/FINDUS", "code_files": [], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "DIY 3D-printed liquid handling workstation", "results_evidence": "Pipetting errors <0.3%; showcase biology and chemistry applications.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom firmware/GUI (GPL-3.0); not Opentrons/PLR.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_XhtKE5t0nOWiZV3YJgBgFJpKrAq"], "found_by": ["amass"]}
+{"id": "flyspresso-embryo-ihc", "title": "An open-source semi-automated robotics pipeline for embryo immunohistochemistry", "doi": "10.1038/s41598-021-89676-5", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8119710/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": "https://github.com/janelia-pypi/hybridizer_python", "code_files": [], "code_license": "not checked", "robot_platform": "other", "api": "other", "protocol_category": "Drosophila embryo fixation and staining robotics", "results_evidence": "Automated embryo fixation, colorimetric/antibody staining and adaptive confocal imaging demonstrated.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom fluidics controller, not a liquid-handler API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_M7a5zpr9onHlfNo2rvYxjaoYQJ8"], "found_by": ["amass"]}
+{"id": "gpcr-livecell-ot2", "title": "GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System", "doi": "10.1021/acssensors.2c01341", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9994309/", "year": 2023, "venue": "ACS sensors", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated compound addition during live-cell cAMP imaging", "results_evidence": "Measured GPR68 cAMP dynamics vs extracellular pH and ogerin modulation using OT-2-integrated microscopy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link found.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_q0Ggo2QEemYLff5LOgORAQYLI4"], "found_by": ["amass"]}
+{"id": "hydra-hydrogel-plates", "title": "Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing", "doi": "10.1038/s44172-025-00575-3", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12749810/", "year": 2025, "venue": "Communications engineering", "open_access_license": "cc-by", "code_url": "https://github.com/Synthetic-Physiology-Lab/hydra-hts-hydrogel-analysis", "code_files": [], "code_license": "none", "robot_platform": "ot2", "api": "other", "protocol_category": "hydrogel coating of 96/384-well plates for cell culture HTS", "results_evidence": "HYDRA produced meniscus-free hydrogel coatings validated by imaging-based anticancer dose-response assays and long-term microscopy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo contains image-analysis scripts only; OT-2 protocol not released.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_Ht5d4BDlmKuczCVx9dH7zd50pLf"], "found_by": ["amass"]}
+{"id": "illumina-dnaprep-flowbot", "title": "Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot", "doi": "10.1038/s41598-024-58963-2", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11001922/", "year": 2024, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "Illumina DNA library prep for WGS (flowbot ONE)", "results_evidence": "Automated libraries had comparable yields (median 1.5-fold diff), similar assembly quality and 100% cgMLST concordance; hands-on time 25 vs 125 min.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Flow Robotics protocol file available only on request; good paper-only porting task.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_6hmaeTZsbAf0xOYBT4JLJPyjYE0"], "found_by": ["amass"]}
+{"id": "kedar-balance-integration", "title": "Opentrons OT-2 mass-balance integration (application note supplement)", "doi": null, "paper_url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance", "year": 2022, "venue": "Opentrons application note", "open_access_license": null, "code_url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance", "code_files": ["OT-2_BalanceAutomation.ipynb (notebook, no .py)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "gravimetric calibration with external balance", "results_evidence": "Gravimetric accuracy of dispensed volumes reported in the application note.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "Notebook-only, external-hardware dependent, no peer-reviewed paper.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "kitfree-rna-extraction", "title": "A high-throughput pipeline for scalable kit-free RNA extraction", "doi": "10.1038/s41598-021-02742-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8636496/", "year": 2021, "venue": "Scientific reports", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "kit-free magnetic-bead RNA extraction for SARS-CoV-2 RT-qPCR", "results_evidence": "Semi-automated kit-free extraction validated by SARS-CoV-2 RT-qPCR without loss of diagnostic sensitivity/accuracy.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link in full text.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_67rBmQVGvZfNxbJQxDsiuEoRZew"], "found_by": ["amass"]}
+{"id": "labdroid-phenol-chloroform", "title": "Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing", "doi": "10.12688/f1000research.109251.1", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8931447/", "year": 2022, "venue": "F1000Research", "open_access_license": "cc-by", "code_url": "https://doi.org/10.5281/zenodo.5733820", "code_files": [], "code_license": "CC-BY-4.0", "robot_platform": "other", "api": "other", "protocol_category": "HMW genomic DNA phenol-chloroform extraction (Maholo LabDroid)", "results_evidence": "Routine extraction of >100 kb gDNA from algae, bacteria, insects and human cells; validated by pulse-field electrophoresis and nanopore read N50.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Proprietary LabDroid job files (.PRJ); humanoid robot not a liquid handler API.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_5RmeQb0DTzqBED9vaGn7r1LhEBe"], "found_by": ["amass"]}
+{"id": "lego-lhr-stem", "title": "Liquid-handling Lego robots and experiments for STEM education and research", "doi": "10.1371/journal.pbio.2001413", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5360201/", "year": 2017, "venue": "PLoS biology", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "educational Lego liquid handling robot", "results_evidence": "Activities tested with school students; build and experiment instructions provided.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Lego EV3 programs; not relevant API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_XmDWjWZyNFqYeaKBXEulafS1PTK"], "found_by": ["amass"]}
+{"id": "maple-fly-robot", "title": "MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping", "doi": "10.7554/eLife.37166", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6193762/", "year": 2018, "venue": "eLife", "open_access_license": "cc-by", "code_url": "https://github.com/FlySorterLLC/MAPLEControlSoftware", "code_files": [], "code_license": "not checked", "robot_platform": "other", "api": "other", "protocol_category": "Drosophila handling robot", "results_evidence": "Automated virgin collection and social-behaviour experiments revealing persistent idiosyncrasies.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom robot, not liquid handling.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_hU5OjLOIAJ8W8VBxIOTQR06Nlr"], "found_by": ["amass"]}
+{"id": "marchantia-agro-transformation", "title": "Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation", "doi": "10.1111/tpj.70118", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11993085/", "year": 2025, "venue": "The Plant journal : for cell and molecular biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Agrobacterium-mediated plant (Marchantia) transformation", "results_evidence": "Semi-automated protocol showed transformation efficiency similar to manual manipulation.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link in full text.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_QTLDXogx16ZOAstLvfRPprCJmTV"], "found_by": ["amass"]}
+{"id": "miniaturized-16s-mosquito", "title": "High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity", "doi": "10.1128/mSystems.00166-18", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6222042/", "year": 2018, "venue": "mSystems", "open_access_license": "cc-by", "code_url": "https://www.protocols.io/view/high-throughput-miniaturized-16s-rrna-amplicon-lib-u2ieyce", "code_files": [], "code_license": "protocols.io (CC-BY)", "robot_platform": "other", "api": "other", "protocol_category": "miniaturised 16S rRNA amplicon library prep (5 uL, Mosquito HV/Echo)", "results_evidence": "Miniaturised 5 uL reactions matched standard 25 uL composition; validated on 46 fish x 5 body sites over seven months.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Step-by-step protocols.io only (TTP Mosquito/Echo); paper-only task possible.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_PDQ9xjdqhxi9EVLaXrTUadiioCv"], "found_by": ["amass"]}
+{"id": "mngs-384-miniaturized", "title": "Miniaturization and optimization of 384-well compatible RNA sequencing library preparation", "doi": "10.1371/journal.pone.0206194", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6328170/", "year": 2019, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "miniaturised 384-well mNGS RNA library prep (Mosquito HTS)", "results_evidence": "ERCC spike-ins showed miniaturised prep fidelity equivalent to full-volume preps at much lower cost/time.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Private protocols.io link; non-Python liquid handler.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_FgoF22qjQ8MieBA6wiWMAws9TF3"], "found_by": ["amass"]}
+{"id": "mobile-robot-burger-2020", "title": "A mobile robotic chemist (Burger et al.)", "doi": "10.1038/s41586-020-2442-2", "paper_url": "https://www.nature.com/articles/s41586-020-2442-2", "year": 2020, "venue": "Nature", "open_access_license": "paywalled", "code_url": "none public (ROS code not released)", "code_files": [], "code_license": "n/a", "language": "Python/ROS", "hardware": ["KUKA KMR iiwa", "GC", "photolysis station"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "688 experiments over 8 days found photocatalyst mixtures 6x more active.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "mxene-aerogel-al", "title": "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties", "doi": "10.1038/s41467-024-49011-8", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11144242/", "year": 2024, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/oshin71/Programmable-MXene-Aerogel", "code_files": [], "code_license": "none (data Zenodo BSD-3-Clause-Clear)", "robot_platform": "ot2", "api": "other", "protocol_category": "materials mixture preparation (MXene/CNF/gelatin) for active learning", "results_evidence": "OT-2 prepared 264 mixtures; 162 conductive aerogels fabricated/characterised over 8 active-learning cycles to train an ANN for inverse design.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo is empty/data only; OT-2 scripts not released; materials science.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_SpCNFN4CK5sOluCy0KLQ4t2mTLD"], "found_by": ["amass", "nonlh"]}
+{"id": "newcastle-neg-opentrons", "title": "Newcastle Network Ecology Group OT-2 protocol and labware collection", "doi": null, "paper_url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons", "year": 2022, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons", "code_files": ["Labware/api_v2/test_*.py", "Protocols/*.py (51 Opentrons-aware files; mix of API v1 and v2)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "mixed lab protocols and custom labware definitions", "results_evidence": "No linked publication found.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "No paper, unlicensed, and many scripts are API v1 labware tests.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "nfkb-luciferase-ot2", "title": "Luciferase reporter assay for NF-kB activation automated by an open-source liquid handling platform", "doi": "10.1016/j.slast.2024.100155", "paper_url": "https://doi.org/10.1016/j.slast.2024.100155", "year": 2024, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell seeding, transfection and luciferase reporter assay", "results_evidence": "OT-2 Python protocols for HeLa seeding, NF-kB reporter transfection and luciferase readout gave quantifiable activation signals with good sample-handling quality.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Python protocols described but no repository located (may be in SI); worth checking SLAS supplementary.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_6JPEUNa4CkA8mVKu3EfuFiMaZlK"], "found_by": ["amass"]}
+{"id": "opentrons-physicalai-hf", "title": "Opentrons/PhysicalAI (Hugging Face dataset of Flex teleoperation episodes)", "doi": null, "paper_url": "https://huggingface.co/datasets/Opentrons/PhysicalAI", "year": 2026, "venue": "Hugging Face dataset (Opentrons)", "open_access_license": "unstated on dataset card", "code_url": "https://huggingface.co/datasets/Opentrons/PhysicalAI", "code_files": ["(HDF5 episodes + GIFs, e.g. flex_to_biotek/inference/*.hdf5; no protocol .py)"], "code_license": "unstated", "robot_platform": "flex", "api": "other", "protocol_category": "Flex plate-handoff manipulation episodes (imitation learning data)", "results_evidence": "Inference session summaries record on-robot execution of plate handoffs to a BioTek reader.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "No protocol code or paper; relevant as embodiment data rather than a paper->code task, and the licence is unstated.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "ot2eye", "title": "OT2Eye: Detection of labware conditions to monitor and extend affordable liquid-handling robots", "doi": "10.1016/j.slast.2026.100410", "paper_url": "https://doi.org/10.1016/j.slast.2026.100410", "year": 2026, "venue": "SLAS technology", "open_access_license": "cc-by (SLAS Technology OA, verify)", "code_url": "https://github.com/bioinfo-tsukuba/ot2eye", "code_files": [], "code_license": "MIT", "robot_platform": "ot2", "api": "other", "protocol_category": "labware/tip detection from OT-2 camera images", "results_evidence": "High accuracy identifying plates and tip racks and their deck positions, and tip presence/absence.", "wet_lab_validated": false, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Computer-vision tool, not a wet-lab protocol (MIT); possible verifier aid.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_67bEY0DCJ8NvYefU4Qifg3lJnc4"], "found_by": ["amass"]}
+{"id": "pipette-show", "title": "Pipette Show: An Open Source Web Application to Support Pipetting into Microplates", "doi": "10.1021/acssynbio.1c00494", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.1c00494", "year": 2022, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Global-Biofoundries-Alliance/pipette-show", "code_files": ["(web app; no robot protocol .py)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "manual pipetting guidance", "results_evidence": "Error rates for manual plate filling with vs without the app.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "No robot code; manual-pipetting aid only.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "plastic-substitutes-al", "title": "Machine intelligence-accelerated discovery of all-natural plastic substitutes", "doi": "10.1038/s41565-024-01635-z", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11186784/", "year": 2024, "venue": "Nature nanotechnology", "open_access_license": "cc-by", "code_url": "https://github.com/chentl/MatAL", "code_files": [], "code_license": "BSD", "robot_platform": "ot2", "api": "other", "protocol_category": "nanocomposite film mixture preparation for active learning", "results_evidence": "OT-2 prepared 286 CNF/MMT/gelatin/glycerol nanocomposites to train models discovering all-natural plastic substitutes.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "MatAL contains ML code only; no OT-2 protocol; BSD.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_XSTjitcXORpdBVLgqh3351fcD7e"], "found_by": ["amass"]}
+{"id": "polymer-protein-hybrids", "title": "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids", "doi": "10.1002/adma.202201809", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1002/adma.202201809", "year": 2022, "venue": "Advanced Materials", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/webbtheosim/PPH_public", "code_files": ["csv data only"], "code_license": "none", "language": "-", "hardware": ["Hamilton liquid handler", "plate reader", "robotic arm"], "domain": "biology", "task_type": "other", "results_evidence": "Enzyme-stabilising copolymers designed and assayed.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Data only.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "pr-pr", "title": "PR-PR: cross-platform laboratory automation system", "doi": "10.1021/sb4001728", "paper_url": "https://doi.org/10.1021/sb4001728", "year": 2014, "venue": "ACS synthetic biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "tecan", "api": "other", "protocol_category": "cross-platform protocol language (Golden Gate, Kunkel mutagenesis, Gibson)", "results_evidence": "Modified Golden Gate assembly run across liquid-handling robot, microfluidic and manual platforms; Kunkel and Gibson also implemented.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "PR-PR DSL compiled to Tecan; historical; no Python protocol.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_XTiO9qwkOd5IRMZcuTRMPGZeqBC"], "found_by": ["amass"]}
+{"id": "protein-corona-ot2", "title": "Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data", "doi": "10.1007/s00216-020-02726-1", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7483600/", "year": 2020, "venue": "Analytical and bioanalytical chemistry", "open_access_license": "cc-by (PMC OA, verify)", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein corona formation and magnetic isolation for proteomics", "results_evidence": "Automated corona isolation with magnetic-core nanoparticles; compared low-cost proteomics workflows.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Protocol only in ESM text; no code.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_B5qpdBu6SwPc7FpkHe7KMJcgnUZ"], "found_by": ["amass"]}
+{"id": "proteoautonet", "title": "ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning", "doi": "10.1038/s41467-026-68484-3", "paper_url": "https://doi.org/10.1038/s41467-026-68484-3", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY 4.0 (to confirm)", "code_url": "https://github.com/guomics-lab/ProteoAutoNet", "code_files": ["(11 analysis python files; no liquid-handler protocol script found)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "automated proteomics sample handling + ML analysis", "results_evidence": "Co-elution networks derived from robot-processed samples validated against known complexes.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "Only ML/analysis code is released; no robot protocol code.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "radiolabeling-psma-ot2", "title": "Automated radiolabeling and handling of 177 Lu- and 225 Ac-PSMA-617 using a robotic pipettor", "doi": "10.1002/jlcr.4085", "paper_url": "https://doi.org/10.1002/jlcr.4085", "year": 2024, "venue": "Journal of labelled compounds & radiopharmaceuticals", "open_access_license": "unknown/likely paywalled", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "radiochemistry (177Lu/225Ac-PSMA-617 labelling)", "results_evidence": "Robotic pipettor performed radiometal labelling with reduced operator exposure and synthesis times (radiochemical yields/purity reported).", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code; niche radiochemistry.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CuOYvsMA0ArgHxEYefJckQamsBl"], "found_by": ["amass"]}
+{"id": "sdl-nano-acsnano", "title": "A Self-Driving Lab for Nano- and Advanced Materials Synthesis", "doi": "10.1021/acsnano.4c17504", "paper_url": "https://pubs.acs.org/doi/10.1021/acsnano.4c17504", "year": 2025, "venue": "ACS Nano", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["xArm", "flow synthesis", "spectroscopy"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Perspective/platform review.", "wet_lab_validated": false, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code; perspective.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "snails-slow-pipetting", "title": "Consistent ultra-long DNA sequencing with automated slow pipetting", "doi": "10.1186/s12864-021-07500-w", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7953553/", "year": 2021, "venue": "BMC genomics", "open_access_license": "cc-by", "code_url": "https://github.com/dholab/SNAILS", "code_files": [], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "ultra-long nanopore library prep slow pipetting (3D-printer based)", "results_evidence": "Across six libraries SNAILS preserved more >100 kb reads and increased average read length vs manual slow pipetting.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Python scripts emit G-code for a modified 3D printer; not a liquid-handler API.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_7qRIj7wDrr98JaRqTAYKUMqfbjA"], "found_by": ["amass"]}
+{"id": "sp3-magbead-protocol-repo", "title": "Automated magnetic bead-based digestion protocols for Opentrons OT-2 (proteomics CNB-CBM)", "doi": null, "paper_url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol", "code_files": ["(no .py in repo; protocol documentation only)"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SP3 bead digestion", "results_evidence": "None published.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "No Python protocol files present despite the MIT licence and OT-2 framing.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "summit-flow", "title": "Summit: benchmarking machine learning methods for reaction optimisation", "doi": "10.1002/cmtd.202000051", "paper_url": "https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmtd.202000051", "year": 2021, "venue": "Chemistry-Methods", "open_access_license": "CC BY", "code_url": "https://github.com/sustainable-processes/summit", "code_files": ["summit/benchmarks/", "summit/strategies/"], "code_license": "MIT", "language": "Python", "hardware": ["(benchmarks/emulators of flow reactors)"], "domain": "chemistry", "task_type": "other", "results_evidence": "Emulators trained on literature flow-chemistry data; no new wet-lab experiments.", "wet_lab_validated": false, "simulatable": "true", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Benchmark software, no lab automation.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "swabseq-flex", "title": "Automated implementation of the SwabSeq COVID-19 diagnostic assay on the opentrons flex liquid-handling robot", "doi": "10.1016/j.diagmicrobio.2026.117519", "paper_url": "https://doi.org/10.1016/j.diagmicrobio.2026.117519", "year": 2026, "venue": "Diagnostic microbiology and infectious disease", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "SwabSeq NGS COVID-19 diagnostic (RT-PCR barcoding, pooling, SPRI cleanup)", "results_evidence": "Flex workflow completed in ~2.5 h with complete agreement on negatives, very high agreement on positives and no discordant calls vs manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Flex protocol code not located (check SI); high-value Flex target if found.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_QpaAmsl6M7rjKC75l8yL5odts5x"], "found_by": ["amass"]}
+{"id": "synthetic-cells-robotics", "title": "Scaling Up Synthetic Cell Production Using Robotics and Machine Learning Toward Therapeutic Applications", "doi": "10.1002/adbi.202400671", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12078883/", "year": 2025, "venue": "Advanced biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/IdoGalil/syn", "code_files": [], "code_license": "unknown (repo not found)", "robot_platform": "tecan", "api": "other", "protocol_category": "synthetic cell production scale-up", "results_evidence": "Robotic scale-up increased synthetic-cell batch size 30-fold; luciferase SCs monitored in mice.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Repo URL dead; Tecan platform.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_ENm6Rp10P1W4yf8WWCUPVhWtn0V"], "found_by": ["amass"]}
+{"id": "takahashi-turbidostat", "title": "A low cost, customizable turbidostat for use in synthetic circuit characterization", "doi": "10.1021/sb500165g", "paper_url": "https://pubs.acs.org/doi/10.1021/sb500165g", "year": 2015, "venue": "ACS Synthetic Biology", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/klavinslab (location unverified)", "code_files": [], "code_license": "unverified", "language": "Arduino/Python", "hardware": ["8-chamber turbidostat"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Circuit characterisation in turbidostats with growth/fluorescence data.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified.", "est_tasks": 0, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "tox-pipetting-robot", "title": "A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays", "doi": "10.1371/journal.pone.0179636", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5473567/", "year": 2017, "venue": "PloS one", "open_access_license": "cc-by", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "water-quality whole-organism bioassay robot", "results_evidence": "Tested precision of automated pipetting for online toxicity bioassays.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Custom open hardware; no Opentrons/PLR code.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_A6M2tuF3phVX1rCESXk3NmVObNT"], "found_by": ["amass"]}
+{"id": "transfection-reagent-agnostic", "title": "A Novel, Fully Automated, and Reagent-Agnostic Transient Transfection Protocol", "doi": "10.1002/cpz1.968", "paper_url": "https://doi.org/10.1002/cpz1.968", "year": 2024, "venue": "Current protocols", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "other", "api": "other", "protocol_category": "automated transient transfection of adherent cells", "results_evidence": "HeLa transfection efficiency 40.9-73.3% and A549 42.2-54%, comparable to manual.", "wet_lab_validated": true, "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code located; platform unclear from abstract.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_69n4c5dgMmotdIjN4UtUde64nHh"], "found_by": ["amass"]}
+{"id": "xchem-opentrons", "title": "XChem Opentrons reaction liquid-handling toolkit", "doi": null, "paper_url": "https://github.com/xchem/opentrons", "year": 2019, "venue": "repository only (XChem crystallography pipeline papers do not release these scripts)", "open_access_license": null, "code_url": "https://github.com/xchem/opentrons", "code_files": ["examples/**/*.py (60 Opentrons-aware files, API v1 era)"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "reaction dispensing arrays for crystallographic screening", "results_evidence": "No single paper ties these scripts to reported results.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "Apache-2.0 but API v1 generated scripts and no paper pairing.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null, "found_by": ["web"]}
+{"id": "moeller-library-dup", "title": "Moeller Lab Opentrons protocol library (Zymo magbead extraction, Hackflex, Quantifluor)", "doi": "10.1186/s13059-022-02777-w", "paper_url": "https://doi.org/10.1186/s13059-022-02777-w", "year": 2022, "venue": "Genome Biology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/tanaes/Moeller_Opentrons_protocol_library", "code_files": ["Extraction/Zymo_fecal-soil_magbead/Zymo_fecal-soil_magbead_B-extraction.py", "Library_Prep/Hackflex/hackflex.py", "Quantification/Quantifluor_DNA_quant/Quantifluor_DNA_four-plates.py", "Transfers/tubes_to_96well.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "magnetic-bead DNA extraction, Hackflex library prep, DNA quantification", "results_evidence": "Hackflex libraries and extractions benchmarked by sequencing yield/quality in the companion paper.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "MIT library with nine OT-2 scripts beyond the Hackflex one already tracked; extraction and quantification protocols are new task material.", "duplicate_of_existing": "moeller-hackflex", "est_tasks": 5, "source_agent": "web", "found_by": ["amass", "github", "web"]}
+{"id": "wei-science-factory", "title": "Towards a modular architecture for science factories (WEI; color-picker + PCR workcells)", "doi": "10.1039/D3DD00142C", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00142c", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/AD-SDL/rpl_wei", "code_files": ["src/wei/core/workflow.py", "src/wei/core/experiment.py", "src/wei/core/interfaces/simulate_interface.py", "src/wei/core/interfaces/ros2_interface.py"], "code_license": "MIT", "language": "Python", "hardware": ["Brooks PF400", "Hudson PlateCrane/Sciclops", "Opentrons OT-2", "A4S sealer", "Brooks peeler", "Bio-Rad thermocycler", "Camera"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Executed closed-loop color-matching and PCR workflows on the ANL RPL workcell with reported timing/throughput and color-error convergence.", "wet_lab_validated": true, "simulatable": "true: built-in simulate_interface lets YAML workflows run with no hardware", "duplicate_of_existing": "glas-preciseflex (related PF400 driver; different repo)", "readiness": "ready", "readiness_reason": "Open paper, MIT code, YAML workflow + module specs run in simulate mode; tasks can be 'methods -> WEI workflow YAML' graded against module/action sequence.", "est_tasks": 6, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "apex-guide-dup", "title": "Opentrons OT-2 Automated Protein Expression and Purification Guide (APEX companion repo)", "doi": "10.1021/acssynbio.5c00189", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.5c00189", "year": 2025, "venue": "ACS Synthetic Biology", "open_access_license": "unclear (journal version)", "code_url": "https://github.com/btx11/opentrons-apex-protein-guide", "code_files": ["(guide/reimplementation of APEX OT-2 steps)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein expression and purification", "results_evidence": "APEX validated by expressing and purifying proteins with yields reported in the paper.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Duplicate of the existing apex source; note that the journal version (ACS Synth Biol 2025) is newer than the bioRxiv entry on file.", "duplicate_of_existing": "apex", "est_tasks": 0, "source_agent": "web", "found_by": ["amass", "web"]}
+{"id": "cbgp-transposon-genotyping-ot2", "title": "High-throughput workflow for the genotypic characterization of transposon library variants (protocols.io, CBGP)", "doi": "10.17504/protocols.io.kqdg394jzg25/v1", "paper_url": "https://doi.org/10.17504/protocols.io.kqdg394jzg25/v1", "year": 2023, "venue": "protocols.io", "open_access_license": "cc-by/4.0", "code_url": "https://github.com/Biocomputation-CBGP/OT2", "code_files": ["AntibioticPlatesGeneration/ScriptPlateGenerationAndIncubation.py", "ColonySelection/ColonySelectionScript.py", "MergingSamplesSourcePlates/ScriptMergeSamplesN1plate.py", "GoldenStandardAssembly/MoCloWithoutMixing.py"], "code_license": "none", "stars": 0, "last_push": "2023-08-22", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "antibiotic plate prep, colony selection, sample merging, MoClo assembly", "results_evidence": "protocols.io workflows from the CBGP group; wet-lab results are in the related transposon-genotyping paper already in corpus.", "wet_lab_validated": "unknown", "duplicate_of_existing": "lap-transposon-genotyping", "readiness": "partial", "readiness_reason": "Same group/workflow as existing lap-transposon-genotyping (BiocomputationLab); no license; custom 3D-printed labware.", "est_tasks": 2, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-assemblytron-assemblytron", "title": "PlantSynBioLab/AssemblyTron (already in corpus as assemblytron)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/PlantSynBioLab/AssemblyTron", "code_files": [], "code_license": "NOASSERTION", "stars": 12, "last_push": "2024-12-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "DNA assembly", "results_evidence": "See existing corpus entry assemblytron.", "wet_lab_validated": true, "duplicate_of_existing": "assemblytron", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-botany-botany", "title": "cvoiniciuc/BOTany (already in corpus as botany)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/cvoiniciuc/BOTany", "code_files": [], "code_license": "none", "stars": 2, "last_push": "2026-03-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plant biology protocols", "results_evidence": "See existing corpus entry botany.", "wet_lab_validated": true, "duplicate_of_existing": "botany", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-chory-2021-hamilton-pyhamilton", "title": "dgretton/pyhamilton (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/pyhamilton", "code_files": [], "code_license": "MIT", "stars": 192, "last_push": "2026-09-05", "robot_platform": "hamilton", "api": "other", "protocol_category": "PyHamilton library", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-chory-2021-hamilton-pyhamilton-population-dyn", "title": "dgretton/pyhamilton_population_dynamics (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/pyhamilton_population_dynamics", "code_files": [], "code_license": "MIT", "stars": 1, "last_push": "2020-11-23", "robot_platform": "hamilton", "api": "other", "protocol_category": "population dynamics (pyhamilton)", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-chory-2021-hamilton-roboplaque", "title": "dgretton/roboplaque (already in corpus as chory-2021-hamilton)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/dgretton/roboplaque", "code_files": [], "code_license": "MIT", "stars": 4, "last_push": "2020-11-30", "robot_platform": "hamilton", "api": "other", "protocol_category": "phage plaque assay (pyhamilton)", "results_evidence": "See existing corpus entry chory-2021-hamilton.", "wet_lab_validated": true, "duplicate_of_existing": "chory-2021-hamilton", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-copick-copick", "title": "sysbio-cnb/COPICK (already in corpus as copick)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/sysbio-cnb/COPICK", "code_files": [], "code_license": "MIT", "stars": 9, "last_push": "2023-03-01", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "colony picking", "results_evidence": "See existing corpus entry copick.", "wet_lab_validated": true, "duplicate_of_existing": "copick", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-covid19clinic-covid19clinic", "title": "CDB-coreBM/covid19clinic (already in corpus as covid19clinic)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/CDB-coreBM/covid19clinic", "code_files": [], "code_license": "GPL-3.0", "stars": 4, "last_push": "2021-04-23", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 RT-qPCR", "results_evidence": "See existing corpus entry covid19clinic.", "wet_lab_validated": true, "duplicate_of_existing": "covid19clinic", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-hulp-rna-extraction-rna-extraction-ot2opentro", "title": "HULPopentrons/RNA_extraction_OT2opentrons (already in corpus as hulp-rna-extraction)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/HULPopentrons/RNA_extraction_OT2opentrons", "code_files": [], "code_license": "none", "stars": 2, "last_push": "2020-07-12", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viral RNA extraction", "results_evidence": "See existing corpus entry hulp-rna-extraction.", "wet_lab_validated": true, "duplicate_of_existing": "hulp-rna-extraction", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-opencell-automation-2024-accs-pub", "title": "czbiohub-sf/2024-accs-pub (already in corpus as opencell-automation)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/czbiohub-sf/2024-accs-pub", "code_files": [], "code_license": "none", "stars": 3, "last_push": "2026-01-22", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated cell culture splitting", "results_evidence": "See existing corpus entry opencell-automation.", "wet_lab_validated": true, "duplicate_of_existing": "opencell-automation", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-ot-mation-ot-mation-repo", "title": "tphoward/OT-Mation_Repo (already in corpus as ot-mation)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/tphoward/OT-Mation_Repo", "code_files": [], "code_license": "Apache-2.0", "stars": 2, "last_push": "2025-03-21", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "synbio automation", "results_evidence": "See existing corpus entry ot-mation.", "wet_lab_validated": true, "duplicate_of_existing": "ot-mation", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-proxy-viscometer-otproxy", "title": "beatricesoh/OTProxyViscometer (Opentrons for Automated and High-Throughput Viscometry)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/beatricesoh/OTProxyViscometer", "code_files": ["OT-2_80FR.py"], "code_license": "none", "stars": 0, "last_push": "2025-01-28", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscometry", "results_evidence": "See existing corpus entry proxy-viscometer.", "wet_lab_validated": true, "duplicate_of_existing": "proxy-viscometer", "readiness": "partial", "readiness_reason": "Second code repo for an existing corpus paper (includes raw mass-profile data).", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "dup-sidekick-liquid-handler", "title": "rodolfokeesey/Liquid-Handler (already in corpus as sidekick)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/rodolfokeesey/Liquid-Handler", "code_files": [], "code_license": "NOASSERTION", "stars": 32, "last_push": "2023-02-06", "robot_platform": "other", "api": "other", "protocol_category": "open-hardware liquid handler", "results_evidence": "See existing corpus entry sidekick.", "wet_lab_validated": true, "duplicate_of_existing": "sidekick", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-slowpoke-slowpoke", "title": "Tom-Ellis-Lab/Slowpoke (already in corpus as slowpoke)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Tom-Ellis-Lab/Slowpoke", "code_files": [], "code_license": "MIT", "stars": 3, "last_push": "2026-02-09", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate + colony PCR", "results_evidence": "See existing corpus entry slowpoke.", "wet_lab_validated": true, "duplicate_of_existing": "slowpoke", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["amass", "github"]}
+{"id": "dup-transporter-screening-transporterscreening", "title": "ljm176/TransporterScreening (already in corpus as transporter-screening)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/ljm176/TransporterScreening", "code_files": [], "code_license": "none", "stars": 1, "last_push": "2024-01-05", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "transporter screening", "results_evidence": "See existing corpus entry transporter-screening.", "wet_lab_validated": true, "duplicate_of_existing": "transporter-screening", "readiness": "partial", "readiness_reason": "Duplicate of existing corpus paper; recorded for completeness only.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "fastkris-crystallisation", "title": "fastKris: Opentrons crystallisation screen protocol builder", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/LucoDevro/fastKris", "code_files": ["protocol.py", "template.py"], "code_license": "MIT", "stars": 1, "last_push": "2022-12-17", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein crystallisation screen setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "protein-crystallization-ot2", "readiness": "partial", "readiness_reason": "MIT generator, no paper; topic overlaps existing protein-crystallization-ot2.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "galaxy-synbiocad", "title": "The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering", "doi": "10.1038/s41467-022-32661-x", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9424320/", "year": 2022, "venue": "Nature communications", "open_access_license": "cc-by", "code_url": "https://github.com/brsynth (Galaxy-SynBioCAD tools; DNA-Bot generator)", "code_files": [], "code_license": "MIT (tools)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "pathway design to automated BASIC DNA assembly and transformation", "results_evidence": "Built a library of lycopene-producing E. coli strains across four sites using DNA-Bot generated OT-2 scripts; 83% success retrieving validated pathways.", "wet_lab_validated": true, "duplicate_of_existing": "dna-bot (OT-2 scripts are DNA-Bot generated)", "readiness": "partial", "readiness_reason": "Robot scripts are generated by DNA-Bot (already in corpus); new element is the lycopene library experiment.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_ChyB9zcT5J8Kd76qDJ3g2faQk1Y"], "found_by": ["amass"]}
+{"id": "isciii-covid-stations", "title": "BU-ISCIII opentrons_covid19 (ISCIII station A/B/C RT-PCR diagnostics)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/BU-ISCIII/opentrons_covid19", "code_files": ["calibration_check/stationA_protocol1_buffer_S3_calibration.py", "calibration_check/stationB_protocol1_extraction_S3_calibration.py", "calibration_check/stationC_protocol1_pcr_S3_calibration.py"], "code_license": "AGPL-3.0", "stars": 0, "last_push": "2021-02-08", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SARS-CoV-2 sample prep, extraction, PCR setup", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "covid-diagnostic-capacity-2021", "readiness": "partial", "readiness_reason": "AGPL; covidWarriors lineage; likely code behind Spanish COVID diagnostic capacity papers already in corpus (no code known there) - check.", "est_tasks": 1, "source_agent": "github", "found_by": ["github"]}
+{"id": "lap-format-repository", "title": "The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology", "doi": "10.1021/acssynbio.3c00397", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.3c00397", "year": 2023, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/Biocomputation-CBGP/LAPrepository", "code_files": ["LAPEntries/**/ScriptsFinal/*.py (37 OT-2 entry scripts)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "library of standardised protocols (colony selection, PCR setup, media distribution, plate merging)", "results_evidence": "Each LAP entry documents wet-lab execution/validation records on OT-2 at the host biofoundry.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Large multi-protocol repo (same code base as the existing lap-transposon-genotyping source) with no licence; the LAP format paper itself is new to the corpus and each entry could become a task after per-entry validation.", "duplicate_of_existing": "lap-transposon-genotyping", "est_tasks": 10, "source_agent": "web", "found_by": ["web"]}
+{"id": "maggielam-digestion-dup", "title": "Shotgun proteomics sample processing automated by an open-source lab robot (standard digestion scripts)", "doi": "10.3791/63092", "paper_url": "https://www.jove.com/t/63092", "year": 2021, "venue": "JoVE", "open_access_license": "unclear (JoVE subscription)", "code_url": "https://github.com/MaggieLam-Lab/StandardDigestion-Opentrons", "code_files": ["digestion_scripts/SP3_digestion.py", "digestion_scripts/NoSP3_digestion.py", "digestion_scripts/SP3_peptide_cleanup.py", "misc_scripts/BCA_protocol.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics digestion, SP3 cleanup, BCA assay", "results_evidence": "Peptide identifications/CVs for automated vs manual digestion reported in the JoVE article.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already represented by shotgun-proteomics-jove; MIT scripts are usable but the JoVE text is not open.", "duplicate_of_existing": "shotgun-proteomics-jove", "est_tasks": 3, "source_agent": "web", "found_by": ["amass", "github", "web"]}
+{"id": "opensampler-dup", "title": "Modification of a low-cost pipetting robot for nanoliter liquid handling and autosampling for LC-MS", "doi": "10.1002/jssc.70379", "paper_url": "https://doi.org/10.1002/jssc.70379", "year": 2026, "venue": "Journal of Separation Science", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/RTKlab-BYU/OpenSampler", "code_files": ["(OpenSampler/OpenLC control python)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "nanoliter autosampling for LC-MS", "results_evidence": "Injection precision and chromatographic performance measured for the modified robot.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already tracked as pipetting-robot-nanoliter; control software is not an Opentrons protocol.", "duplicate_of_existing": "pipetting-robot-nanoliter", "est_tasks": 0, "source_agent": "web", "found_by": ["amass", "web"]}
+{"id": "opentrons-accs-dup", "title": "Open-source cell culture automation system with integrated cell counting for passaging microplate cultures", "doi": "10.1093/pnasnexus/pgaf385", "paper_url": "https://doi.org/10.1093/pnasnexus/pgaf385", "year": 2025, "venue": "PNAS Nexus", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/czbiohub-sf/accs-protocol-software-pub", "code_files": ["cal_dummy_scripts/cal_cell_splitting.py", "cal_dummy_scripts/cal_96to8x12.py", "accs-protocols/accs_npf/resources/sim_proxy_script/run.py"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell culture passaging / cell counting", "results_evidence": "Automated passaging maintained cell cultures over weeks with counting accuracy benchmarked against manual counts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already in the corpus as opencell-automation, but this second BSD-3 repo (protocol framework, calibration scripts, simulation proxy) was not ingested and could yield runnable tasks.", "duplicate_of_existing": "opencell-automation", "est_tasks": 3, "source_agent": "web", "found_by": ["amass", "github", "web"]}
+{"id": "pioneer-ngs-plr", "title": "ngs_library_prep (Illumina library prep on Hamilton STARlet with PyLabRobot)", "doi": null, "paper_url": null, "year": null, "venue": null, "open_access_license": null, "code_url": "https://github.com/Pioneer-Research-Labs/ngs_library_prep", "code_files": ["methods/startup.py"], "code_license": "none", "stars": 12, "last_push": "2026-04-02", "robot_platform": "hamilton", "api": "pylabrobot", "protocol_category": "NGS library prep", "results_evidence": null, "wet_lab_validated": "unknown", "duplicate_of_existing": "pioneer-ngs", "readiness": "partial", "readiness_reason": "Already in corpus (pioneer-ngs); no paper, no license.", "est_tasks": 0, "source_agent": "github", "found_by": ["github"]}
+{"id": "proxy-viscometer-dup", "title": "Opentrons for automated and high-throughput viscometry (supplementary protocol files)", "doi": "10.1039/d2dd00126h", "paper_url": "https://doi.org/10.1039/d2dd00126h", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Kedar-Materials-by-Design-Lab/Opentrons-ProxyViscometer", "code_files": ["(protocol files for proxy viscometer; see also beatricesoh/OTProxyViscometer)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscosity measurement by timed aspiration", "results_evidence": "Measured viscosities correlated with reference rheometer values.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Duplicate of proxy-viscometer; a second mirror repo (beatricesoh/OTProxyViscometer) exists with the same content.", "duplicate_of_existing": "proxy-viscometer", "est_tasks": 0, "source_agent": "web", "found_by": ["github", "web"]}
+{"id": "pylabrobot-paper", "title": "PyLabRobot: An Open-Source, Hardware Agnostic Interface for Liquid-Handling Robots and Accessories", "doi": "10.1101/2023.07.10.547733", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10369895/", "year": 2023, "venue": "bioRxiv : the preprint server for biology", "open_access_license": "cc-by (bioRxiv, verify)", "code_url": "https://github.com/PyLabRobot/pylabrobot", "code_files": ["(library; demos in rickwierenga/plr-game-of-life, pylabrobot-art-studio)"], "code_license": "MIT", "robot_platform": "pylabrobot", "api": "pylabrobot", "protocol_category": "hardware-agnostic liquid-handling interface (Hamilton STAR, Tecan EVO, OT-2)", "results_evidence": "Validated via unit tests and application demos (browser simulator, position calibration, path teaching); no biological assay results.", "wet_lab_validated": false, "duplicate_of_existing": "covered by PyLabRobot/LH agents", "readiness": "partial", "readiness_reason": "MIT library with simulator, useful as an execution backend for PLR tasks but no paper-specific wet-lab protocol to reproduce.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_1j8eO8dsJWaiiSG8DhA3CmhWjU8"], "found_by": ["amass", "nonlh"]}
+{"id": "uc2-esp", "title": "UC2-ESP: A general-purpose framework for open-source microscopy control", "doi": "10.1111/jmi.70147", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.70147", "year": 2026, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://github.com/openUC2/UC2-REST", "code_files": ["uc2rest/ (Python REST client)", "ESP32 firmware (youseetoo/uc2-esp32)"], "code_license": "(LICENSE present, unrecognised)", "language": "Python/C++", "hardware": ["UC2 modular microscope", "ESP32 motors/LEDs"], "domain": "biology", "task_type": "imaging", "results_evidence": "Firmware/REST control demonstrated across UC2 microscope builds.", "wet_lab_validated": true, "simulatable": "partial: REST client mockable; firmware needs ESP32", "duplicate_of_existing": "uc2-hi2 (same UC2 ecosystem, different paper)", "readiness": "partial", "readiness_reason": "Close to existing uc2-hi2 entry.", "est_tasks": 1, "source_agent": "nonlh", "found_by": ["nonlh"]}
+{"id": "uc2-platereader-dup", "title": "UC2 Opentrons imaging unit / automated immunostaining (OT-2 + UC2 microscope)", "doi": null, "paper_url": "https://www.protocols.io/view/uc2-automated-immunostaining-protocol-using-the-op-bw8dphs6", "year": 2022, "venue": "protocols.io + openUC2 docs", "open_access_license": "CC BY 4.0 (protocols.io)", "code_url": "https://github.com/beniroquai/Opentrons-Microscope-Platereader", "code_files": ["IMJOY/main_opentrons.py"], "code_license": "NOASSERTION", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated immunostaining with in-situ imaging", "results_evidence": "Immunostained plates imaged on the UC2 microscope with staining quality shown in the protocol record.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already covered by uc2-hi2; the protocols.io immunostaining entry is a CC BY NL source that could still be paired with the control script.", "duplicate_of_existing": "uc2-hi2", "est_tasks": 2, "source_agent": "web", "found_by": ["web"]}
+{"id": "y1h-yeast-lap", "title": "Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast", "doi": "10.1002/cpz1.70059", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11580771/", "year": 2024, "venue": "Current protocols", "open_access_license": "cc-by (Current Protocols OA, verify)", "code_url": "https://github.com/BiocomputationLab/LAPrepository", "code_files": ["LAPEntries/LAP-PCR-OT2-2.0.0/ScriptPCR_v200.py", "LAPEntries/LAP-PCR-OT2-1.0.0/ScriptPCR.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-2.0.0/CounterSelectionScript_v200.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.0.0/CounterSelectionScript.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.0.0/ScriptPlateGenerationAndIncubation_v200.py", "LAPEntries/LAP-CellMediaInoculation-OT2-1.0.0/ScriptPlateGenerationAndIncubation.py", "LAPEntries/LAP-MoCloAssembly-OT2-2.0.0/ScriptMoCloConstructAssembly_v200.py", "LAPEntries/LAP-MoCloAssembly-OT2-1.0.1/ScriptMoCloConstructAssembly_v101.py", "LAPEntries/LAP-CellMediaInoculation-OT2-2.0.0/ScriptPlateGenerationAndIncubation_v200.py", "LAPEntries/LAP-MoCloAssembly-OT2-1.0.0/ScriptMoCloConstructAssembly.py", "LAPEntries/LAP-CustomReagentMixingMultiSinglePip-OT2-1.0.0/ScriptMixingReagents_v100.py", "LAPEntries/LAP-ColonyCounterSelection-OT2-1.1.0/CounterSelectionScript_v110.py", "LAPEntries/LAP-NplateMerging-OT2-2.0.0/ScriptMergePlates_v200.py", "LAPEntries/LAP-NplateMerging-OT2-1.0.0/ScriptMergePlates.py", "SetFunctions/define_tiprack.py", "SetFunctions/check_tip_and_pick.py", "SetFunctions/setting_labware.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "yeast transformation / arrayed library inoculation (Y1H screening)", "results_evidence": "Robotized yeast one-hybrid workflow for screening arrayed Arabidopsis TF libraries against promoter fragment baits (interaction readouts reported).", "wet_lab_validated": true, "duplicate_of_existing": "lap-transposon-genotyping (same LAPrepository code repo; different paper)", "readiness": "partial", "readiness_reason": "Uses LAP-CellMediaInoculation-OT2 scripts (apiLevel) driven by Excel variables files; repo has no license file; repo already in corpus via lap-transposon-genotyping.", "est_tasks": 2, "source_agent": "amass", "amass_ids": ["AMBC_3uwG18vtShB9zqOfI0Cku0a0czs"], "found_by": ["amass"]}
+{"id": "dup-actinomation", "title": "ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp", "doi": "10.1016/j.synbio.2025.03.005", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11999424/", "year": 2025, "venue": "Synthetic and systems biotechnology", "open_access_license": "see corpus", "code_url": "https://github.com/kedar", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "actinomation", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'actinomation'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_77MocSkO1RbfRmv3jKNi1ab0MCj"], "found_by": ["amass"]}
+{"id": "dup-assemblytron", "title": "AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots", "doi": "10.1093/synbio/ysac032", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9832943/", "year": 2022, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "see corpus", "code_url": "http://doi.org/10.5281/zenodo.7250273", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "assemblytron", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'assemblytron'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_8xuxgObx5ypgVt6sA0FbA54CFPd"], "found_by": ["amass"]}
+{"id": "dup-assemblytron-4220-7_8", "title": "Biofoundry-Assisted Golden Gate Cloning with AssemblyTron", "doi": "10.1007/978-1-0716-4220-7_8", "paper_url": "https://doi.org/10.1007/978-1-0716-4220-7_8", "year": 2025, "venue": "Methods in molecular biology (Clifton, N.J.)", "open_access_license": "see corpus", "code_url": "http://doi.org/10.5281/zenodo.7250273", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "assemblytron", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'assemblytron'; recorded for dedup, not a new candidate. (different DOI/version of the same work)", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_1JIgBBpQddQw7RVtolfypecj219"], "found_by": ["amass"]}
+{"id": "dup-auto-qpcr", "title": "Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data", "doi": "10.1038/s41598-021-99727-6", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8556264/", "year": 2021, "venue": "Scientific reports", "open_access_license": "see corpus", "code_url": "https://github.com/neuroeddu/auto-qpcr", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "auto-qpcr", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'auto-qpcr'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Qo3BjINV5mV7gE8itVvQtlwh8Co"], "found_by": ["amass"]}
+{"id": "dup-covid-diagnostic-capacity-2021", "title": "Optimization and adaptation of the diagnostic capacity for the performance of large volumes of SARS-CoV-2 RT-PCR", "doi": "10.1016/j.eimc.2021.01.014", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7877244/", "year": 2021, "venue": "Enfermedades infecciosas y microbiologia clinica (English ed.)", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "covid-diagnostic-capacity-2021", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'covid-diagnostic-capacity-2021'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_OdVlxGttXtc1mrMiDYLJZWOV5oi"], "found_by": ["amass"]}
+{"id": "dup-covid-diagnostic-capacity-2022", "title": "Optimization and adaptation of the diagnostic capacity for the performance of large volumes of SARS-CoV-2 RT-PCR", "doi": "10.1016/j.eimce.2022.05.001", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9127703/", "year": 2022, "venue": "Enfermedades infecciosas y microbiologia clinica (English ed.)", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "covid-diagnostic-capacity-2022", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'covid-diagnostic-capacity-2022'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_S5GHvIO0WeJq52cLQHfWVJVzhqy"], "found_by": ["amass"]}
+{"id": "dup-dna-bot", "title": "DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology", "doi": "10.1093/synbio/ysaa010", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7476404/", "year": 2020, "venue": "Synthetic biology (Oxford, England)", "open_access_license": "see corpus", "code_url": "https://github.com/basic-dna-assembly/dna-bot/tree/oup_synbio", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "dna-bot", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'dna-bot'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_NmKFNEvS0wjBcYrMLAmr2nphJLQ"], "found_by": ["amass"]}
+{"id": "dup-ht-mic", "title": "Development of a high-throughput minimum inhibitory concentration (HT-MIC) testing workflow", "doi": "10.3389/fmicb.2023.1079033", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10249070/", "year": 2023, "venue": "Frontiers in microbiology", "open_access_license": "see corpus", "code_url": "https://github.com/suman921/ht-mic", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "ht-mic", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'ht-mic'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_PlvV7JLJokbyIWF5oxnNLHphr3S"], "found_by": ["amass"]}
+{"id": "dup-infectious-disease-diagnostic-workflow", "title": "An Automated Versatile Diagnostic Workflow for Infectious Disease Detection in Low-Resource Settings", "doi": "10.3390/mi15060708", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11205418/", "year": 2024, "venue": "Micromachines", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "infectious-disease-diagnostic-workflow", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'infectious-disease-diagnostic-workflow'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_4Jr7X2fDzRWReAtldmDVqGS5JKk"], "found_by": ["amass"]}
+{"id": "dup-low-cost-pipetting-robot-slas", "title": "Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling", "doi": "10.1177/2472630320973591", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8143861/", "year": 2020, "venue": "SLAS technology", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "low-cost-pipetting-robot-slas", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'low-cost-pipetting-robot-slas'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_Etubiyg36H4b1fVLvDugE61OFbs"], "found_by": ["amass"]}
+{"id": "dup-maldi-surface-throughput", "title": "Customized Surface Design to Increase Throughput of Ambient Ionization Mass Spectrometry Lipidomics", "doi": "10.1021/jasms.3c00062", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12765230/", "year": 2023, "venue": "Journal of the American Society for Mass Spectrometry", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "maldi-surface-throughput", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'maldi-surface-throughput'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_TQC6jMfNFzVQSd7e84TLXQxW8OF"], "found_by": ["amass"]}
+{"id": "dup-personal-pipetting-robots", "title": "Open-source personal pipetting robots with live-cell incubation and microscopy compatibility", "doi": "10.1038/s41467-022-30643-7", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9151679/", "year": 2022, "venue": "Nature communications", "open_access_license": "see corpus", "code_url": "https://github.com/csdgroup/phil", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "personal-pipetting-robots", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'personal-pipetting-robots'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_EUHMTk0r9F4O02hzFCYQA7Ed61h"], "found_by": ["amass"]}
+{"id": "dup-pipette-tool-change", "title": "Leveraging flexible pipette-based tool changes to transform liquid handling systems into dual-function sample preparation and imaging platforms", "doi": "10.1016/j.ohx.2025.e00653", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12181777/", "year": 2025, "venue": "HardwareX", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "pipette-tool-change", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'pipette-tool-change'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_BdogUnnIJ6d8G6DQNcIfOnauaqO"], "found_by": ["amass"]}
+{"id": "dup-pipetting-speed-ot2", "title": "Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq", "doi": "10.17912/micropub.biology.001566", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12117386/", "year": 2025, "venue": "microPublication biology", "open_access_license": "see corpus", "code_url": "https://github.com/bioinfo-tsukuba/ot2_pipspd_paper", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "pipetting-speed-ot2", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'pipetting-speed-ot2'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_RGU4qmDzfSwSXHM42J56x3dqbUw"], "found_by": ["amass"]}
+{"id": "dup-polymerisation-kinetics-robot", "title": "A robotic approach to polymerisation kinetics: a case study on copolymerisation parameter estimation", "doi": "10.1039/d6sc02232d", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13103962/", "year": 2026, "venue": "Chemical science", "open_access_license": "see corpus", "code_url": "https://github.com/prdmonash/a-robotic-approach-to-polymerization-kinetics-a-case-study-on-copolymerization-parameter-estimation", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "polymerisation-kinetics-robot", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'polymerisation-kinetics-robot'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_M8z99yDb5EkvjYFzUescLig11w1"], "found_by": ["amass"]}
+{"id": "dup-protein-crystallization-ot2", "title": "Automation of protein crystallization scaleup via Opentrons-2 liquid handling", "doi": "10.1016/j.slast.2025.100268", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12229254/", "year": 2025, "venue": "SLAS technology", "open_access_license": "see corpus", "code_url": "https://github.com/jbderoo/opentrons2-protein-crystallization", "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "protein-crystallization-ot2", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'protein-crystallization-ot2'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CDkn5snHqKQ1YO4dNo8xoEuxSfN"], "found_by": ["amass"]}
+{"id": "dup-proteomics-digestion-workflow", "title": "Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics", "doi": "10.1016/j.mcpro.2024.100790", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11251069/", "year": 2024, "venue": "Molecular & cellular proteomics : MCP", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "proteomics-digestion-workflow", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'proteomics-digestion-workflow'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_DJEOKs7MNxMyVNZAFpE6NioOj4"], "found_by": ["amass"]}
+{"id": "dup-sars-cov-2-magbead-extraction", "title": "SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP", "doi": "10.3390/v12080863", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7472728/", "year": 2020, "venue": "Viruses", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "sars-cov-2-magbead-extraction", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'sars-cov-2-magbead-extraction'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_CCNZbFA2sV6RQLfqeerWgwiVdHB"], "found_by": ["amass"]}
+{"id": "dup-sars-cov-2-rtqpcr-jove", "title": "Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots", "doi": "10.3791/63395", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9199378/", "year": 2022, "venue": "Journal of visualized experiments : JoVE", "open_access_license": "see corpus", "code_url": null, "code_files": [], "code_license": "see corpus", "robot_platform": null, "api": null, "protocol_category": "(already in corpus)", "results_evidence": "See corpus entry.", "wet_lab_validated": null, "duplicate_of_existing": "sars-cov-2-rtqpcr-jove", "readiness": "no", "readiness_reason": "Duplicate of existing corpus paper 'sars-cov-2-rtqpcr-jove'; recorded for dedup, not a new candidate.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_DZyA4PnsIe8DnhiCvLzdcTnLAds"], "found_by": ["amass"]}
+{"id": "facs-automation", "title": "An open-source FACS automation system for high-throughput cell biology", "doi": "10.1371/journal.pone.0299402", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10956866/", "year": 2024, "venue": "PloS one", "open_access_license": "cc-by", "code_url": "https://github.com/czbiohub-sf/2023-facs-automation-pub", "code_files": [], "code_license": "BSD", "robot_platform": "other", "api": "other", "protocol_category": "FACS sample handling and autonomous sorting/gating", "results_evidence": "Walkaway sequential FACS of many samples with algorithmic gating; reduced operator variation and hands-on time (sort purity/yield reported).", "wet_lab_validated": true, "duplicate_of_existing": "opencell-automation (same CZ Biohub group, separate paper)", "readiness": "no", "readiness_reason": "Python GUI-automation of instrument software and Hamilton/robot arm integration; no liquid-handling protocol file.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_2ng2mytae0v23coWE16OdsGd9pR"], "found_by": ["amass"]}
+{"id": "modular-pipetting-imaging-uc2", "title": "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications", "doi": "10.1002/adbi.202101063", "paper_url": "https://doi.org/10.1002/adbi.202101063", "year": 2021, "venue": "Advanced biology", "open_access_license": "unknown", "code_url": null, "code_files": [], "code_license": "n/a (no repo)", "robot_platform": "ot2", "api": "other", "protocol_category": "automated sample prep + imaging (Opentrons + OpenFlexure/UC2/ImJoy)", "results_evidence": "Demonstrated automated pipetting-imaging feedback pipeline with low-cost microscopes.", "wet_lab_validated": true, "duplicate_of_existing": "uc2-hi2 (related openUC2 group; different paper)", "readiness": "no", "readiness_reason": "Code not verified via Amass text; paywalled.", "est_tasks": 1, "source_agent": "amass", "amass_ids": ["AMBC_DSCQ9BbNl9zmxKKsvmsPTC2Tvdi"], "found_by": ["amass"]}
+{"id": "oscar-ur-arm", "title": "OSCAR: A Modular Open-Source Robotic Platform for Biological Laboratories", "doi": "10.1021/acssynbio.5c00733", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13010791/", "year": 2026, "venue": "ACS synthetic biology", "open_access_license": "cc-by (PMC OA, verify)", "code_url": "https://github.com/rodrigue-laboratory/oscar", "code_files": [], "code_license": "BSD (oscar_task)", "robot_platform": "other", "api": "other", "protocol_category": "robot-arm pipetting of plasmid assembly workflow (PCR, assembly, transformation)", "results_evidence": "OSCAR executed a representative plasmid assembly workflow from PCR through enzymatic assembly and transformation using human lab equipment.", "wet_lab_validated": true, "duplicate_of_existing": "pipette-tool-change (same Rodrigue lab pipette tool)", "readiness": "no", "readiness_reason": "ROS/C++ MoveIt task code for a UR arm; not a liquid-handler protocol API.", "est_tasks": 0, "source_agent": "amass", "amass_ids": ["AMBC_7CMiao3MoyrlOaW8MxiwS5SEj8j"], "found_by": ["amass"]}
diff --git a/research/expansion/nonlh_candidates.jsonl b/research/expansion/nonlh_candidates.jsonl
new file mode 100644
index 0000000..fef1bce
--- /dev/null
+++ b/research/expansion/nonlh_candidates.jsonl
@@ -0,0 +1,82 @@
+{"id": "wei-science-factory", "title": "Towards a modular architecture for science factories (WEI; color-picker + PCR workcells)", "doi": "10.1039/D3DD00142C", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00142c", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/AD-SDL/rpl_wei", "code_files": ["src/wei/core/workflow.py", "src/wei/core/experiment.py", "src/wei/core/interfaces/simulate_interface.py", "src/wei/core/interfaces/ros2_interface.py"], "code_license": "MIT", "language": "Python", "hardware": ["Brooks PF400", "Hudson PlateCrane/Sciclops", "Opentrons OT-2", "A4S sealer", "Brooks peeler", "Bio-Rad thermocycler", "Camera"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Executed closed-loop color-matching and PCR workflows on the ANL RPL workcell with reported timing/throughput and color-error convergence.", "wet_lab_validated": true, "simulatable": "true: built-in simulate_interface lets YAML workflows run with no hardware", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Open paper, MIT code, YAML workflow + module specs run in simulate mode; tasks can be 'methods -> WEI workflow YAML' graded against module/action sequence.", "est_tasks": 6, "source_agent": "nonlh"}
+{"id": "madsci-ad-sdl", "title": "MADSci: A modular Python-based framework to enable autonomous science", "doi": "10.21105/joss.09416", "paper_url": "https://doi.org/10.21105/joss.09416", "year": 2026, "venue": "Journal of Open Source Software", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/AD-SDL/MADSci", "code_files": ["examples/example_experiment.py", "examples/example_lab/compose.yaml", "examples/example_lab/example_modules/liquidhandler.py"], "code_license": "MIT", "language": "Python", "hardware": ["Brooks PF400", "OT-2/Flex", "plate readers", "sealers", "thermocyclers"], "domain": "other", "task_type": "scheduling", "results_evidence": "Framework; experiments reported via ANL RPL deployments but no single peer-reviewed results paper verified.", "wet_lab_validated": false, "simulatable": "true: example_lab ships virtual example modules via docker compose", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "JOSS software paper (no wet-lab results paper of its own); simulatable example lab makes it a good execution substrate for WEI/RPL-derived tasks.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "ad-sdl-pf400-module", "title": "AD-SDL PF400 / PlateCrane / Sciclops module drivers (WEI workcell modules)", "doi": "10.1039/D3DD00142C", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00142c", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/AD-SDL/pf400_module", "code_files": ["src/pf400_interface/pf400.py", "src/pf400_rest_node.py", "(hudson_platecrane_module) src/platecrane_driver/platecrane_driver.py", "(sciclops_module) src/sciclops_interface.py"], "code_license": "MIT", "language": "Python", "hardware": ["Brooks PF400", "Hudson PlateCrane EX", "Hudson Sciclops"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Same experiments as WEI paper (plate moves between OT-2, sealer, thermocycler, camera).", "wet_lab_validated": true, "simulatable": "partial: TCP drivers need hardware; must be stubbed (WEI simulate mode bypasses them)", "duplicate_of_existing": "glas-preciseflex (related PF400 driver; different repo)", "readiness": "partial", "readiness_reason": "Overlaps glas-preciseflex style PF400 control; low-level TCP command strings need a mock server for grading.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "polybot-pedot", "title": "Autonomous platform for solution processing of electronic polymers (Polybot)", "doi": "10.1038/s41467-024-55655-3", "paper_url": "https://www.nature.com/articles/s41467-024-55655-3", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/polybot-nexus/PEDOT_PSS_supporting_data", "code_files": ["*.ipynb (analysis only)"], "code_license": "MIT", "language": "Python", "hardware": ["Chemspeed", "UR5e", "N9 robot", "film coater", "annealing", "probe station", "camera"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Autonomously optimised PEDOT:PSS film conductivity/defects over closed-loop campaigns; conductivities reported.", "wet_lab_validated": true, "simulatable": "false: only analysis notebooks released; orchestration code not public", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Results + data public but robot orchestration (Polybot/WEI) not released for this paper.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "chemos-2020", "title": "ChemOS: An orchestration software to democratize autonomous discovery", "doi": "10.1371/journal.pone.0229862", "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229862", "year": 2020, "venue": "PLoS ONE", "open_access_license": "CC BY", "code_url": "https://github.com/aspuru-guzik-group/ChemOS", "code_files": ["Experiments/_dummy_dump/", "DatabaseManager/interfaces.py", "Communicator/"], "code_license": "Apache-2.0", "language": "Python", "hardware": ["robotic bartender (barmixvah)", "HPLC (in demos)"], "domain": "chemistry", "task_type": "scheduling", "results_evidence": "Demonstrates closed-loop optimisation on a cocktail-mixing robot and HPLC calibration, with reported optimisation traces.", "wet_lab_validated": true, "simulatable": "partial: dummy experiment folders; py2-era code, needs revival", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Old code (pyc, Python2-era); grading via dummy instrument possible but setup heavy.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "chemos2-atlas", "title": "Atlas: a brain for self-driving laboratories (BO library used in ChemOS 2.0 campaigns)", "doi": "10.1039/D4DD00115J", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d4dd00115j", "year": 2025, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/aspuru-guzik-group/atlas", "code_files": ["src/atlas/planners/", "examples/"], "code_license": "MIT", "language": "Python", "hardware": [], "domain": "chemistry", "task_type": "other", "results_evidence": "BO planners benchmarked on emulators and deployed on SDL campaigns (e.g., electrochemistry with ChemOS 2.0).", "wet_lab_validated": true, "simulatable": "true: pure software, Olympus emulators", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Planner library only; hardware-free but task would be optimisation config, not lab-automation code.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "baybe", "title": "BayBE: Bayesian Back End for design of experiments", "doi": "10.1039/D5DD00050E", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d5dd00050e", "year": 2025, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/emdgroup/baybe", "code_files": ["baybe/campaign.py", "examples/"], "code_license": "Apache-2.0", "language": "Python", "hardware": [], "domain": "chemistry", "task_type": "other", "results_evidence": "Campaign API with benchmarks; industrial case studies reported, few with released wet-lab data.", "wet_lab_validated": false, "simulatable": "true: pure software", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Not hardware-automation code; only adjunct planner.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "coscientist", "title": "Autonomous chemical research with large language models (Coscientist)", "doi": "10.1038/s41586-023-06792-0", "paper_url": "https://www.nature.com/articles/s41586-023-06792-0", "year": 2023, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://github.com/gomesgroup/coscientist", "code_files": ["simple_implementation/coscientist.py", "simple_implementation/tools.py", "simple_implementation/run.py"], "code_license": "(LICENSE present, unrecognised text)", "language": "Python", "hardware": ["Opentrons OT-2", "Emerald Cloud Lab", "UV-Vis plate reader (via OT-2/heater-shaker)", "Heater-shaker"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Suzuki/Sonogashira couplings executed and confirmed by GC-MS; plate-reader colour tasks executed.", "wet_lab_validated": true, "simulatable": "partial: OT-2 simulate for LH parts; ECL SLL steps not simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Heavily overlaps LH (OT-2); non-LH element is ECL cloud-lab and plate-reader calls; released code is a reduced implementation.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "chemcrow", "title": "Augmenting large language models with chemistry tools (ChemCrow)", "doi": "10.1038/s42256-024-00832-8", "paper_url": "https://www.nature.com/articles/s42256-024-00832-8", "year": 2024, "venue": "Nature Machine Intelligence", "open_access_license": "CC BY", "code_url": "https://github.com/ur-whitelab/chemcrow-public", "code_files": ["chemcrow/agents/", "chemcrow/tools/rxn4chem.py", "(chemcrow-runs) notebooks"], "code_license": "MIT", "language": "Python", "hardware": ["IBM RoboRXN cloud synthesis platform"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Executed syntheses of DEET and three thioureas plus a chromophore on RoboRXN, with characterisation.", "wet_lab_validated": true, "simulatable": "false: RoboRXN cloud API required (no simulator)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Execution is via proprietary cloud API; could grade generated RXN action sequences offline.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "clairify-xdl", "title": "Large language models for chemistry robotics (CLAIRify: NL -> XDL)", "doi": "10.1007/s10514-023-10136-2", "paper_url": "https://link.springer.com/article/10.1007/s10514-023-10136-2", "year": 2023, "venue": "Autonomous Robots", "open_access_license": "CC BY", "code_url": "https://github.com/ac-rad/xdl-generation", "code_files": ["xdlgenerator/nlp2xdl.py", "web-interface/verify.py", "dataset/ (chem-eval .txt protocols)"], "code_license": "MIT", "language": "Python", "hardware": ["Franka Panda", "Chemputer (via XDL)"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Generated XDL executed on a Franka robot for solubility/recrystallisation; expert-evaluated XDL validity on 108 protocols.", "wet_lab_validated": true, "simulatable": "true: XDL verifier (syntax/static checks) runs offline; robot execution via simulation", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Directly a 'methods text -> XDL' task with a bundled verifier and ~100 protocol texts; MIT.", "est_tasks": 10, "source_agent": "nonlh"}
+{"id": "organa", "title": "ORGANA: a robotic assistant for automated chemistry experimentation and characterization", "doi": "10.1016/j.matt.2024.10.015", "paper_url": "https://arxiv.org/abs/2401.06949", "year": 2025, "venue": "Matter (arXiv 2401.06949)", "open_access_license": "arXiv non-exclusive / journal TBD", "code_url": "https://github.com/ac-rad/organa", "code_files": ["clairify/xdlgenerator/nlp2xdl.py", "moveit_pddlstream/xdl_parse.py", "output/plan_*.xdl"], "code_license": "none", "language": "Python", "hardware": ["Franka Panda", "pH meter", "electrochemistry potentiostat", "camera", "Isaac Sim digital twin"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Solubility, pH, recrystallisation and electrochemistry (quinone) experiments executed with reported user-study times and measured values.", "wet_lab_validated": true, "simulatable": "partial: XDL plans + PDDLStream/MoveIt planning simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence on repo; XDL plans gradeable, robot layer needs ROS/MoveIt.", "est_tasks": 4, "source_agent": "nonlh"}
+{"id": "chemputer-acra", "title": "Verification and execution of the scientific literature via chemputation augmented by large language models", "doi": "10.1038/s42004-026-01993-w", "paper_url": "https://www.nature.com/articles/s42004-026-01993-w", "year": 2026, "venue": "Communications Chemistry", "open_access_license": "CC BY", "code_url": "https://github.com/croningp/acra", "code_files": ["acra/agents/agents/xdl_generator.py", "acra/agents/prompts/xdl_prompt.py", "acra/data/xdls/CHEMIFY-*.xdl"], "code_license": "(LICENSE present, unrecognised text)", "language": "Python / XDL", "hardware": ["Chemputer"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "LLM-generated XDL from literature procedures executed on the Chemputer with yields reported; >100 reference XDLs released.", "wet_lab_validated": true, "simulatable": "true: chemputer XDL compiles/simulates against a graph (xdl dry-run)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Ready-made literature->XDL pairs with executed results; check licence text before vendoring.", "est_tasks": 15, "source_agent": "nonlh"}
+{"id": "chemputer-blueprints", "title": "Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer", "doi": "10.1038/s41467-024-54238-6", "paper_url": "https://www.nature.com/articles/s41467-024-54238-6", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://gitlab.com/croningroup/chemputer/xdl", "code_files": ["xdl v2.0.0 (blueprints)", "SI XDL files"], "code_license": "see GitLab (unverified)", "language": "Python / XDL", "hardware": ["Chemputer"], "domain": "chemistry", "task_type": "protocol_language", "results_evidence": "Parallel chiral syntheses executed with reported yields/ee using XDL blueprints.", "wet_lab_validated": true, "simulatable": "true: XDL 2.0 compile + simulate mode", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "XDL procedures in SI map to methods text; xdl package supports simulation without hardware.", "est_tasks": 4, "source_agent": "nonlh"}
+{"id": "chemputer-peptide", "title": "Universal peptide synthesis via solid-phase methods fused with chemputation", "doi": "10.1038/s41467-025-62344-2", "paper_url": "https://www.nature.com/articles/s41467-025-62344-2", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.15948769", "code_files": ["Zenodo XDL archive"], "code_license": "Zenodo (check)", "language": "XDL", "hardware": ["Chemputer", "SPPS module"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Synthesised multiple peptides (incl. semaglutide-type) with purity/yield reported.", "wet_lab_validated": true, "simulatable": "true: XDL simulation", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "XDL in Zenodo + methods text; good protocol_language tasks.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "chemputer-modules-acscs", "title": "Robotic Modules for the Programmable Chemputation of Molecules and Materials", "doi": "10.1021/acscentsci.3c00304", "paper_url": "https://pubs.acs.org/doi/10.1021/acscentsci.3c00304", "year": 2023, "venue": "ACS Central Science", "open_access_license": "CC BY", "code_url": "https://gitlab.com/croningroup/chemputer", "code_files": ["SI XDL/graph files"], "code_license": "unverified", "language": "XDL", "hardware": ["Chemputer modules"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Several syntheses executed on new modules with yields reported.", "wet_lab_validated": true, "simulatable": "true: XDL simulation", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Code link not in full text; relies on SI.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "mobile-robots-dai-2024", "title": "Autonomous mobile robots for exploratory synthetic chemistry", "doi": "10.1038/s41586-024-08173-7", "paper_url": "https://www.nature.com/articles/s41586-024-08173-7", "year": 2024, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.11174257", "code_files": ["Zenodo: workflow + decision-maker code, Chemspeed scripts, robot ROS code (several records)"], "code_license": "Zenodo (check per record)", "language": "Python", "hardware": ["KUKA KMR iiwa mobile robots", "Chemspeed ISynth", "UPLC-MS", "benchtop NMR"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "Supramolecular/structural diversification chemistry run autonomously with UPLC-MS/NMR-based decisions; hits reported.", "wet_lab_validated": true, "simulatable": "partial: decision-maker runs on released data; robot/ROS code needs hardware or Gazebo stub", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Strong triple; Zenodo code bundle sizeable; grading via decision logic or workflow script structure.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "evolver-2018", "title": "Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER", "doi": "10.1038/nbt.4151", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035058/", "year": 2018, "venue": "Nature Biotechnology", "open_access_license": "author manuscript (PMC); journal paywalled", "code_url": "https://github.com/FYNCH-BIO/dpu", "code_files": ["experiment/template/eVOLVER.py", "experiment/template/custom_script.py", "(FYNCH-BIO/evolver) evolver/evolver.py server"], "code_license": "MIT", "language": "Python", "hardware": ["eVOLVER continuous-culture array (16 vials)", "OD/temp sensors", "peristaltic pumps"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Turbidostat/chemostat growth curves and selection experiments across 16 vials reported with fitness measurements.", "wet_lab_validated": true, "simulatable": "partial: custom_script.py control loop is pure Python over OD arrays; can be driven by a fake socket server/replayed OD logs", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT; turbidostat/chemostat control functions are small and gradeable by replaying OD traces to check pump commands; paper PDF is PMC author manuscript.", "est_tasks": 5, "source_agent": "nonlh"}
+{"id": "evolver-ddr-elife", "title": "Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community (eVOLVER)", "doi": "10.7554/eLife.67175", "paper_url": "https://elifesciences.org/articles/67175", "year": 2021, "venue": "eLife", "open_access_license": "CC BY", "code_url": "https://github.com/khalillab/DDR-eVOLVER-model", "code_files": ["*.ipynb (model)", "DPU custom_script variants in SI (unverified)"], "code_license": "MIT", "language": "Python", "hardware": ["eVOLVER"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Fluctuating dilution regimes run on eVOLVER with community composition measured by sequencing.", "wet_lab_validated": true, "simulatable": "partial: eVOLVER custom_script logic replayable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Released repo is the model, not the eVOLVER control script; would need reconstructing the dilution program from methods.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "chibio-2020", "title": "In situ characterisation and manipulation of biological systems with Chi.Bio", "doi": "10.1371/journal.pbio.3000794", "paper_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000794", "year": 2020, "venue": "PLoS Biology", "open_access_license": "CC BY", "code_url": "https://github.com/HarrisonSteel/ChiBio", "code_files": ["app.py (single-file Flask controller incl. turbidostat, optogenetics, custom programs)"], "code_license": "none (no LICENSE file)", "language": "Python", "hardware": ["Chi.Bio reactors (BeagleBone)", "LEDs", "spectrometer", "pumps"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Turbidostat growth, optogenetic feedback control and fluorescence measurements demonstrated with reported traces.", "wet_lab_validated": true, "simulatable": "partial: hardware I2C calls must be stubbed; control functions (Turbidostat, CustomProgram) are pure logic", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence on code; single large app.py; otherwise excellent methods->control-program tasks.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "chibio-cocultures-evotron", "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback", "doi": "10.1038/s41467-022-32392-z", "paper_url": "https://www.nature.com/articles/s41467-022-32392-z", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/santkumar/evotron", "code_files": ["arduino/mega/main/main.ino", "evolver/software/ (modified eVOLVER)", "controller Python in Zenodo 10.5281/zenodo.6908131"], "code_license": "none", "language": "C++/Python", "hardware": ["custom eVOLVER/Chi.Bio-like bioreactors", "optogenetic LEDs", "OD/fluorescence sensors"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Closed-loop optogenetic control held E. coli co-culture ratios at setpoints over days; measured composition reported.", "wet_lab_validated": true, "simulatable": "partial: controller logic simulatable with a growth model; firmware needs hardware", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; mixed Arduino/Python; controller logic good grading target.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "reacsight", "title": "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight", "doi": "10.1038/s41467-022-31033-9", "paper_url": "https://www.nature.com/articles/s41467-022-31033-9", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.4776009", "code_files": ["Zenodo: ReacSight orchestration (Flask instrument servers, OT-2 sampling, cytometer driving)"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Chi.Bio/eVOLVER bioreactors", "Opentrons OT-2 (sampling robot)", "Guava flow cytometer"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Automated cytometry-based optogenetic control of yeast populations and co-cultures with reported dynamics.", "wet_lab_validated": true, "simulatable": "partial: instrument servers are HTTP; mockable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Combines bioreactor + cytometer scheduling; partial LH overlap (OT-2 sampler).", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "pioreactor", "title": "Pioreactor open-source bioreactor software (used in published studies)", "doi": null, "paper_url": "https://docs.pioreactor.com", "year": 2025, "venue": "software (no primary paper; cited in e.g. Microb Cell Fact 2025, Nature 2026)", "open_access_license": null, "code_url": "https://github.com/pioreactor/pioreactor", "code_files": ["core/pioreactor/automations/dosing/turbidostat.py", "core/pioreactor/actions/leader/experiment_profile.py", "experiment profile YAMLs"], "code_license": "MIT", "language": "Python", "hardware": ["Pioreactor 20/40 mL bioreactor (Raspberry Pi)"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "No first-party results paper; third-party papers (e.g., 10.1186/s12934-025-02670-8) use it for culture experiments.", "wet_lab_validated": false, "simulatable": "true: built-in testing/fake hardware mode (TESTING env var) runs automations without hardware", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Highly simulatable experiment-profile YAMLs, but no paper with its own released profile + results; could pair with a citing paper's methods.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "bio-spec-hardwarex", "title": "BIO-SPEC: An open-source bench-top parallel bioreactor system", "doi": "10.1016/j.ohx.2025.e00670", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067225000690", "year": 2025, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "see paper repository (OSF/Zenodo, not verified)", "code_files": [], "code_license": "CC BY (hardware, per HardwareX)", "language": "Python/Arduino", "hardware": ["parallel bioreactors", "OD sensor"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Validation growth experiments reported in HardwareX.", "wet_lab_validated": true, "simulatable": "false: firmware", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified; hardware-centric.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "photobioreactor-fluorescence", "title": "Integration of Fluorescence Spectroscopy into a Photobioreactor for the Monitoring of Cyanobacteria", "doi": "10.3390/bios15030128", "paper_url": "https://www.mdpi.com/2079-6374/15/3/128", "year": 2025, "venue": "Biosensors", "open_access_license": "CC BY", "code_url": "https://github.com/borjaggarcia/fluorescence-monitoring", "code_files": ["(not probed)"], "code_license": "unverified", "language": "Python", "hardware": ["Pioreactor-based photobioreactor", "spectrometer"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Cyanobacterial growth monitored by fluorescence with reported correlation to OD.", "wet_lab_validated": true, "simulatable": "partial: Pioreactor plugin runs in testing mode", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Small repo; licence unverified.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "pycromanager-2021", "title": "Pycro-Manager: open-source software for customized and reproducible microscope control", "doi": "10.1038/s41592-021-01087-6", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532176/", "year": 2021, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/micro-manager/pycro-manager", "code_files": ["pycromanager/acquisition/", "misc/examples/", "docs/source/*.ipynb (application notebooks)"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["Micro-Manager-controlled microscopes (cameras, stages, light sources)"], "domain": "biology", "task_type": "imaging", "results_evidence": "Applications in paper (adaptive illumination, light-sheet, high-throughput imaging) with acquired data.", "wet_lab_validated": true, "simulatable": "true: Micro-Manager Demo config (DemoCamera/DemoStage) via pymmcore / Java backend", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Demo hardware lets acquisition events be executed and checked (axes, positions, exposures, hooks).", "est_tasks": 5, "source_agent": "nonlh"}
+{"id": "pymmcore-plus-mda", "title": "pymmcore-plus + useq-schema (multi-dimensional acquisition engine)", "doi": null, "paper_url": "https://pymmcore-plus.github.io/pymmcore-plus/", "year": 2024, "venue": "software (used by Mantis/shrimPy and others)", "open_access_license": null, "code_url": "https://github.com/pymmcore-plus/pymmcore-plus", "code_files": ["examples/run_mda.py", "examples/event_driven_acquisition.py", "(useq-schema) src/useq/_mda_sequence.py"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["Micro-Manager devices"], "domain": "biology", "task_type": "imaging", "results_evidence": "Software; validated through downstream papers (e.g., Mantis PNAS Nexus 2024).", "wet_lab_validated": false, "simulatable": "true: loadSystemConfiguration() demo config, fully headless", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Best grading substrate for imaging tasks: MDASequence is declarative and comparable; pair with papers' imaging methods.", "est_tasks": 4, "source_agent": "nonlh"}
+{"id": "mantis-shrimpy", "title": "Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells", "doi": "10.1093/pnasnexus/pgae323", "paper_url": "https://academic.oup.com/pnasnexus/article/3/9/pgae323/7742297", "year": 2024, "venue": "PNAS Nexus", "open_access_license": "CC BY-NC", "code_url": "https://github.com/czbiohub-sf/shrimPy", "code_files": ["archive/pycromanager/acquisition_settings/*.yaml", "archive/pycromanager/cli/run_acquisition.py", "mantis acquisition engine"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["custom light-sheet + label-free microscope", "Micro-Manager stages/cameras"], "domain": "biology", "task_type": "imaging", "results_evidence": "Multi-well 4D imaging of cell lines acquired and analysed with reported throughput.", "wet_lab_validated": true, "simulatable": "true: demo acquisition settings YAML + Micro-Manager demo config", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Acquisition settings YAMLs map directly to methods text; demo config enables dry-run.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "navigate-2024", "title": "Navigate: an open-source platform for smart light-sheet microscopy", "doi": "10.1038/s41592-024-02413-4", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540721/", "year": 2024, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/TheDeanLab/navigate", "code_files": ["src/navigate/controller/controller.py", "src/navigate/model/features/ (feature lists = smart acquisition programs)", "config/configuration.yaml (synthetic hardware)"], "code_license": "BSD-style (LICENSE.md)", "language": "Python", "hardware": ["light-sheet microscopes (ASLM, OPM)", "stages", "cameras", "galvos"], "domain": "biology", "task_type": "imaging", "results_evidence": "Smart acquisition (autofocus, tiling, decision-based imaging) demonstrated on multiple microscopes with images.", "wet_lab_validated": true, "simulatable": "true: ships 'synthetic' hardware devices for every device class", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Feature-list programs are a compact DSL; synthetic hardware enables execution-based grading.", "est_tasks": 4, "source_agent": "nonlh"}
+{"id": "eda-event-driven", "title": "Event-driven acquisition for content-enriched microscopy", "doi": "10.1038/s41592-022-01589-x", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613693/", "year": 2022, "venue": "Nature Methods", "open_access_license": "author manuscript (PMC, CC BY)", "code_url": "https://github.com/wl-stepp/eda_plugin", "code_files": ["eda_plugin/examples/main.py", "eda_plugin/examples/actuators.py", "eda_plugin/examples/interpreters.py", "(LEB-EPFL/EDA) analysis"], "code_license": "BSD-3-Clause", "language": "Python", "hardware": ["iSIM microscope", "Micro-Manager"], "domain": "biology", "task_type": "imaging", "results_evidence": "Adaptive frame-rate imaging of mitochondrial and bacterial division events with reported photobleaching reduction.", "wet_lab_validated": true, "simulatable": "true: Micro-Manager demo config + recorded data replay", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Feedback rule (interpreter thresholds -> frame rate) is checkable by replaying image streams.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "etsted", "title": "Event-triggered STED imaging", "doi": "10.1038/s41592-022-01588-y", "paper_url": "https://www.nature.com/articles/s41592-022-01588-y", "year": 2022, "venue": "Nature Methods", "open_access_license": "CC BY", "code_url": "https://github.com/jonatanalvelid/etSTED-widget", "code_files": ["EtSTEDController.py", "mockcamera.py", "analysis_pipelines/pipeline_fake.py"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["STED microscope", "ImSwitch"], "domain": "biology", "task_type": "imaging", "results_evidence": "Event-triggered STED of vesicle/synaptic events with reported detection rates.", "wet_lab_validated": true, "simulatable": "true: mockcamera + fake pipeline included", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Mock camera bundled; GPL limits vendoring but can be referenced.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "pysted", "title": "Development of AI-assisted microscopy frameworks through realistic simulation with pySTED", "doi": "10.1038/s42256-024-00903-w", "paper_url": "https://www.nature.com/articles/s42256-024-00903-w", "year": 2024, "venue": "Nature Machine Intelligence", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/FLClab/pySTED", "code_files": ["pysted/base.py", "(gym-sted) gym_sted/envs/"], "code_license": "CC (Attribution, check NC)", "language": "Python", "hardware": ["STED microscope (real validation)", "simulator"], "domain": "biology", "task_type": "imaging", "results_evidence": "RL policies trained in simulation were deployed on a real STED microscope with image quality reported.", "wet_lab_validated": true, "simulatable": "true: the code is a simulator (gym environment)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Simulator itself rather than lab-automation code; good as a grader for imaging-parameter tasks; NC licences.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "imswitch", "title": "ImSwitch: generalizing microscope control in Python", "doi": "10.21105/joss.03394", "paper_url": "https://joss.theoj.org/papers/10.21105/joss.03394", "year": 2021, "venue": "JOSS", "open_access_license": "CC BY", "code_url": "https://github.com/ImSwitch/ImSwitch", "code_files": ["imswitch/imcontrol/", "imswitch/_data/user_defaults/imcontrol_setups/example_virtual_microscope.json"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["many microscope devices"], "domain": "biology", "task_type": "imaging", "results_evidence": "Software paper; underpins etSTED and UC2 experiments.", "wet_lab_validated": false, "simulatable": "true: virtual microscope setup", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Software paper; results via downstream papers.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "uc2-esp", "title": "UC2-ESP: A general-purpose framework for open-source microscopy control", "doi": "10.1111/jmi.70147", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.70147", "year": 2026, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://github.com/openUC2/UC2-REST", "code_files": ["uc2rest/ (Python REST client)", "ESP32 firmware (youseetoo/uc2-esp32)"], "code_license": "(LICENSE present, unrecognised)", "language": "Python/C++", "hardware": ["UC2 modular microscope", "ESP32 motors/LEDs"], "domain": "biology", "task_type": "imaging", "results_evidence": "Firmware/REST control demonstrated across UC2 microscope builds.", "wet_lab_validated": true, "simulatable": "partial: REST client mockable; firmware needs ESP32", "duplicate_of_existing": "uc2-hi2 (same UC2 ecosystem, different paper)", "readiness": "partial", "readiness_reason": "Close to existing uc2-hi2 entry.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "openframe-openaf", "title": "openFrame: modular open microscopy platform with single-shot optical autofocus", "doi": "10.1111/jmi.13219", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13219", "year": 2023, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://github.com/ImperialCollegeLondon/openAF", "code_files": ["Java Micro-Manager plugin + Python scripts"], "code_license": "BSD", "language": "Java/Python", "hardware": ["openFrame microscope", "autofocus module"], "domain": "biology", "task_type": "imaging", "results_evidence": "Autofocus accuracy/stability characterised and used in HCA imaging.", "wet_lab_validated": true, "simulatable": "partial: Micro-Manager demo for plugin shell only", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Autofocus algorithm checkable on images; Java plugin.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "openflexure-autofocus", "title": "Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope", "doi": "10.1111/jmi.13064", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13064", "year": 2022, "venue": "Journal of Microscopy", "open_access_license": "CC BY", "code_url": "https://gitlab.com/openflexure/openflexure-microscope-server", "code_files": ["openflexure_microscope/api/default_extensions/autofocus.py", "scan extension"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["OpenFlexure Microscope", "Raspberry Pi camera", "Sangaboard stage"], "domain": "biology", "task_type": "imaging", "results_evidence": "Automated malaria blood-smear tiling scans with autofocus success rates reported.", "wet_lab_validated": true, "simulatable": "true: server has a simulation/mock camera+stage mode (dev)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "GitLab server includes mock hardware; scan/autofocus parameters gradeable.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "alabos-alab", "title": "AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories (A-Lab)", "doi": "10.1039/d4dd00129j", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/dd/d4dd00129j", "year": 2024, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://github.com/CederGroupHub/alab_management", "code_files": ["alab_management/builders/experimentbuilder.py", "examples/alab_example/alab_example/devices/box_furnace.py", "examples/alab_example/alab_example/tasks/", "tests/fake_lab/"], "code_license": "MIT", "language": "Python", "hardware": ["A-Lab: UR5e arms", "box/tube furnaces", "powder dosing (Labman)", "XRD", "ball mill", "capping grippers"], "domain": "materials", "task_type": "scheduling", "results_evidence": "AlabOS ran A-Lab for months (>3500 samples) of solid-state synthesis; A-Lab Nature 2023 reported 41 synthesized targets (later disputed).", "wet_lab_validated": true, "simulatable": "true: fake_lab devices + example device classes run without hardware (needs MongoDB)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "MIT, fake devices, experiment builder API; tasks: 'synthesis recipe text -> ExperimentBuilder task graph (heating profile, dosing, XRD)'.", "est_tasks": 5, "source_agent": "nonlh"}
+{"id": "a-lab-2023", "title": "An autonomous laboratory for the accelerated synthesis of novel materials (A-Lab)", "doi": "10.1038/s41586-023-06734-w", "paper_url": "https://www.nature.com/articles/s41586-023-06734-w", "year": 2023, "venue": "Nature", "open_access_license": "CC BY", "code_url": "https://github.com/njszym/ARROWS", "code_files": ["ARROWS (active-learning synthesis planner)", "XRD-AutoAnalyzer"], "code_license": "none (ARROWS); see repos", "language": "Python", "hardware": ["UR5e", "furnaces", "XRD", "powder dosing"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Claimed 41/58 novel compounds synthesized in 17 days (phase claims later contested).", "wet_lab_validated": true, "simulatable": "partial: planning/XRD analysis code runs offline; robot control via AlabOS", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Robot code is AlabOS (separate entry); contested results lower ground-truth reliability.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "ada-thin-films", "title": "Self-driving laboratory for accelerated discovery of thin-film materials (Ada)", "doi": "10.1126/sciadv.aaz8867", "paper_url": "https://www.science.org/doi/10.1126/sciadv.aaz8867", "year": 2020, "venue": "Science Advances", "open_access_license": "CC BY-NC", "code_url": "https://github.com/berlinguette/ada", "code_files": ["per-paper folders: campaign data, user_config.py, transformations_config.py, analysis scripts"], "code_license": "MIT", "language": "Python", "hardware": ["N9 robot arm (North Robotics)", "spin coater", "annealing", "UV-Vis-NIR", "4-point probe", "camera"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Optimised hole-transport-layer pseudomobility via closed-loop BO; data released per campaign.", "wet_lab_validated": true, "simulatable": "false: robot orchestration (ChemOS/N9) not released; only configs/data", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Campaign configs + data released but not hardware control code.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "ada-pareto-2022", "title": "A self-driving laboratory advances the Pareto front for material properties (Ada combustion synthesis)", "doi": "10.1038/s41467-022-28580-6", "paper_url": "https://www.nature.com/articles/s41467-022-28580-6", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/berlinguette/ada", "code_files": ["2022 folders (data + luigi pipeline configs)"], "code_license": "MIT", "language": "Python", "hardware": ["N9 arm", "spray coater", "XRF", "conductivity probe"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Pareto fronts of conductivity vs annealing temperature for Pd films reported.", "wet_lab_validated": true, "simulatable": "false: data/config only", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Same as Ada: no control code.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "afion-plasmonic", "title": "Self-driving lab for the photochemical synthesis of plasmonic nanoparticles (AFION)", "doi": "10.1038/s41467-025-56788-9", "paper_url": "https://www.nature.com/articles/s41467-025-56788-9", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/Taylorwutianyi/AFION-LAB", "code_files": ["General_AFION_Platform_Control_Software_Code/PythonLab/microreactor_v12.py", "pylab/instruments/pumps/hamilton_pump.py", "pylab/instruments/thorlabs_spectrometer/ccs.py"], "code_license": "none", "language": "Python", "hardware": ["flow microreactors", "syringe pumps", "UV LEDs (Arduino stepper)", "Thorlabs spectrometer"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Targeted Ag nanoparticle morphologies/spectra achieved autonomously with reported spectra.", "wet_lab_validated": true, "simulatable": "partial: instrument classes need serial stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; instrument-level Python is clear; flow chemistry rig.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "bear-mechanics", "title": "Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership (BEAR)", "doi": "10.1038/s41467-024-48534-4", "paper_url": "https://www.nature.com/articles/s41467-024-48534-4", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/KelseyEng/BEAR_ADTS", "code_files": ["*.m MATLAB orchestration", "*.py printer control", "gcode"], "code_license": "(LICENSE present, unrecognised)", "language": "MATLAB/Python", "hardware": ["FDM 3D printers", "UR5e arm", "Instron compression tester", "scale"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Record 75% energy-absorbing efficiency structures discovered; >25,000 experiments.", "wet_lab_validated": true, "simulatable": "partial: MATLAB orchestration with hardware calls; geometry generation simulatable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "MATLAB; arm/printer sequencing could be stubbed.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "clio-electrolytes", "title": "Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation (Clio)", "doi": "10.1038/s41467-022-32938-1", "paper_url": "https://www.nature.com/articles/s41467-022-32938-1", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/BattModels/Clio-PythonAPI", "code_files": ["Experiment.py", "demo_electrolytecomp.py", "(Clio-LabViewControl) LabVIEW VIs"], "code_license": "none", "language": "Python/LabVIEW", "hardware": ["Clio: pumps, mixing, conductivity cell", "pouch cells"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Found electrolyte with 13% higher conductivity in 42 experiments; pouch-cell validation.", "wet_lab_validated": true, "simulatable": "partial: Python API sends to LabVIEW; demo script mockable", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; LabVIEW backend.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "ahtech-electrochem", "title": "A high-throughput experimentation platform for data-driven discovery in electrochemistry (AHTech)", "doi": "10.1126/sciadv.adu4391", "paper_url": "https://www.science.org/doi/10.1126/sciadv.adu4391", "year": 2025, "venue": "Science Advances", "open_access_license": "CC BY-NC", "code_url": "https://github.com/Liu-Lab-JHU/AHTech", "code_files": ["Code/AHTech Operation/AHTech_run.py", "Code/AHTech Operation/OpentronsClient.py", "easy-biologic potentiostat driver"], "code_license": "MIT", "language": "Python", "hardware": ["Opentrons OT-2 (electrode carrier)", "BioLogic multichannel potentiostat"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Thousands of CVs on redox mediators with discovered reactivity trends reported.", "wet_lab_validated": true, "simulatable": "partial: OT-2 HTTP client mockable; potentiostat via easy-biologic needs stub", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Electrochemistry is non-LH but OT-2 used as robot; MIT.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "panda-bear", "title": "PANDA: a self-driving lab for studying electrodeposited polymer films", "doi": "10.1039/d4mh00797b", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/mh/d4mh00797b", "year": 2024, "venue": "Materials Horizons", "open_access_license": "CC BY", "code_url": "https://github.com/BU-KABlab/PANDA-BEAR", "code_files": ["examples/run_experiment.py", "src/panda_lib/hardware/grbl_cnc_mill/mock.py", "src/panda_lib/hardware/gamry_potentiostat/gamry_control_mock.py", "src/panda_lib/hardware/emstat_potentiostat/emstat_control_mock.py"], "code_license": "GPL-3.0", "language": "Python", "hardware": ["CNC gantry (GRBL)", "syringe pump", "Gamry/EmStat potentiostat", "telecentric camera"], "domain": "materials", "task_type": "characterisation", "results_evidence": "BO campaign optimised PEDOT:PSS electrochromic switching; data reported.", "wet_lab_validated": true, "simulatable": "true: mock CNC, mock potentiostats, path simulation shipped", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Mocks for every instrument; experiment definitions translate from methods (deposition potential/time, CV params).", "est_tasks": 4, "source_agent": "nonlh"}
+{"id": "robochem", "title": "Automated self-optimization, intensification, and scale-up of photocatalysis in flow (RoboChem)", "doi": "10.1126/science.adj1817", "paper_url": "https://www.science.org/doi/10.1126/science.adj1817", "year": 2024, "venue": "Science", "open_access_license": "paywalled (UvA repository copy)", "code_url": "https://github.com/Noel-Research-Group/Robochem_v1.0", "code_files": ["ML_GUI/run_optimization.py", "ML_GUI/Dragonfly_BO.py", "Platform_/Eagle_Reactor/Eagle_control.py", "Platform_/Liquid_Handler/GX_241_Liquid_Handler.py"], "code_license": "MIT", "language": "Python", "hardware": ["Gilson GX-241 liquid handler", "Vapourtec/Eagle flow photoreactor", "benchtop NMR", "pumps"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "19 photocatalytic transformations self-optimised; yields often exceeded literature.", "wet_lab_validated": true, "simulatable": "partial: BO loop runnable; instrument classes need serial stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Paper paywalled; code MIT; flow chemistry rig with no built-in mocks.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "llm-rdf", "title": "An automatic end-to-end chemical synthesis development platform powered by large language models (LLM-RDF)", "doi": "10.1038/s41467-024-54457-x", "paper_url": "https://www.nature.com/articles/s41467-024-54457-x", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/Ruan-Yixiang/LLM-RDF", "code_files": ["agent web app (JS/TS)", "hardware executor scripts"], "code_license": "none", "language": "JavaScript/Python", "hardware": ["HTE liquid handler", "GC", "robot arm"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Cu/TEMPO aerobic oxidation developed end-to-end with HTE screening, kinetics and scale-up.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; huge vendored node_modules; partial LH.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "mxene-aerogel", "title": "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties", "doi": "10.1038/s41467-024-49011-8", "paper_url": "https://www.nature.com/articles/s41467-024-49011-8", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/oshin71/Programmable-MXene-Aerogel", "code_files": ["*.py ML pipeline", "*.ipynb"], "code_license": "BSD", "language": "Python", "hardware": ["pipetting robot (OT-2)", "freeze-caster"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Aerogels with predicted conductivity/EMI shielding fabricated and measured.", "wet_lab_validated": true, "simulatable": "false: ML only", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Released code is ML, not automation.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "sdl-demo-clslab", "title": "What is a minimal working example for a self-driving laboratory? (SDL-Demo / CLSLab:Light)", "doi": "10.1016/j.matt.2022.11.007", "paper_url": "https://www.cell.com/matter/fulltext/S2590-2385(22)00651-1", "year": 2022, "venue": "Matter", "open_access_license": "author accepted (NSF PAR)", "code_url": "https://github.com/sparks-baird/self-driving-lab-demo", "code_files": ["src/self_driving_lab_demo/", "notebooks/2.2-sensor-simulator.ipynb", "scripts/bayesian_optimization_basic.py"], "code_license": "MIT", "language": "Python/MicroPython", "hardware": ["Raspberry Pi Pico W", "RGB LEDs", "AS7341 spectral sensor"], "domain": "other", "task_type": "characterisation", "results_evidence": "Optimisation of LED mixing to match target spectra; simulator vs hardware comparison reported.", "wet_lab_validated": true, "simulatable": "true: SensorSimulator class mirrors hardware", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Built-in simulator; tasks like 'set up BO campaign / MQTT commands per methods'; low biology relevance.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "ac-training-lab", "title": "Acceleration Consortium Training Lab (remote-access SDL modules incl. Hello-World, sample transfer)", "doi": null, "paper_url": "https://github.com/AccelerationConsortium/ac-training-lab", "year": 2025, "venue": "software (several Digital Discovery / ChemRxiv tutorials)", "open_access_license": null, "code_url": "https://github.com/AccelerationConsortium/ac-training-lab", "code_files": ["scripts/prefect_scripts/my_gh_sample_transfer_workflow.py", "src/ac_training_lab/"], "code_license": "MIT", "language": "Python", "hardware": ["xArm/MyCobot arms", "Cobra sample transfer", "Raspberry Pi devices", "3D-printer gantries"], "domain": "other", "task_type": "plate_transport", "results_evidence": "Educational SDL modules; no single results paper verified.", "wet_lab_validated": false, "simulatable": "partial: Prefect workflows run with MQTT mocks", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No canonical results paper.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "helao-async", "title": "HELAO-async: autonomous electrochemistry/high-throughput experimentation orchestration (Caltech/TRI)", "doi": "10.1039/d3dd00193h", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00193h", "year": 2023, "venue": "Digital Discovery (DOI unverified)", "open_access_license": "CC BY", "code_url": "https://github.com/High-Throughput-Experimentation/helao-async", "code_files": ["helao/deploy/hexagon/servers/action/ws_simulator.py", "helao/deploy/hexagon/servers/action/sim_db_server.py", "sequences/ & experiments/ libraries"], "code_license": "MIT", "language": "Python", "hardware": ["scanning droplet cell", "potentiostats", "PAL autosampler", "XY stages"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Used for autonomous electrocatalyst/OER composition screening with reported datasets.", "wet_lab_validated": true, "simulatable": "true: simulator action servers in repo", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "DOI not verified here; complex multi-server deployment; experiment/sequence functions are gradeable.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "enzyme-sdl", "title": "Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab", "doi": "10.1002/bit.70038", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1002/bit.70038", "year": 2025, "venue": "Biotechnology and Bioengineering", "open_access_license": "CC BY", "code_url": "https://github.com/putzsebastian/sdl-enzymes-optimization", "code_files": ["*.py optimisation", "csv campaign data"], "code_license": "MIT", "language": "Python", "hardware": ["liquid handler", "plate reader", "robotic arm (SDL)"], "domain": "biology", "task_type": "other", "results_evidence": "Enzymatic reaction conditions optimised autonomously; campaign data released.", "wet_lab_validated": true, "simulatable": "partial: optimiser only", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code is ML/optimiser only.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "memplex-printing", "title": "Designer artificial environments for membrane protein synthesis", "doi": "10.1038/s41467-025-59471-1", "paper_url": "https://www.nature.com/articles/s41467-025-59471-1", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://github.com/ccmeyer/printing-platform", "code_files": ["Scripts/control_platform.py", "Scripts/Dobot/DobotControl.py", "Scripts/Precigenome/PGMFC/control_c.py"], "code_license": "MIT", "language": "Python", "hardware": ["Dobot arm", "piezo droplet printer", "pressure controller", "plate reader"], "domain": "biology", "task_type": "other", "results_evidence": "Thousands of cell-free membrane-protein reactions printed and measured; formulations identified.", "wet_lab_validated": true, "simulatable": "partial: Dobot/pressure DLL calls need stubs", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Nanolitre droplet printing = liquid dispensing (overlap); arm control is non-LH.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "polymer-protein-hybrids", "title": "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids", "doi": "10.1002/adma.202201809", "paper_url": "https://onlinelibrary.wiley.com/doi/10.1002/adma.202201809", "year": 2022, "venue": "Advanced Materials", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/webbtheosim/PPH_public", "code_files": ["csv data only"], "code_license": "none", "language": "-", "hardware": ["Hamilton liquid handler", "plate reader", "robotic arm"], "domain": "biology", "task_type": "other", "results_evidence": "Enzyme-stabilising copolymers designed and assayed.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Data only.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "raft-polymerization-platform", "title": "A fully automated platform for photoinitiated RAFT polymerization", "doi": "10.1039/d2dd00100d", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d2dd00100d", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.7379060", "code_files": ["Zenodo: Chemspeed/robot scripts + data"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Chemspeed SWING", "UV photoreactor", "GPC/NMR"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "Automated photo-RAFT polymerisations with Mn/\u0110 characterisation reported.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Zenodo contents unverified.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "solubility-hein", "title": "Automated solubility screening platform using computer vision", "doi": "10.1016/j.isci.2021.102176", "paper_url": "https://www.cell.com/iscience/fulltext/S2589-0042(21)00144-0", "year": 2021, "venue": "iScience", "open_access_license": "CC BY-NC-ND", "code_url": "https://gitlab.com/heingroup/automated_solubility_h1", "code_files": ["N9 robot scripts", "HeinSight turbidity CV"], "code_license": "unverified", "language": "Python", "hardware": ["North Robotics N9 arm", "camera", "dosing", "hotplate"], "domain": "chemistry", "task_type": "characterisation", "results_evidence": "Solubility of compounds determined by CV turbidity with comparison to HPLC.", "wet_lab_validated": true, "simulatable": "partial: N9 'north' package has a simulation mode (unverified)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "GitLab licence unverified.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "mobile-robot-burger-2020", "title": "A mobile robotic chemist (Burger et al.)", "doi": "10.1038/s41586-020-2442-2", "paper_url": "https://www.nature.com/articles/s41586-020-2442-2", "year": 2020, "venue": "Nature", "open_access_license": "paywalled", "code_url": "none public (ROS code not released)", "code_files": [], "code_license": "n/a", "language": "Python/ROS", "hardware": ["KUKA KMR iiwa", "GC", "photolysis station"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "688 experiments over 8 days found photocatalyst mixtures 6x more active.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No public code.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "archemist", "title": "ARChemist: Autonomous Robotic Chemistry System Architecture (Fakhruldeen et al.)", "doi": "10.1109/ICRA46639.2022.9811996", "paper_url": "https://arxiv.org/abs/2204.13571", "year": 2022, "venue": "ICRA 2022", "open_access_license": "arXiv", "code_url": "https://github.com/ARChemist (unverified)", "code_files": [], "code_license": "unverified", "language": "Python/ROS", "hardware": ["KUKA KMR", "Franka", "solubility/crystallisation stations"], "domain": "chemistry", "task_type": "plate_transport", "results_evidence": "Solubility screening and crystallisation workflows demonstrated.", "wet_lab_validated": true, "simulatable": "partial: ROS", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "summit-flow", "title": "Summit: benchmarking machine learning methods for reaction optimisation", "doi": "10.1002/cmtd.202000051", "paper_url": "https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmtd.202000051", "year": 2021, "venue": "Chemistry-Methods", "open_access_license": "CC BY", "code_url": "https://github.com/sustainable-processes/summit", "code_files": ["summit/benchmarks/", "summit/strategies/"], "code_license": "MIT", "language": "Python", "hardware": ["(benchmarks/emulators of flow reactors)"], "domain": "chemistry", "task_type": "other", "results_evidence": "Emulators trained on literature flow-chemistry data; no new wet-lab experiments.", "wet_lab_validated": false, "simulatable": "true", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Benchmark software, no lab automation.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "labop", "title": "LabOP (Laboratory Open Protocol language, formerly PAML) - iGEM interlab growth-curve/calibration protocols", "doi": null, "paper_url": "https://bioprotocols.github.io/labop/", "year": 2023, "venue": "software + iGEM Interlab use (journal paper not verified)", "open_access_license": null, "code_url": "https://github.com/Bioprotocols/labop", "code_files": ["examples/protocols/growth-curve/growth_curve.py", "examples/protocols/iGEM/interlab-endpoint.py", "examples/protocols/calibration/", "labop_convert/ (to Opentrons/Autoprotocol/markdown)"], "code_license": "MIT", "language": "Python", "hardware": ["plate reader", "incubator", "liquid handlers (via converters)"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Protocols used in the iGEM Interlab study (results published separately); executable via converters.", "wet_lab_validated": true, "simulatable": "true: execution engine runs protocols abstractly and emits markdown/Autoprotocol without hardware", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Protocol DSL with a hardware-free execution engine; 'methods text -> LabOP protocol' graded by executed trace.", "est_tasks": 5, "source_agent": "nonlh"}
+{"id": "autoprotocol-dnada", "title": "Automated Platform for the Plasmid Construction Process (DNAda -> Autoprotocol)", "doi": "10.1021/acssynbio.3c00292", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.3c00292", "year": 2023, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY", "code_url": "https://github.com/JBEI/dnada", "code_files": ["backend/app/app/core/autoprotocols.py", "backend/app/app/api/utils/pcrrun_helper.py", "backend/app/app/api/utils/assemblyrun_helper.py"], "code_license": "Apache-2.0", "language": "Python", "hardware": ["Strateos-style Autoprotocol targets", "thermocyclers", "plate sealers", "liquid handlers"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Hundreds of plasmid constructions executed with reported success rates.", "wet_lab_validated": true, "simulatable": "true: Autoprotocol JSON is generated offline (autoprotocol-python)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Autoprotocol JSON (seal/thermocycle/spin/incubate instructions) is an inspectable non-LH target; Apache-2.0.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "autoprotocol-python", "title": "Autoprotocol-python (Strateos/Transcriptic protocol IR)", "doi": null, "paper_url": "https://autoprotocol.org", "year": 2016, "venue": "specification/software", "open_access_license": null, "code_url": "https://github.com/autoprotocol/autoprotocol-python", "code_files": ["autoprotocol/protocol.py", "autoprotocol/instruction.py", "autoprotocol/harness.py"], "code_license": "BSD-3-Clause (LICENSE.rst)", "language": "Python", "hardware": ["Strateos cloud lab: thermocycler, plate reader, sealer, centrifuge, incubator"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Specification; experimental results come from cloud-lab papers (e.g., SD2 replication papers).", "wet_lab_validated": false, "simulatable": "true: emits JSON without hardware", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Substrate rather than paper; pair with DNAda/SD2 papers.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "sd2-yeast-replication", "title": "Highly-automated, high-throughput replication of yeast-based logic circuit design assessments (SD2/Strateos/Aquarium)", "doi": "10.1093/synbio/ysac018", "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac018/6703309", "year": 2022, "venue": "Synthetic Biology", "open_access_license": "CC BY", "code_url": "https://github.com/rpgoldman/replication-paper-data-analysis", "code_files": ["analysis notebooks", "(SD2E/pysd2cat, jvrana/Terrarium for Aquarium planning)"], "code_license": "none", "language": "Python", "hardware": ["Strateos cloud lab", "Aquarium (UW BIOFAB)", "flow cytometer", "plate reader"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Logic-circuit assays replicated across labs with cytometry results compared.", "wet_lab_validated": true, "simulatable": "partial: protocol plans not released as executable code", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Released code is analysis; cloud-lab protocols not public.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "aquarium", "title": "Aquarium laboratory operating system (UW BIOFAB) - used in SD2 robustness studies", "doi": "10.1093/synbio/ysad005", "paper_url": "https://academic.oup.com/synbio/article/8/1/ysad005/7069301", "year": 2023, "venue": "Synthetic Biology (usage paper)", "open_access_license": "CC BY-NC", "code_url": "https://github.com/aquariumbio/aquarium", "code_files": ["Ruby operation types (protocols run by technicians)"], "code_license": "MIT", "language": "Ruby", "hardware": ["human-executed bench protocols", "plate readers", "cytometers"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Aquarium-run yeast logic circuit experiments with cytometry outcomes reported.", "wet_lab_validated": true, "simulatable": "partial: Aquarium docker runs protocols with simulated technician", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Ruby, heavy docker; mostly human-in-loop protocols.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "teemi", "title": "teemi: open-source literate programming for iterative DBTL cycles", "doi": "10.1371/journal.pcbi.1011929", "paper_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011929", "year": 2024, "venue": "PLoS Computational Biology", "open_access_license": "CC0", "code_url": "https://github.com/hiyama341/teemi", "code_files": ["teemi/build/", "teemi/lims/", "notebooks for G8H/CPR yeast library"], "code_license": "MIT", "language": "Python", "hardware": ["Flowbot/OT-2 (LH)", "plate reader", "colony picking (manual/robot)"], "domain": "biology", "task_type": "other", "results_evidence": "Yeast strain library built and screened with titres reported.", "wet_lab_validated": true, "simulatable": "true: pure Python", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Mostly design/LIMS; minor non-LH content.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "slab-scheduling", "title": "Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints", "doi": "10.1177/24726303211021790", "paper_url": "https://journals.sagepub.com/doi/10.1177/24726303211021790", "year": 2021, "venue": "SLAS Technology", "open_access_license": "CC BY-NC", "code_url": "https://github.com/labauto/SLab.jl", "code_files": ["src/*.jl (MIP scheduler)", "tsv job/instrument definitions"], "code_license": "MIT", "language": "Julia", "hardware": ["LabDroid Maholo robot", "incubators", "centrifuges"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Schedules for cell-culture protocols computed and compared to baseline; executed on Maholo.", "wet_lab_validated": true, "simulatable": "true: pure scheduler", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Scheduling-as-code: methods text with time constraints -> job/time-constraint spec; makespan verifiable.", "est_tasks": 3, "source_agent": "nonlh"}
+{"id": "labdroid-cell-culture", "title": "Robotic search for optimal cell culture in regenerative medicine (LabDroid Maholo, iPSC-RPE)", "doi": "10.7554/eLife.77007", "paper_url": "https://elifesciences.org/articles/77007", "year": 2022, "venue": "eLife", "open_access_license": "CC BY", "code_url": "https://github.com/labauto/LabDroid_optimizer", "code_files": ["src/ (GPyOpt-based BO driver)", "parameter csvs"], "code_license": "none", "language": "Python", "hardware": ["LabDroid Maholo dual-arm robot", "incubator", "microscope"], "domain": "biology", "task_type": "other", "results_evidence": "BO over 7 culture parameters improved iPSC-RPE differentiation scores (pigmentation) in 111 days.", "wet_lab_validated": true, "simulatable": "partial: optimizer only; robot protocols proprietary (Maholo)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; robot program not released.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "openworkstation", "title": "OpenWorkstation: A modular open-source technology for automated in vitro workflows", "doi": "10.1016/j.ohx.2020.e00152", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067220300468", "year": 2020, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "https://github.com/SebastianEggert/OpenWorkstation", "code_files": ["api/openworkstation/robot/robot.py", "api/openworkstation/drivers/smoothie_drivers/v2_0_0/virtual_smoothie.py", "examples/microphysiometry-setup/camera.py"], "code_license": "CC BY-SA (repo)", "language": "Python", "hardware": ["modular gantry", "plate handling modules", "camera", "incubation"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Automated microphysiometry/cell-culture workflow demonstrated with measurements.", "wet_lab_validated": true, "simulatable": "true: virtual_smoothie driver (Opentrons-derived simulator)", "duplicate_of_existing": null, "readiness": "ready", "readiness_reason": "Virtual driver bundled; scripts are short and gradeable.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "zhao-autonomous-enzyme", "title": "A generalized platform for artificial intelligence-powered autonomous enzyme engineering (iBioFAB)", "doi": "10.1038/s41467-025-61209-y", "paper_url": "https://www.nature.com/articles/s41467-025-61209-y", "year": 2025, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/Zhao-Group/closed-loop", "code_files": ["demo.py", "src/utils/experiment_utils.py", "(Primer_Design_and_Worklists) worklist generators"], "code_license": "MIT", "language": "Python", "hardware": ["iBioFAB: Thermo F5 arm", "thermocyclers", "incubators", "plate readers", "liquid handlers"], "domain": "biology", "task_type": "scheduling", "results_evidence": "Engineered AtHMT and YmPhytase variants with 16-26x improvements in 4 rounds.", "wet_lab_validated": true, "simulatable": "partial: ML + worklist generation offline; iBioFAB scheduling proprietary (Thermo Momentum)", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Robot-scheduler code not public; worklists are LH-centric.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "sample-protein-sdl", "title": "Self-driving laboratories to autonomously navigate the protein fitness landscape (SAMPLE)", "doi": "10.1038/s44286-023-00002-4", "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926838/", "year": 2024, "venue": "Nature Chemical Engineering", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.10048592", "code_files": ["Zenodo: agent code + Strateos protocols/data"], "code_license": "check Zenodo", "language": "Python", "hardware": ["Strateos cloud lab (Golden Gate, PCR, cell-free expression, thermostability assays on plate readers/thermocyclers)"], "domain": "biology", "task_type": "protocol_language", "results_evidence": "Four agents converged on glycoside hydrolases >12 C more thermostable.", "wet_lab_validated": true, "simulatable": "partial: Autoprotocol JSON generation offline", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Cloud-lab program; Zenodo contents need inspection.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "cloudlab-chiral-perovskite", "title": "Autonomous discovery of optically active chiral inorganic perovskite nanocrystals through an intelligent cloud lab", "doi": "10.1038/s41467-020-15728-5", "paper_url": "https://www.nature.com/articles/s41467-020-15728-5", "year": 2020, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["cloud lab robotic synthesis + CD spectroscopy"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Chiral perovskite NCs with CD responses discovered.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code link.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "pylabrobot-nonlh", "title": "PyLabRobot non-LH backends (plate readers, centrifuges, incubators, arms, sealers)", "doi": "10.1016/j.device.2023.100111", "paper_url": "https://www.cell.com/device/fulltext/S2666-9986(23)00170-3", "year": 2023, "venue": "Device", "open_access_license": "CC BY (open access; verify)", "code_url": "https://github.com/PyLabRobot/pylabrobot", "code_files": ["pylabrobot/plate_reading/", "pylabrobot/centrifuge/", "pylabrobot/incubators/", "pylabrobot/arms/", "pylabrobot/sealing/"], "code_license": "MIT", "language": "Python", "hardware": ["BMG CLARIOstar", "Agilent VSpin", "Liconic/Cytomat incubators", "PreciseFlex arm", "A4S sealer"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Paper validates LH; non-LH backends validated in later lab use, not in the paper.", "wet_lab_validated": false, "simulatable": "true: chatterbox/simulator backends for most device classes", "duplicate_of_existing": "covered by PyLabRobot/LH agents", "readiness": "partial", "readiness_reason": "Overlaps other agents' PyLabRobot coverage; best used as the execution substrate for non-LH tasks.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "star-hardwarex", "title": "Sequential Treatment Application Robot (STAR) for high-replication marine experimentation", "doi": "10.1016/j.ohx.2024.e00524", "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067224000178", "year": 2024, "venue": "HardwareX", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.10048123", "code_files": ["Zenodo: xArm control scripts"], "code_license": "check Zenodo", "language": "Python", "hardware": ["UFACTORY xArm", "dosing"], "domain": "biology", "task_type": "plate_transport", "results_evidence": "Marine organism treatment experiments with high replication reported.", "wet_lab_validated": true, "simulatable": "partial: xArm SDK has no official sim; stub required", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "xArm script readable; Zenodo licence unverified.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "brightfield-biofilm", "title": "Label-free microscopy enables high-throughput identification of genes controlling biofilm development", "doi": "10.1128/mbio.00448-26", "paper_url": "https://journals.asm.org/doi/10.1128/mbio.00448-26", "year": 2026, "venue": "mBio", "open_access_license": "CC BY", "code_url": "https://github.com/BridgesLabCMU/Brightfield-biofilm-assay", "code_files": ["*.jl analysis", "acquisition settings"], "code_license": "none", "language": "Julia", "hardware": ["automated widefield microscope", "plate handling"], "domain": "biology", "task_type": "imaging", "results_evidence": "Genome-wide biofilm screen with hit genes reported.", "wet_lab_validated": true, "simulatable": "partial: analysis only", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "No licence; mostly analysis.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "phage-cocktails-robotics", "title": "High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails", "doi": "10.1038/s41467-026-68684-x", "paper_url": "https://www.nature.com/articles/s41467-026-68684-x", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY", "code_url": "https://doi.org/10.5281/zenodo.17594564", "code_files": ["Zenodo: robot scripts + CV pipeline"], "code_license": "check Zenodo", "language": "Python", "hardware": ["robotic arm", "plate reader", "imaging"], "domain": "biology", "task_type": "imaging", "results_evidence": "Phage cocktails designed and validated with plaque/plate-reader data.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Zenodo contents unverified.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "culturomics-colony-picking", "title": "High-throughput microbial culturomics using automation and machine learning (CAMII colony picker)", "doi": "10.1038/s41587-023-01674-2", "paper_url": "https://www.nature.com/articles/s41587-023-01674-2", "year": 2023, "venue": "Nature Biotechnology", "open_access_license": "CC BY", "code_url": "see paper code availability (not verified)", "code_files": ["colony imaging + morphology-guided picking code"], "code_license": "unverified", "language": "Python", "hardware": ["custom imaging + colony-picking robot"], "domain": "biology", "task_type": "imaging", "results_evidence": "Isolated >26,000 gut isolates with morphology-guided picking efficiency reported.", "wet_lab_validated": true, "simulatable": "partial: picking selection runs on images", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Code link not verified; strong colony-picking triple if code available.", "est_tasks": 2, "source_agent": "nonlh"}
+{"id": "takahashi-turbidostat", "title": "A low cost, customizable turbidostat for use in synthetic circuit characterization", "doi": "10.1021/sb500165g", "paper_url": "https://pubs.acs.org/doi/10.1021/sb500165g", "year": 2015, "venue": "ACS Synthetic Biology", "open_access_license": "author manuscript (PMC)", "code_url": "https://github.com/klavinslab (location unverified)", "code_files": [], "code_license": "unverified", "language": "Arduino/Python", "hardware": ["8-chamber turbidostat"], "domain": "biology", "task_type": "bioreactor", "results_evidence": "Circuit characterisation in turbidostats with growth/fluorescence data.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Code location not verified.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "fish-fluidics", "title": "An open source 16-channel fluidics system for automating sequential FISH-based imaging", "doi": "10.1016/j.ohx.2022.e00343", "paper_url": "https://www.sciencedirect.com/science/article/pii/S246806722200088X", "year": 2022, "venue": "HardwareX", "open_access_license": "CC BY-NC-ND", "code_url": "https://github.com/dzhaojie/Fluidics-system-for-FISH", "code_files": ["fluidics control + imaging sync scripts"], "code_license": "unverified", "language": "Python", "hardware": ["valves", "pumps", "microscope"], "domain": "biology", "task_type": "imaging", "results_evidence": "seqFISH rounds automated with imaging results.", "wet_lab_validated": true, "simulatable": "partial", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Fluidics overlaps LH; licence unverified.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "daxi-lightsheet", "title": "DaXi: high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy", "doi": "10.1038/s41592-022-01417-2", "paper_url": "https://www.nature.com/articles/s41592-022-01417-2", "year": 2022, "venue": "Nature Methods", "open_access_license": "CC BY", "code_url": "https://github.com/royerlab/daxi", "code_files": ["Micro-Manager beanshell (.bsh) acquisition scripts", "python control"], "code_license": "CC BY (repo)", "language": "Python/BeanShell", "hardware": ["custom light-sheet", "Micro-Manager"], "domain": "biology", "task_type": "imaging", "results_evidence": "Zebrafish/drosophila volumetric imaging reported.", "wet_lab_validated": true, "simulatable": "partial: Micro-Manager demo for scripts", "duplicate_of_existing": null, "readiness": "partial", "readiness_reason": "Small scripts; mostly hardware-specific.", "est_tasks": 1, "source_agent": "nonlh"}
+{"id": "aurora-materials", "title": "AURORA - An Automatic Robotic Platform for Materials Discovery", "doi": "10.1021/acsami.5c02605", "paper_url": "https://pubs.acs.org/doi/10.1021/acsami.5c02605", "year": 2025, "venue": "ACS Applied Materials & Interfaces", "open_access_license": "CC BY", "code_url": "https://github.com/PalmSens/MethodSCRIPT_Examples", "code_files": ["(vendor MethodSCRIPT examples only)"], "code_license": "vendor", "language": "Python", "hardware": ["xArm", "potentiostat (PalmSens)"], "domain": "materials", "task_type": "characterisation", "results_evidence": "Electrochemical materials screening reported.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Platform code not released.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "sdl-nano-acsnano", "title": "A Self-Driving Lab for Nano- and Advanced Materials Synthesis", "doi": "10.1021/acsnano.4c17504", "paper_url": "https://pubs.acs.org/doi/10.1021/acsnano.4c17504", "year": 2025, "venue": "ACS Nano", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["xArm", "flow synthesis", "spectroscopy"], "domain": "materials", "task_type": "synthesis", "results_evidence": "Perspective/platform review.", "wet_lab_validated": false, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code; perspective.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "ai-chemist-ustc", "title": "An all-round AI-Chemist with a scientific mind", "doi": "10.1093/nsr/nwac190", "paper_url": "https://academic.oup.com/nsr/article/9/10/nwac190/6694179", "year": 2022, "venue": "National Science Review", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": ["mobile robot", "workstations"], "domain": "chemistry", "task_type": "synthesis", "results_evidence": "OER catalysts discovered autonomously.", "wet_lab_validated": true, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "No code.", "est_tasks": 0, "source_agent": "nonlh"}
+{"id": "adept-framework", "title": "The ADePT framework for assessing autonomous laboratory robotics", "doi": "10.1038/s42004-026-01932-9", "paper_url": "https://www.nature.com/articles/s42004-026-01932-9", "year": 2026, "venue": "Communications Chemistry", "open_access_license": "CC BY", "code_url": "none found", "code_files": [], "code_license": "n/a", "language": "-", "hardware": [], "domain": "other", "task_type": "other", "results_evidence": "Assessment framework; useful for rubric design, not tasks.", "wet_lab_validated": false, "simulatable": "false", "duplicate_of_existing": null, "readiness": "no", "readiness_reason": "Framework paper, no code.", "est_tasks": 0, "source_agent": "nonlh"}
diff --git a/research/expansion/nonlh_notes.md b/research/expansion/nonlh_notes.md
new file mode 100644
index 0000000..fed00d6
--- /dev/null
+++ b/research/expansion/nonlh_notes.md
@@ -0,0 +1,125 @@
+# Non-liquid-handling (non-LH) candidates: notes
+
+Source agent: `nonlh`. Data file: `nonlh_candidates.jsonl` (82 candidates, one JSON object per line).
+
+## How the search was run
+
+GitHub API access was unavailable: the `gh` token was invalid, and unauthenticated calls are limited to 60 per hour. Web search was rate-limited for part of the session. The search used these methods instead:
+
+- **Europe PMC REST search** (journals plus bioRxiv/ChemRxiv preprints). Queries:
+  - `"self-driving laboratory" AND github`
+  - `"robotic arm" AND "plate reader" AND github`
+  - `"PF400" OR "PreciseFlex"`
+  - `"xArm" AND laboratory AND automation`
+  - turbidostat/morbidostat/continuous culture + github
+  - pycro-manager / Micro-Manager smart microscopy
+  - colony picking (twice)
+  - SiLA 2
+  - Chemputer/XDL titles
+  - mobile robotic chemist
+  - Pioreactor / eVOLVER / Chi.Bio
+  - autofocus microscopy
+  - event-driven acquisition
+  - cloud lab / Emerald Cloud Lab / Strateos
+  - LabOP / Autoprotocol
+  - self-driving lab titles
+  - flow chemistry self-optimising
+  - LLM + robot + chemistry/biology
+  - HardwareX robotic arm / incubator / microscope
+  - plate reader + python
+  - smart/feedback/adaptive microscopy
+  - Opentrons + robotic arm
+  - digital twin lab robot
+  - electrochemistry SDL + github
+  - powder dispensing
+- **Code links from full text.** For about 75 DOIs, the Europe PMC full-text XML was scanned for links to GitHub, GitLab, Zenodo and figshare.
+- **Repository checks.** About 90 repos were checked with a shallow, blob-less `git clone` of the file tree only. This confirmed each repo exists, gave the file list, and identified the licence from the LICENSE file text. I searched each file list for mock/simulator/fake/virtual/demo files to judge whether it can be simulated.
+- **DOI confirmation.** DOIs I was unsure of were checked on Crossref: Atlas, BayBE, ORGANA, MADSci, AlabOS, ChemOS 2.0, PyLabRobot, PANDA and RoboChem.
+- **Web searches** for code locations: RoboChem, PANDA, SDL-Demo, SAMPLE and WEI.
+
+**Duplicate check against `docs/task-sources.md`:** no paper overlaps exactly. Related entries are marked in `duplicate_of_existing`:
+- `ad-sdl-pf400-module` is related to `glas-preciseflex` (both are PF400 drivers).
+- `uc2-esp` is in the same UC2 ecosystem as `uc2-hi2`.
+- `pylabrobot-nonlh` is covered by the PyLabRobot/LH agents.
+
+Existing corpus entries that are partly non-LH were not re-added: aros-cellpainting, optoplate-ml, lustro, wrmxpress, proxy-viscometer and polymerisation-kinetics-robot.
+
+**Caveats:**
+- Fields marked "unverified" or "check Zenodo" were not opened.
+- The HELAO DOI and Pioreactor's testing mode are taken from memory and not confirmed.
+- A licence recorded as "LICENSE present, unrecognised" needs reading before any code is vendored (Coscientist, ACRA, BEAR, UC2-REST).
+
+## Counts
+
+By readiness: **ready 20**, partial 48, no 14. Estimated tasks: 89 from ready candidates, 169 in total.
+
+| task_type | n | ready | partial | no |
+|---|---|---|---|---|
+| imaging | 16 | 7 | 9 | 0 |
+| synthesis | 16 | 1 | 11 | 4 |
+| protocol_language | 10 | 5 | 5 | 0 |
+| bioreactor | 9 | 1 | 6 | 2 |
+| other | 9 | 0 | 4 | 5 |
+| plate_transport | 8 | 1 | 5 | 2 |
+| characterisation | 8 | 2 | 5 | 1 |
+| scheduling | 6 | 3 | 3 | 0 |
+
+By domain: biology 43, chemistry 22, materials 13, other 4.
+
+## Which categories best extend Text2WetLab
+
+1. **Protocol languages that compile to hardware (XDL/χDL, LabOP, Autoprotocol): best fit.**
+   - The target is text, so the grader can parse it and check its structure: step and parameter matching, plus compile or simulate checks.
+   - XDL ships a static verifier and simulation mode. Cronin's ACRA repo has more than 100 reference XDLs from literature procedures that were executed on the Chemputer, with yields reported.
+   - CLAIRify ships a verifier and about 100 protocol texts.
+   - LabOP has a hardware-free execution engine. DNAda emits Autoprotocol JSON with seal, thermocycle, spin and incubate steps.
+   - The task shape is the same as Text2WetLab ("methods -> code"). It adds chemistry and also covers non-pipetting bio steps such as thermocycling, sealing and spinning.
+   - Overlap with PyLabRobot is low.
+2. **Automated microscopy acquisition: high fit, almost no overlap.**
+   - The Micro-Manager demo configuration (through pymmcore-plus or pycro-manager), Navigate's "synthetic" devices, ImSwitch's virtual microscope and the mock camera in etSTED all let acquisition code run headless.
+   - A grader can check the event sequence: axes, positions, z-stacks, channels, exposures, intervals, and the feedback rules used in smart microscopy.
+   - Imaging methods sections are precise and number-heavy, which suits grading.
+   - PyLabRobot does not cover microscopes.
+3. **Bioreactor/turbidostat control programs: good fit once small stubs are written.**
+   - eVOLVER `custom_script.py`, Chi.Bio custom programs and Pioreactor automations/experiment profiles are small control loops.
+   - Grading can replay recorded OD traces and check pump and LED commands against the methods text: dilution thresholds, setpoints and light programs.
+   - Licences are the main issue: Chi.Bio and evotron have none, while eVOLVER and Pioreactor are MIT.
+4. **Workcell scheduling/orchestration (WEI/MADSci, AlabOS, SLab.jl): good fit.**
+   - WEI has a `simulate_interface`, MADSci has virtual example modules, and AlabOS has `fake_lab` devices.
+   - Workflow YAML and task graphs can be compared step by step: module, action and arguments.
+   - This overlaps PyLabRobot's arm, reader, incubator and centrifuge backends at the device level, but not at the workflow-language level. Grade the workflow and keep PyLabRobot for device execution.
+5. **Chemistry/materials SDLs with custom rigs (flow, electrochemistry, gantries): mixed fit.**
+   - Most release the optimiser and data but not runnable instrument code, or they use serial drivers with no mocks (RoboChem, AFION, Clio).
+   - The exception is PANDA-BEAR, which ships mocks for its CNC and potentiostats.
+   - Use selectively.
+6. **Arms moving plates (PF400, xArm, UR, mobile robots): low fit on their own.**
+   - Driver code is low-level (TCP command strings, joint positions) and depends on site teach-points, so methods text cannot specify it.
+   - It is better to grade at the workflow layer (point 4). This category also overlaps glas-preciseflex and PyLabRobot most heavily.
+7. **LLM-agent papers (Coscientist, ChemCrow, ORGANA, LLM-RDF): weak sources of reference code.** Execution goes through proprietary clouds (RoboRXN, ECL) or depends on LH. They are useful as related work and baselines.
+
+**Recommendation:** add three new task families:
+- methods text to XDL (ACRA, CLAIRify, blueprints, peptide)
+- imaging-methods text to Micro-Manager MDA or Navigate feature lists (pycro-manager, Mantis, EDA, OpenFlexure)
+- methods text to workcell workflow (WEI, AlabOS, LabOP)
+
+Grade each against a simulator-backed trace.
+
+## Top 15 candidates
+
+1. `chemputer-acra`: more than 100 literature-to-XDL pairs executed on the Chemputer; xdl dry-run is possible. Check the licence text.
+2. `clairify-xdl`: NL-to-XDL with a bundled verifier and about 100 protocol texts; MIT; executed on a Franka.
+3. `wei-science-factory`: open Digital Discovery paper; MIT; WEI workflow YAML runs in simulate mode (PF400, sealer, thermocycler, camera).
+4. `alabos-alab`: MIT; fake-lab devices; solid-state synthesis recipes become task graphs (furnace profiles, XRD).
+5. `navigate-2024`: Nature Methods; synthetic hardware for every device class; smart light-sheet feature lists.
+6. `pycromanager-2021`: Nature Methods; BSD; Micro-Manager demo config; acquisition events are checkable.
+7. `mantis-shrimpy`: open PNAS Nexus; acquisition-settings YAML maps directly to the methods; BSD.
+8. `labop`: protocol language with a hardware-free execution engine; iGEM interlab growth-curve and calibration protocols.
+9. `autoprotocol-dnada`: ACS Synth Biol (CC BY); Apache-2.0; Autoprotocol JSON with thermocycle, seal and spin steps.
+10. `panda-bear`: open Materials Horizons paper; mocks for CNC and potentiostats; electrodeposition and CV parameters.
+11. `eda-event-driven`: Nature Methods; BSD; a feedback rule controls the imaging rate, checked by replaying image streams.
+12. `evolver-2018`: MIT DPU `custom_script.py`; turbidostat/chemostat logic is checked by replaying OD traces.
+13. `chemputer-blueprints`: Nature Communications (CC BY); XDL 2.0 blueprints with chiral syntheses executed.
+14. `openflexure-autofocus`: J Microscopy (CC BY); GPL server with mock hardware; tiled scans with autofocus.
+15. `slab-scheduling`: SLAS Technology; MIT Julia scheduler; time constraints in the methods text can be checked against makespan.
+
+Next tier (partial): `madsci-ad-sdl`, `chibio-2020` (no licence), `pioreactor` (no first-party paper), `mobile-robots-dai-2024` (Zenodo bundle), `robochem` (paywalled paper), `etsted` (GPL), `openworkstation`.
diff --git a/research/expansion/tools/fault_detect.py b/research/expansion/tools/fault_detect.py
new file mode 100644
index 0000000..57bd65e
--- /dev/null
+++ b/research/expansion/tools/fault_detect.py
@@ -0,0 +1,144 @@
+"""Align a model's Opentrons run log against the oracle's and list faults, deterministically.
+
+usage: fault_detect.py <logs_dir> <task> [--md]
+Fault kinds (each tied to the model event index where it first shows, and the wells it touches):
+  volume      same source -> destination well, total volume off by >5% from the oracle
+  missing     a source -> destination flow the oracle has and the model never does
+  extra       a source -> destination flow the model does and the oracle never does
+  order       reagents reach a destination in a different first-addition order
+  mix         pipette-mixing in a well the oracle never mixes
+  timing      total protocol delays < 60% of the oracle's
+  magnet      fewer magnet engage cycles than the oracle
+"""
+import collections, json, re, sys
+
+ROWS = "ABCDEFGH"
+
+
+def slot(key):
+  return int(re.findall(r"on (\d+)$", key)[0])
+
+
+def short(key):
+  return re.sub(r" on .*$", "", key)
+
+
+def parse(path):
+  log = json.load(open(path))
+  ev, loads = log["events"], {slot(k): v for k, v in log["labware"].items()}
+  plate96 = lambda key: "96" in loads.get(slot(key), "") and "tiprack" not in loads.get(slot(key), "")
+  transfers, mixes, delay, engages, sources = [], [], 0.0, 0, set()
+  pending = None
+  for i, e in enumerate(ev):
+    k = e["kind"]
+    if k == "delay":
+      delay += e["seconds"]
+    elif k == "engage":
+      engages += 1
+    elif k == "aspirate":
+      pending = e
+    elif k == "dispense" and pending is not None:
+      a, ch = pending, e["channels"]
+      cols = lambda w, key: [f"{r}{re.findall(r'\d+', w)[0]}" for r in ROWS] if ch == 8 and plate96(key) else [w]
+      if slot(a["labware"]) == slot(e["labware"]) and a["well"] == e["well"]:
+        mixes.append(dict(i=i, slot=slot(e["labware"]), wells=cols(e["well"], e["labware"]), name=short(e["labware"])))
+      else:
+        src = (slot(a["labware"]), "*" if plate96(a["labware"]) or "tuberack" in loads.get(slot(a["labware"]), "") else a["well"])
+        sources.add((slot(a["labware"]), a["well"]))
+        for w in cols(e["well"], e["labware"]):
+          transfers.append(dict(i=i, src=src, src_name=short(a["labware"]), dst=slot(e["labware"]),
+                                dst_well=w, dst_name=short(e["labware"]), vol=e["volume"]))
+      pending = None
+  return dict(n=len(ev), transfers=transfers, mixes=mixes, delay=delay, engages=engages, sources=sources)
+
+
+def src_label(t):
+  s, w = t["src"]
+  return f"{t['src_name']}" + (f" {w}" if w != "*" else "") + f" (slot {s})"
+
+
+def faults(oracle, model):
+  out = []
+  # total volume and well count per (source, destination slot): well layouts may legitimately differ
+  def agg(run):
+    tot, wells, first = collections.Counter(), collections.defaultdict(set), {}
+    for t in run["transfers"]:
+      k = (t["src"], t["dst"])
+      tot[k] += t["vol"]; wells[k].add(t["dst_well"]); first.setdefault(k, t)
+    return tot, wells, first
+  vo, wo, fo = agg(oracle)
+  vm, wm, first = agg(model)
+  groups = {}
+  for k in set(vo) | set(vm):
+    a, b = vo.get(k, 0), vm.get(k, 0)
+    if a and b and abs(a - b) > 0.05 * a:
+      groups[k] = ("volume", a / len(wo[k]), b / len(wm[k]), sorted(wm[k]))
+    elif a and not b:
+      groups[k] = ("missing", a / len(wo[k]), 0, [])
+    elif b and not a:
+      groups[k] = ("extra", 0, b / len(wm[k]), sorted(wm[k]))
+  o_src_names = {t["src"]: src_label(t) for t in oracle["transfers"]}
+  for (src, dst), (kind, a, b, wells) in groups.items():
+    t0 = first.get((src, dst)) or fo.get((src, dst))
+    i = first[(src, dst)]["i"] if (src, dst) in first else None
+    name, dname = src_label(t0), t0["dst_name"]
+    if kind == "volume":
+      tm, to = vm[(src, dst)], vo[(src, dst)]
+      msg = (f"{b:g} uL {name} -> {dname} per well; oracle {a:g} uL" if len(wm[(src, dst)]) == len(wo[(src, dst)])
+             else f"{tm:,.0f} uL total {name} -> {dname}; oracle {to:,.0f} uL ({(tm - to) / to:+.0%})")
+    elif kind == "missing":
+      msg = f"never moves {name} -> {dname} (oracle {a:g} uL into each of {len(wo[(src, dst)])} wells)"
+    else:
+      msg = f"extra transfer {name} -> {dname} ({b:g} uL x {len(wells)} wells; oracle none)"
+    out.append(dict(kind=kind, i=i, slot=dst, wells=wells, msg=msg))
+  # first-addition order into each destination slot
+  def order(run):
+    seen = collections.defaultdict(list)
+    for t in run["transfers"]:
+      if t["src"] not in [s for s, _ in seen[t["dst"]]]:
+        seen[t["dst"]].append((t["src"], t))
+    return seen
+  oo, mo = order(oracle), order(model)
+  for dst in mo:
+    common = [s for s, _ in oo.get(dst, []) if s in [x for x, _ in mo[dst]]]
+    mseq = [(s, t) for s, t in mo[dst] if s in common]
+    for pos, (s, t) in enumerate(mseq):
+      if s != common[pos]:
+        expected = next(t2 for s2, t2 in oo[dst] if s2 == common[pos])
+        out.append(dict(kind="order", i=t["i"], slot=dst, wells=[t["dst_well"]],
+                        msg=f"adds {src_label(t)} to {t['dst_name']} before {src_label(expected)} (oracle order differs)"))
+        break
+  # mixing where the oracle never mixes
+  omix = {(m["slot"], w) for m in oracle["mixes"] for w in m["wells"]}
+  flagged = set()
+  for m in model["mixes"]:
+    new = [w for w in m["wells"] if (m["slot"], w) not in omix and (m["slot"], w) not in flagged
+           and (m["slot"], w) not in model["sources"]]
+    if new:
+      flagged |= {(m["slot"], w) for w in new}
+      out.append(dict(kind="mix", i=m["i"], slot=m["slot"], wells=new,
+                      msg=f"pipette-mixes {m['name']} {','.join(new[:4])} (oracle never mixes here)"))
+  if oracle["delay"] and model["delay"] < 0.6 * oracle["delay"]:
+    out.append(dict(kind="timing", i=None, slot=None, wells=[],
+                    msg=f"total waits {model['delay']/60:.0f} min vs oracle {oracle['delay']/60:.0f} min", severity="note"))
+  if model["engages"] < oracle["engages"]:
+    out.append(dict(kind="magnet", i=None, slot=None, wells=[],
+                    msg=f"magnet engaged {model['engages']}x vs oracle {oracle['engages']}x", severity="note"))
+  # collapse repeated per-well mix faults into one entry per slot
+  return sorted(out, key=lambda f: (f["i"] is None, f["i"] or 0))
+
+
+MODELS = {"claude-opus-5-5": "Opus 5.5", "claude-sonnet-5-5": "Sonnet 5.5", "claude-fable-5-1": "Fable 5.1"}
+
+if __name__ == "__main__":
+  logs, task = sys.argv[1], sys.argv[2]
+  o = parse(f"{logs}/{task}.oracle.json")
+  result = {}
+  for m, name in MODELS.items():
+    fs = faults(o, parse(f"{logs}/{task}.{m}.json"))
+    result[m] = fs
+    json.dump(fs, open(f"{logs}/{task}.{m}.faults.json", "w"), indent=1)
+    if "--md" in sys.argv:
+      print(f"- **{name}**: " + ("no faults vs oracle" if not fs else ""))
+      for f in fs:
+        print(f"  - {'note' if f.get('severity') == 'note' else 'FAULT'} `{f['kind']}` {f['msg']}")
diff --git a/research/expansion/tools/hamilton_replay.py b/research/expansion/tools/hamilton_replay.py
new file mode 100644
index 0000000..e323ea2
--- /dev/null
+++ b/research/expansion/tools/hamilton_replay.py
@@ -0,0 +1,148 @@
+"""3D replay of a Hamilton STARlet run log (from the t2w-sim container) on PyLabRobot's STARlet model.
+
+usage: hamilton_replay.py <log.json> <label> <seconds_per_event> <out.mp4>
+Rebuilds the authors' APE deck on a simulated STARlet (with its meshes), moves the X-arm to each target,
+updates tip and volume trackers, and moves the binding plate onto the magnet and back.
+"""
+import asyncio, json, sys
+
+import replay_log
+from pylabrobot.hamilton.star.device import STARlet
+from pylabrobot.resources import Coordinate, Resource, set_tip_tracking, set_volume_tracking
+from pylabrobot.resources.agenbio.plates import AGenBio_1_troughplate_100000uL_Fl
+from pylabrobot.resources.alpaqua.magnetic_racks import Alpaqua_96_magnum_flx
+from pylabrobot.resources.bioer.plates import BioER_96_wellplate_Vb_2200uL
+from pylabrobot.resources.diy.grindbio.modules import Hamilton_MFX_plateholder_DWP_metal_tapped_10mm_3dprint
+from pylabrobot.resources.hamilton.mfx_carriers import MFX_CAR_L5_base
+from pylabrobot.resources.hamilton.mfx_modules import Hamilton_MFX_plateholder_DWP_metal_tapped
+from pylabrobot.resources.hamilton.tip_carriers import TIP_CAR_480_A00
+from pylabrobot.resources.hamilton.tip_racks import hamilton_96_tiprack_1000uL
+from pylabrobot.visualizer3D.facility import Facility
+
+
+class HamiltonReplay:
+  def __init__(self, log, task):
+    set_tip_tracking(True)
+    set_volume_tracking(True)
+    self.facility = Facility(name="facility", size_x=2000, size_y=1200, size_z=1000)
+    self.star = STARlet(simulation=True)
+    self.facility.assign_child_resource(self.star, location=Coordinate(0, 0, 0))
+    deck = self.star.deck
+    self.focus_name = deck.name
+    tip_car = TIP_CAR_480_A00("tip_car")
+    deck.assign_child_resource(tip_car, rails=25)
+    for i in range(3):
+      tip_car[i] = hamilton_96_tiprack_1000uL(f"tips_0{i}")
+    m13 = {i: Hamilton_MFX_plateholder_DWP_metal_tapped_10mm_3dprint(n) for i, n in enumerate(
+      ["rail13_mag_module", "rail13_waste_module", "rail13_elution_plate_module", "rail13_wash1_module", "rail13_wash2_module"])}
+    deck.assign_child_resource(MFX_CAR_L5_base("car_13", modules=m13), rails=13)
+    for i, r in enumerate([Alpaqua_96_magnum_flx("mag_plate"), AGenBio_1_troughplate_100000uL_Fl("waste_trough"),
+                           BioER_96_wellplate_Vb_2200uL("elution_plate"), AGenBio_1_troughplate_100000uL_Fl("wash1_trough"),
+                           AGenBio_1_troughplate_100000uL_Fl("wash2_trough")]):
+      m13[i].assign_child_resource(r)
+    m19 = {i: Hamilton_MFX_plateholder_DWP_metal_tapped(n) for i, n in enumerate(
+      ["rail19_binding_module", "rail19_source_module", "rail19_flowthrough_module", "rail19_binding_trough_module", "rail19_elution_trough_module"])}
+    deck.assign_child_resource(MFX_CAR_L5_base("car_19", modules=m19), rails=19)
+    for i, r in enumerate([BioER_96_wellplate_Vb_2200uL("binding_plate"), BioER_96_wellplate_Vb_2200uL("source_plate"),
+                           BioER_96_wellplate_Vb_2200uL("flowthrough_plate"), AGenBio_1_troughplate_100000uL_Fl("binding_trough"),
+                           AGenBio_1_troughplate_100000uL_Fl("elution_trough")]):
+      m19[i].assign_child_resource(r)
+    for name in ("source_plate",):
+      for w in deck.get_resource(name).get_all_items():
+        w.tracker.set_volume(350)
+    for name in ("binding_trough", "wash1_trough", "wash2_trough", "elution_trough"):
+      for w in deck.get_resource(name).get_all_items():
+        w.tracker.set_volume(w.max_volume * 0.9)
+    self.head = Resource(name="channels", size_x=20, size_y=70, size_z=120, category="pipette")
+    self.facility.assign_child_resource(self.head, location=Coordinate(800, 300, 450))
+    self.events = log["events"]
+    self.caption = lambda t: None
+    self.delay = 0.05
+    self.topped_up = 0
+
+  def get(self, name):
+    deck = self.star.deck
+    return deck.get_resource(name) if deck.has_resource(name) else None
+
+  async def move_to(self, res):
+    loc = res.get_absolute_location() + Coordinate(res.get_size_x() / 2 - 10, -20, res.get_size_z() + 40)
+    self.facility.unassign_child_resource(self.head)
+    self.facility.assign_child_resource(self.head, location=loc)
+    try:
+      await self.star.x_arm.move_to_x_position(round(min(max(loc.x, 0), 1000), 1))
+    except Exception:
+      pass
+    await asyncio.sleep(self.delay)
+
+  async def run(self, label):
+    try:
+      await self.star.setup()
+    except Exception:
+      pass
+    self.caption(f"{label}: start")
+    await asyncio.sleep(1.5)
+    last_move = None
+    for ev in self.events:
+      k = ev["kind"]
+      if k == "comment":
+        self.caption(f"{label} | {ev['text'][:110]}")
+        await asyncio.sleep(0.15)
+      elif k == "delay":
+        await asyncio.sleep(0.1)
+      elif k == "pick":
+        spots = [self.get(n) for n in ev["spots"]]
+        spots = [s for s in spots if s is not None]
+        if spots:
+          await self.move_to(spots[0])
+          for s in spots:
+            if s.tracker.has_tip:
+              s.tracker.remove_tip()
+      elif k == "drop":
+        spots = [self.get(n) for n in ev["spots"]]
+        spots = [s for s in spots if s is not None and hasattr(s, "tracker")]
+        if spots:
+          await self.move_to(spots[0])
+          for s in spots:
+            if not s.tracker.has_tip:
+              s.tracker.add_tip(s.make_tip())
+      elif k in ("aspirate", "dispense"):
+        wells = [(self.get(n), v) for n, v in zip(ev["wells"], ev["vols"])]
+        wells = [(w, v) for w, v in wells if w is not None and hasattr(w, "tracker")]
+        if not wells:
+          continue
+        await self.move_to(wells[0][0])
+        for w, v in wells:
+          if k == "aspirate":
+            if w.tracker.get_used_volume() < v:
+              w.tracker.set_volume(min(w.max_volume, v))
+              self.topped_up += 1
+            w.tracker.remove_liquid(min(v, w.tracker.get_used_volume()))
+          else:
+            w.tracker.add_liquid(min(v, w.tracker.get_free_volume()))
+      elif k == "move":
+        key = (ev["plate"], ev["to"])
+        if key == last_move:
+          continue
+        last_move = key
+        plate, dest = self.get(ev["plate"]), self.get(ev["to"])
+        if plate is None or dest is None:
+          continue
+        await self.move_to(plate)
+        plate.parent.unassign_child_resource(plate)
+        dest.assign_child_resource(plate)
+        self.caption(f"{label} | CoRe gripper: {ev['plate']} -> {ev['to']}")
+        await asyncio.sleep(0.8)
+    self.caption(f"{label}: finished ({len(self.events)} robot events)")
+    await asyncio.sleep(3.0)
+
+  def final_state(self):
+    return {}
+
+
+async def main(log_path, label, per_event, out):
+  replay_log.LogReplay = HamiltonReplay
+  await replay_log.main(log_path, "hamilton", label, per_event, out, out + ".state.json")
+
+
+if __name__ == "__main__":
+  asyncio.run(main(*sys.argv[1:5]))
diff --git a/research/expansion/tools/mj_render.py b/research/expansion/tools/mj_render.py
new file mode 100644
index 0000000..dd173ce
--- /dev/null
+++ b/research/expansion/tools/mj_render.py
@@ -0,0 +1,88 @@
+"""Render a run log (eval/runlog.py event format) in the opentrons-mujoco-viz scene.
+
+usage: mj_render.py <events.json> <out.mp4> [target_seconds=45]
+Every event updates the scene state; only a sample of events is animated and rendered, so a
+6,000-event protocol and a 10-event one both come out near the target length (12 fps).
+"""
+import json, re, sys, time
+import imageio
+import numpy as np
+from PIL import Image, ImageDraw, ImageFont
+
+try:
+    FONT = ImageFont.truetype("/System/Library/Fonts/Helvetica.ttc", 20)
+except Exception:
+    FONT = ImageFont.load_default()
+
+
+def caption(frame, text):
+    img = Image.fromarray(frame).convert("RGB")
+    d = ImageDraw.Draw(img, "RGBA")
+    w, h = img.size
+    d.rectangle([8, h - 44, w - 8, h - 8], fill=(0, 0, 0, 190))
+    d.text((18, h - 38), text[:100], font=FONT, fill=(255, 255, 255, 255))
+    return np.asarray(img)
+
+
+def describe(e):
+    k = e["kind"]
+    if k in ("aspirate", "dispense"):
+        return f"{k} {e['volume'] * e.get('channels', 1):g} uL  {e['well']} of {e['labware']}"
+    if k == "delay":
+        return f"delay {e['seconds']:.0f} s"
+    return {"pick": "pick up tip", "drop": "drop tip", "engage": "magnet engaged", "disengage": "magnet disengaged"}.get(k, k)
+from opentrons.visualization import WetLabScene
+
+FPS = 12
+
+
+def convert(e):
+    k = e["kind"]
+    if k in ("aspirate", "dispense"):
+        m = re.search(r" on (?:slot )?(\d+)$", e["labware"])
+        return {"type": k, "volume": e["volume"] * e.get("channels", 1), "well": e["well"], "slot": int(m[1]) if m else None}
+    if k in ("pick", "drop"):
+        return {"type": k}
+    if k == "delay":
+        return {"type": "delay", "minutes": int(e["seconds"] // 60), "seconds": e["seconds"] % 60}
+    if k == "engage":
+        return {"type": "engage", "height": 13.0}
+    if k == "disengage":
+        return {"type": "disengage"}
+    if k == "temp":
+        return {"type": "temp_set", "celsius": e["celsius"]}
+    return None
+
+
+def main(src, out, target=45.0, label=""):
+    raw = json.load(open(src))["events"]
+    pairs, note = [], ""
+    for e in raw:
+        if e["kind"] == "comment":
+            note = e["text"][:60]
+            continue
+        c = convert(e)
+        if c:
+            pairs.append((c, f"{label} | " + (note + " | " if note else "") + describe(e)))
+    evs = [c for c, _ in pairs]
+    budget = max(24, int(float(target) * FPS))
+    per = 3                                   # frames per animated event
+    stride = max(1, -(-len(evs) * per // budget))
+    t0 = time.time()
+    with WetLabScene() as s:
+        frames = [caption(s.render_with_hud("free"), f"{label}: start")] * 6
+        for i, e in enumerate(evs):
+            if i % stride:
+                s.state.apply_event(e)        # state only: no gantry motion, no render
+                continue
+            s.apply_event(e, motion_steps=40)
+            f = caption(s.render_with_hud("free"), pairs[i][1])
+            frames.extend([f] * per)
+        s._sync_visuals()
+        frames.extend([caption(s.render_with_hud("free"), f"{label}: finished ({len(evs)} robot events)")] * (FPS * 2))
+        imageio.mimsave(out, frames, fps=FPS, macro_block_size=1)
+    print(f"{len(evs)} events, stride {stride}, {len(frames)} frames, {time.time() - t0:.0f}s -> {out}")
+
+
+if __name__ == "__main__":
+    main(*sys.argv[1:5])
diff --git a/research/expansion/tools/mylog.py b/research/expansion/tools/mylog.py
new file mode 100644
index 0000000..3f6f6db
--- /dev/null
+++ b/research/expansion/tools/mylog.py
@@ -0,0 +1,13 @@
+"""eval/runlog.py, but keeping protocol comments as caption events."""
+import json, sys
+sys.path.insert(0, sys.argv[4])
+import runlog
+_parse = runlog.parse
+def parse(text, payload):
+    if text.startswith("COMMENT: "):
+        return {"kind": "comment", "text": text[9:], "instrument": "", "channels": 1}
+    return _parse(text, payload)
+runlog.parse = parse
+out = runlog.main(sys.argv[1], sys.argv[2])
+open(sys.argv[3], "w").write(json.dumps(out))
+print(sys.argv[1].split("results/")[-1], "ok" if out["ok"] else out["error"][:200], len(out.get("events", [])))
diff --git a/research/expansion/tools/otdef.py b/research/expansion/tools/otdef.py
new file mode 100644
index 0000000..72b7d47
--- /dev/null
+++ b/research/expansion/tools/otdef.py
@@ -0,0 +1,55 @@
+"""Build a PyLabRobot resource from any Opentrons labware definition (official library or a repo's custom JSON)."""
+import glob, json, os
+from pylabrobot.resources import Coordinate, Plate, Well
+from pylabrobot.resources.opentrons import load_ot_tip_rack
+
+OT_DEFS = os.path.join(os.path.dirname(__file__), "otvenv/lib/python3.10/site-packages/opentrons_shared_data/data/labware/definitions/2")
+_custom = {}
+
+
+def register_custom(root):
+  """Index custom labware JSON files under a repo (loadName -> definition)."""
+  for f in glob.glob(os.path.join(root, "**", "*.json"), recursive=True):
+    try:
+      d = json.load(open(f, errors="replace"))
+    except Exception:
+      continue
+    if isinstance(d, dict) and "wells" in d and "parameters" in d:
+      _custom[d["parameters"].get("loadName")] = d
+
+
+def definition(load_name):
+  if load_name in _custom:
+    return _custom[load_name]
+  versions = sorted(glob.glob(os.path.join(OT_DEFS, load_name, "*.json")))
+  return json.load(open(versions[-1])) if versions else None
+
+
+def from_definition(d, name):
+  dims = d["dimensions"]
+  items = {}
+  for well_name, w in d["wells"].items():
+    if w.get("shape") == "circular":
+      sx = sy = w["diameter"]
+    else:
+      sx, sy = w.get("xDimension", 8), w.get("yDimension", 8)
+    well = Well(name=f"{name}_{well_name}", size_x=sx, size_y=sy, size_z=w["depth"],
+                max_volume=w.get("totalLiquidVolume") or 1000.0,
+                cross_section_type="circle" if w.get("shape") == "circular" else "rectangle")
+    well.location = Coordinate(w["x"] - sx / 2, w["y"] - sy / 2, w["z"])
+    items[well_name] = well
+  return Plate(name=name, size_x=dims["xDimension"], size_y=dims["yDimension"], size_z=dims["zDimension"],
+               ordered_items=items, model=d["parameters"].get("loadName"))
+
+
+def load(load_name, name):
+  """A PLR resource for an Opentrons load name: tip racks via PLR's loader, everything else as a plate of wells."""
+  d = definition(load_name)
+  if d and d["parameters"].get("isTiprack"):
+    try:
+      return load_ot_tip_rack(load_name, name)
+    except Exception:
+      pass
+  if d is None:
+    return None
+  return from_definition(d, name)
diff --git a/research/expansion/tools/render_candidates.sh b/research/expansion/tools/render_candidates.sh
new file mode 100755
index 0000000..c67b71a
--- /dev/null
+++ b/research/expansion/tools/render_candidates.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+# Render the passing third-party Opentrons protocols (logs from the t2w-sim container) as 3D replay videos.
+S=/private/tmp/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/plr
+B=~/Desktop/Text2WetLab_PLR_3D/candidates; L=$B/logs; V=$B/videos; mkdir -p $V $B/clips
+CODE=~/.cache/text2wetlab-ingest/code/experimental
+cd $S
+python3 - "$L" > $B/render_plan.tsv <<'PY'
+import json, os, sys
+L = sys.argv[1]
+for cand in sorted(os.listdir(L)):
+    runs = []
+    for f in os.listdir(os.path.join(L, cand)):
+        p = os.path.join(L, cand, f)
+        try:
+            d = json.load(open(p))
+        except Exception:
+            continue
+        if not d.get("ok"):
+            continue
+        n = sum(1 for e in d["events"] if e["kind"] in ("aspirate", "dispense"))
+        if n >= 6:
+            runs.append((n, f, p))
+    for n, f, p in sorted(runs, reverse=True)[:3]:
+        moves = sum(1 for e in json.load(open(p))["events"] if e["kind"] in ("pick", "drop", "aspirate", "dispense"))
+        print(f"{cand}\t{f}\t{p}\t{min(0.35, max(0.004, 40.0 / max(moves, 1)))}")
+PY
+while IFS=$'\t' read -r cand f p per; do
+  name="${f%.json}"; out="$V/${cand}__${name}.mp4"
+  [ -s "$out" ] && continue
+  venv/bin/python replay_candidate.py "$p" "$CODE/$cand" "$cand | ${name}" "$per" "$out" < /dev/null 2>&1 | grep -v "^viewer" | tail -1
+done < $B/render_plan.tsv
+# highlights: 15 s from the middle of each candidate's first video
+ls $V/*.mp4 | awk -F'__' '!seen[$1]++' > $B/clips/list.txt
+: > $B/clips/concat.txt
+while read -r v; do
+  d=$(ffprobe -v error -show_entries format=duration -of csv=p=0 "$v"); st=$(python3 -c "print(max(0, $d/2 - 7.5))")
+  c="$B/clips/$(basename "$v")"; ffmpeg -nostdin -loglevel error -y -ss "$st" -t 15 -i "$v" -c:v libx264 -pix_fmt yuv420p -r 25 "$c" && echo "file '$c'" >> $B/clips/concat.txt
+done < $B/clips/list.txt
+ffmpeg -loglevel error -y -f concat -safe 0 -i $B/clips/concat.txt -c copy $B/HIGHLIGHTS_all_candidates.mp4 && echo "highlights $(ffprobe -v error -show_entries format=duration -of csv=p=0 $B/HIGHLIGHTS_all_candidates.mp4)s"
diff --git a/research/expansion/tools/replay3d.py b/research/expansion/tools/replay3d.py
new file mode 100644
index 0000000..d1677b1
--- /dev/null
+++ b/research/expansion/tools/replay3d.py
@@ -0,0 +1,327 @@
+"""Replay a Text2WetLab task in PyLabRobot's 3D viewer and record it to a video.
+
+usage: replay3d.py <task_dir> <out_dir> [--live]
+Builds the task's OT-2 deck from tests/deck.json, fills it from tests/ir.json, then walks the IR
+steps: a pipette marker moves tip rack -> source -> destination while the volume and tip trackers
+update, which the viewer draws. Manual (non-pipetting) steps are shown as captions.
+"""
+import asyncio, json, os, re, sys, string, shutil
+
+from pylabrobot.resources import set_volume_tracking, set_tip_tracking, Coordinate, Resource, Tube
+from pylabrobot.resources.opentrons import (
+  OTDeck, opentrons_96_tiprack_20ul, opentrons_96_tiprack_300ul, opentrons_96_filtertiprack_200ul,
+  opentrons_96_filtertiprack_1000ul)
+from pylabrobot.resources.opentrons.tube_racks import (
+  opentrons_24_tuberack_eppendorf_1_5ml_safelock_snapcap,
+  opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap, opentrons_6_tuberack_falcon_50ml_conical,
+  opentrons_15_tuberack_falcon_15ml_conical)
+from pylabrobot.resources.corning import cor_96_wellplate_360uL_Fb
+from pylabrobot.resources.biorad import biorad_96_wellplate_200uL_Vb
+from pylabrobot.resources.nest import (
+  nest_1_troughplate_195000uL_Vb, nest_12_troughplate_15000uL_Vb, NEST_96_wellplate_2200uL_Ub)
+from pylabrobot.visualizer3D.server import Viewer3D
+from pylabrobot.visualizer3D.facility import Facility
+
+LABWARE = {
+  "corning_96_wellplate_360ul_flat": cor_96_wellplate_360uL_Fb,
+  "biorad_96_wellplate_200ul_pcr": biorad_96_wellplate_200uL_Vb,
+  "nest_1_reservoir_195ml": nest_1_troughplate_195000uL_Vb,
+  "nest_12_reservoir_15ml": nest_12_troughplate_15000uL_Vb,
+  "opentrons_96_tiprack_20ul": opentrons_96_tiprack_20ul,
+  "opentrons_96_tiprack_300ul": opentrons_96_tiprack_300ul,
+  "opentrons_96_filtertiprack_200ul": opentrons_96_filtertiprack_200ul,
+  "opentrons_96_filtertiprack_1000ul": opentrons_96_filtertiprack_1000ul,
+  "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap": opentrons_24_tuberack_eppendorf_1_5ml_safelock_snapcap,
+  "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap": opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap,
+  "opentrons_6_tuberack_falcon_50ml_conical": opentrons_6_tuberack_falcon_50ml_conical,
+  "opentrons_15_tuberack_falcon_15ml_conical": opentrons_15_tuberack_falcon_15ml_conical,
+  # stand-ins (no exact PyLabRobot definition)
+  "usascientific_96_wellplate_2.4ml_deep": NEST_96_wellplate_2200uL_Ub,
+  "thermo_96_wellplate_200ul": biorad_96_wellplate_200uL_Vb,
+}
+
+ROWS = string.ascii_uppercase
+
+
+def expand(spec):
+  """['A1:H12'] -> column-major well names; plain names pass through."""
+  out = []
+  for s in spec:
+    m = re.fullmatch(r"([A-P])(\d+):([A-P])(\d+)", s)
+    if not m:
+      out.append(s)
+      continue
+    r0, c0, r1, c1 = ROWS.index(m[1]), int(m[2]), ROWS.index(m[3]), int(m[4])
+    for c in range(c0, c1 + 1):
+      for r in range(r0, r1 + 1):
+        out.append(f"{ROWS[r]}{c}")
+  return out
+
+
+class Replay:
+  def __init__(self, deck_spec, ir):
+    set_volume_tracking(True)
+    set_tip_tracking(True)
+    self.ir = ir
+    self.facility = Facility(name="lab", size_x=800, size_y=700, size_z=400)
+    self.deck = OTDeck(with_trash=True)
+    self.facility.assign_child_resource(self.deck, location=Coordinate(0, 0, 0))
+    self.labware, self.containers, self.tipracks = {}, {}, {}
+    for slot, s in sorted(deck_spec["slots"].items(), key=lambda kv: int(kv[0])):
+      lw = LABWARE[s["load_name"]](name=s["label"])
+      self.deck.assign_child_at_slot(lw, int(slot))
+      self.labware[s["label"]] = lw
+    for key, t in deck_spec["tips"].items():
+      rack = LABWARE[t["load_name"]](name=f"tips_{key}ul")
+      self.deck.assign_child_at_slot(rack, int(t["slot"]))
+      self.tipracks[key] = rack
+    for name, c in deck_spec.get("containers", {}).items():
+      self.containers[name] = (c["label"], c.get("well"))
+    self.head = Resource(name="pipette", size_x=14, size_y=14, size_z=90, category="pipette")
+    self.facility.assign_child_resource(self.head, location=Coordinate(300, 300, 160))
+    self.caption = lambda text: None
+    self.delay = 0.1
+
+  def wells(self, container, spec):
+    label, default_well = self.containers.get(container, (container, None))
+    lw = self.labware[label]
+    names = expand(spec) if spec else [default_well or "A1"]
+    return [self._vessel(lw, n) for n in names]
+
+  @staticmethod
+  def _vessel(lw, well):
+    item = lw.get_item(well)
+    if hasattr(item, "tracker"):
+      return item
+    if item.children:  # a tube already sits in this rack position
+      return item.children[0]
+    cap = 50000 if "50ml" in lw.name or "50" in str(lw.model) else (
+      15000 if "15ml" in str(lw.model) else 2000 if "2ml" in str(lw.model) else 1500)
+    tube = Tube(name=f"{lw.name}_{well}_tube", size_x=item.get_size_x() * 0.8,
+                size_y=item.get_size_y() * 0.8, size_z=max(20.0, lw.get_size_z() * 0.9), max_volume=cap)
+    item.assign_child_resource(tube)
+    return tube
+
+  def fill(self):
+    for c in self.ir["initial_contents"]:
+      for w in self.wells(c["container"], c["wells"]):
+        cap = w.max_volume
+        vol = c["volume_ul"] if c["volume_ul"] is not None else cap * 0.8
+        w.tracker.set_volume(min(vol, cap))
+
+  async def move_to(self, resource, dz=30.0):
+    loc = resource.get_absolute_location() + Coordinate(
+      resource.get_size_x() / 2 - 7, resource.get_size_y() / 2 - 7, resource.get_size_z() + dz)
+    self.facility.unassign_child_resource(self.head)
+    self.facility.assign_child_resource(self.head, location=loc)
+    await asyncio.sleep(self.delay)
+
+  def rack_for(self, vol):
+    keys = sorted(self.tipracks, key=float)
+    for k in keys:
+      if vol <= float(k):
+        return self.tipracks[k]
+    return self.tipracks[keys[-1]]
+
+  async def pick_tip(self, vol):
+    rack = self.rack_for(vol)
+    spots = [s for s in rack.get_all_items() if s.tracker.has_tip]
+    if not spots:  # reset_tipracks(): the operator refills the rack
+      for s in rack.get_all_items():
+        s.tracker.add_tip(s.make_tip())
+      spots = rack.get_all_items()
+    await self.move_to(spots[0])
+    spots[0].tracker.remove_tip()
+
+  async def drop_tip(self):
+    trash = self.deck.get_trash_area() if hasattr(self.deck, "get_trash_area") else None
+    if trash is not None:
+      await self.move_to(trash)
+
+  @staticmethod
+  def move_liquid(src, dst, vol):
+    have = src.tracker.get_used_volume()
+    if have < vol:  # "plenty" sources: top up rather than fail
+      src.tracker.set_volume(min(src.max_volume, have + vol))
+    src.tracker.remove_liquid(vol)
+    room = dst.tracker.get_free_volume()
+    dst.tracker.add_liquid(min(vol, room))
+
+  def count_ops(self):
+    n = 0
+    for s in self.ir["steps"]:
+      if s["kind"] == "transfer":
+        n += max(len(expand(s["source_wells"]) or [1]), len(expand(s["dest_wells"]) or [1]))
+      elif s["kind"] == "mix":
+        n += len(expand(s["dest_wells"]) or [1])
+    return n
+
+  async def run(self, seconds=50.0):
+    ops = max(1, self.count_ops())
+    self.delay = min(0.5, max(0.025, seconds / ops / 3))
+    self.fill()
+    self.caption(self.ir.get("title", ""))
+    await asyncio.sleep(2.0)
+    for i, s in enumerate(self.ir["steps"], 1):
+      if s["kind"] == "manual":
+        self.caption(f"Step {i} (manual, not pipetted): {s['action']}")
+        await asyncio.sleep(1.8)
+        continue
+      if s["kind"] == "mix":
+        self.caption(f"Step {i}: mix {s['dest']} {', '.join(s['dest_wells']) or ''} x{s['mix_cycles']}")
+        await self.pick_tip(s["volume_ul"] or 20)
+        for w in self.wells(s["dest"], s["dest_wells"]):
+          await self.move_to(w, dz=5)
+          await self.move_to(w, dz=25)
+        await self.drop_tip()
+        continue
+      vol = float(s["volume_ul"])
+      src = self.wells(s["source"], s["source_wells"])
+      dst = self.wells(s["dest"], s["dest_wells"])
+      mix = f", mix x{s['mix_cycles']}" if s.get("mix_cycles") else ""
+      self.caption(f"Step {i}: {vol:g} uL {s.get('reagent') or ''} {s['source']} -> {s['dest']} "
+                   f"({max(len(src), len(dst))} wells{mix})")
+      if len(src) == 1:
+        pairs = [(src[0], d) for d in dst]
+      elif len(dst) == 1:
+        pairs = [(sw, dst[0]) for sw in src]
+      else:
+        pairs = list(zip(src, dst))
+      one_tip = len(src) == 1  # shared reagent: one tip for the step
+      if one_tip:
+        await self.pick_tip(vol)
+      for sw, dw in pairs:
+        if not one_tip:
+          await self.pick_tip(vol)
+        await self.move_to(sw, dz=5)
+        await self.move_to(dw, dz=5)
+        self.move_liquid(sw, dw, vol)
+        if not one_tip:
+          await self.drop_tip()
+      if one_tip:
+        await self.drop_tip()
+    self.caption("Done: final volumes shown on the deck")
+    await asyncio.sleep(3.0)
+
+
+RNA_DECK = {
+  "slots": {
+    "1": {"load_name": "usascientific_96_wellplate_2.4ml_deep", "label": "waste_plate"},
+    "4": {"load_name": "usascientific_96_wellplate_2.4ml_deep", "label": "mag_plate"},
+    "5": {"load_name": "nest_12_reservoir_15ml", "label": "reservoir"},
+    "6": {"load_name": "thermo_96_wellplate_200ul", "label": "elution_plate"},
+    "10": {"load_name": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap", "label": "samples_1_24"},
+    "7": {"load_name": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap", "label": "samples_25_48"},
+  },
+  "tips": {"200": {"load_name": "opentrons_96_filtertiprack_200ul", "slot": 2},
+           "1000": {"load_name": "opentrons_96_filtertiprack_1000ul", "slot": 11}},
+  "containers": {},
+}
+ODD = [f"{r}{c}" for c in (1, 3, 5, 7, 9, 11) for r in "ABCDEFGH"]
+TUBES = [f"{r}{c}" for c in range(1, 7) for r in "ABCD"]
+
+
+def rna_ir():
+  t = lambda src, sw, dst, dw, v, reagent, mix=None: {
+    "kind": "transfer", "source": src, "source_wells": sw, "dest": dst, "dest_wells": dw,
+    "volume_ul": v, "reagent": reagent, "mix_cycles": mix}
+  m = lambda a: {"kind": "manual", "action": a}
+  return {
+    "title": "Magnetic-bead SARS-CoV-2 RNA extraction, 48 samples (PLOS ONE 2021)",
+    "initial_contents": [
+      {"container": "reservoir", "wells": ["A2", "A4", "A6", "A7", "A9", "A10", "A11", "A12"],
+       "volume_ul": None},
+      {"container": "samples_1_24", "wells": TUBES, "volume_ul": 300},
+      {"container": "samples_25_48", "wells": TUBES, "volume_ul": 300},
+    ],
+    "steps": [
+      m("Magnet disengaged; temperature module to 4 C"),
+      t("reservoir", ["A2"], "mag_plate", ODD, 40, "magnetic beads"),
+      t("reservoir", ["A6"], "mag_plate", ODD[:24], 250, "isopropanol"),
+      t("reservoir", ["A7"], "mag_plate", ODD[24:], 250, "isopropanol"),
+      t("samples_1_24", TUBES, "mag_plate", ODD[:24], 250, "sample", 5),
+      t("samples_25_48", TUBES, "mag_plate", ODD[24:], 250, "sample", 5),
+      m("Incubate 5 min at room temperature"),
+      m("Engage magnet, wait 4 min"),
+      t("mag_plate", ODD, "waste_plate", ODD, 540, "supernatant"),
+      t("reservoir", ["A9"], "mag_plate", ODD[:24], 500, "70% ethanol"),
+      t("reservoir", ["A10"], "mag_plate", ODD[24:], 500, "70% ethanol"),
+      t("mag_plate", ODD, "waste_plate", ODD, 500, "ethanol wash 1"),
+      t("reservoir", ["A11"], "mag_plate", ODD[:24], 500, "70% ethanol"),
+      t("reservoir", ["A12"], "mag_plate", ODD[24:], 500, "70% ethanol"),
+      t("mag_plate", ODD, "waste_plate", ODD, 500, "ethanol wash 2"),
+      m("Air-dry beads 4 min, magnet engaged"),
+      m("Disengage magnet"),
+      t("reservoir", ["A4"], "mag_plate", ODD, 100, "elution buffer", 5),
+      m("Wait 30 s, engage magnet 90 s"),
+      t("mag_plate", ODD, "elution_plate", ODD, 80, "eluate (RNA)"),
+      m("Disengage magnet; eluate held at 4 C"),
+    ],
+  }
+
+
+async def main(task_dir, out_dir, live):
+  name = os.path.basename(task_dir.rstrip("/"))
+  if name.startswith("opentrons-rna-extraction"):
+    deck_spec, ir = RNA_DECK, rna_ir()
+  else:
+    deck_spec = json.load(open(os.path.join(task_dir, "tests", "deck.json")))
+    ir = json.load(open(os.path.join(task_dir, "tests", "ir.json")))
+  rp = Replay(deck_spec, ir)
+  viewer = Viewer3D(rp.facility, open_browser=live, name=name)
+  await viewer.start()
+  if live:
+    await viewer.wait_for_browser()
+    await rp.run()
+    await viewer.stop()
+    return
+
+  from playwright.async_api import async_playwright
+  tmp = os.path.join(out_dir, f".rec_{name}")
+  shutil.rmtree(tmp, ignore_errors=True)
+  async with async_playwright() as p:
+    browser = await p.chromium.launch(headless=True, args=["--use-angle=metal", "--enable-gpu", "--ignore-gpu-blocklist"])
+    ctx = await browser.new_context(viewport={"width": 1280, "height": 720},
+                                    record_video_dir=tmp, record_video_size={"width": 1280, "height": 720})
+    page = await ctx.new_page()
+    page.on("console", lambda msg: msg.type == "error" and print("  console:", msg.text[:200]))
+    url = viewer.url.replace("/#", "/?view=iso#")
+    await page.goto(url)
+    await viewer.wait_for_browser(timeout=60)
+    for _ in range(120):  # until the scene has actually arrived and been drawn
+      if await page.evaluate("() => (window.plrViewer?.resources() || []).length > 0"):
+        break
+      await asyncio.sleep(0.25)
+    for btn in ("#toolbar-right-toggle", "#toolbar-left-toggle"):
+      try:
+        await page.click(btn, timeout=2000)
+      except Exception:
+        pass
+    await page.add_style_tag(content="#stats-panel,#scale-bar,#zoom-controls,#home-button{display:none!important}")
+    await asyncio.sleep(1.0)
+    await page.evaluate("() => plrViewer.focus('ot2_deck', 'iso')")
+    await asyncio.sleep(0.5)
+    await page.keyboard.press("Escape")  # close the inspector the focus opened
+    await asyncio.sleep(1.0)
+    await page.evaluate("""() => { const d = document.createElement('div'); d.id = 'cap';
+      d.style.cssText = 'position:fixed;left:16px;right:16px;bottom:16px;padding:10px 14px;' +
+        'background:rgba(0,0,0,.7);color:#fff;font:600 18px system-ui;border-radius:8px;z-index:99999';
+      document.body.appendChild(d); }""")
+    loop = asyncio.get_running_loop()
+    rp.caption = lambda text: loop.create_task(
+      page.evaluate("t => { document.getElementById('cap').textContent = t; }", text))
+    await rp.run()
+    video = page.video
+    await ctx.close()
+    await browser.close()
+    src = await video.path()
+  os.makedirs(out_dir, exist_ok=True)
+  dst = os.path.join(out_dir, f"{name}.mp4")
+  os.system(f'ffmpeg -loglevel error -y -i "{src}" -c:v libx264 -pix_fmt yuv420p -crf 23 "{dst}"')
+  shutil.rmtree(tmp, ignore_errors=True)
+  await viewer.stop()
+  print("wrote", dst)
+
+
+if __name__ == "__main__":
+  asyncio.run(main(sys.argv[1], sys.argv[2], "--live" in sys.argv))
diff --git a/research/expansion/tools/replay_candidate.py b/research/expansion/tools/replay_candidate.py
new file mode 100644
index 0000000..4161648
--- /dev/null
+++ b/research/expansion/tools/replay_candidate.py
@@ -0,0 +1,87 @@
+"""3D replay of a third-party Opentrons protocol's run log (from the t2w-sim container).
+
+usage: replay_candidate.py <events.json> <repo_dir> <label> <seconds_per_event> <out.mp4>
+The deck comes from the labware the protocol loaded (benchmark map, then the Opentrons library, then
+custom labware JSON in the repo). No starting volumes are known, so a source is filled the first time
+it is drawn from (counted as `topped_up`).
+"""
+import asyncio, re, sys
+
+import otdef
+import replay_log
+from replay3d import LABWARE, Facility
+from replay_log import LogReplay, slot_of
+from pylabrobot.resources import set_volume_tracking, set_tip_tracking, Coordinate, Resource
+from pylabrobot.resources.opentrons import OTDeck
+
+
+class CandidateReplay(LogReplay):
+  def __init__(self, log, task):
+    set_volume_tracking(True)
+    set_tip_tracking(True)
+    self.facility = Facility(name="lab", size_x=800, size_y=700, size_z=400)
+    self.deck = OTDeck(with_trash=True)
+    self.facility.assign_child_resource(self.deck, location=Coordinate(0, 0, 0))
+    self.by_slot, self.key_to_slot, self.missing = {}, {}, []
+    for key, load in log["labware"].items():
+      try:
+        slot = slot_of(key)
+      except IndexError:
+        continue
+      self.key_to_slot[key] = slot
+      if slot in self.by_slot or not 1 <= slot <= 11:
+        continue
+      name = f"s{slot}_{load}"
+      lw = LABWARE[load](name=name) if load in LABWARE else otdef.load(load, name)
+      if lw is None:
+        self.missing.append(load)
+        continue
+      try:
+        self.deck.assign_child_at_slot(lw, slot)
+        self.by_slot[slot] = lw
+      except Exception:
+        self.missing.append(load)
+    self.head = Resource(name="pipette", size_x=14, size_y=14, size_z=90, category="pipette")
+    self.facility.assign_child_resource(self.head, location=Coordinate(300, 300, 160))
+    self.events, self.task = log["events"], task
+    self.caption = lambda t: None
+    self.delay = 0.02
+    self.topped_up = 0
+
+  def fill(self):
+    pass  # no starting volumes are known for third-party protocols
+
+  def racks_for(self, instrument):
+    racks = [lw for lw in self.by_slot.values() if "tiprack" in lw.name]
+    size = re.findall(r"P(\d+)", instrument)
+    want = {"20": ("20ul", "10ul"), "300": ("300ul", "200ul"), "50": ("50ul",), "1000": ("1000ul",)}.get(size[0] if size else "", ())
+    sized = [lw for lw in racks if any(w in lw.name for w in want)]
+    return sized or racks
+
+  def targets(self, ev):
+    if slot_of(ev["labware"]) not in self.by_slot:
+      return [], 1
+    return super().targets(ev)
+
+  async def run(self, label):
+    usable = [e for e in self.events if e["kind"] not in ("aspirate", "dispense") or slot_of(e["labware"]) in self.by_slot]
+    self.events = usable
+    await super().run(label)
+
+
+def resolve(self, labware_key):
+  return self.by_slot[slot_of(labware_key)]
+
+
+CandidateReplay.resolve = resolve
+
+
+async def main(events, repo, label, per_event, out):
+  otdef.register_custom(repo)
+  replay_log.LogReplay = CandidateReplay
+  replay_log.initial_fill = lambda task: []
+  await replay_log.main(events, "candidate", label, per_event, out, out + ".state.json")
+
+
+if __name__ == "__main__":
+  asyncio.run(main(*sys.argv[1:6]))
diff --git a/research/expansion/tools/replay_fault.py b/research/expansion/tools/replay_fault.py
new file mode 100644
index 0000000..9be1eea
--- /dev/null
+++ b/research/expansion/tools/replay_fault.py
@@ -0,0 +1,102 @@
+"""replay_log.py plus fault annotation: red caption at the faulty event, red pins on affected wells.
+
+usage: replay_fault.py <events.json> <faults.json> <task> <label> <seconds_per_event> <out.mp4>
+"""
+import asyncio, json, sys
+import replay_log
+from replay_log import LogReplay
+from pylabrobot.resources import Coordinate, Resource
+
+
+class FaultReplay(LogReplay):
+  def __init__(self, log, task, faults):
+    super().__init__(log, task)
+    self.faults = faults
+    self.at = {}
+    for f in faults:
+      if f["i"] is not None:
+        self.at.setdefault(f["i"], []).append(f)
+    self.pins = 0
+    self.red = lambda on: None
+
+  def pin(self, slot, well):
+    lw = self.by_slot.get(slot)
+    if lw is None:
+      return
+    v = self._vessel(lw, well)
+    loc = v.get_absolute_location() + Coordinate(v.get_size_x() / 2 - 4, v.get_size_y() / 2 - 4, v.get_size_z() + 10)
+    self.pins += 1
+    self.facility.assign_child_resource(
+      Resource(name=f"fault_{self.pins}", size_x=8, size_y=8, size_z=45, category="finger"), location=loc)
+
+  async def run(self, label):
+    self.fill()
+    n = sum(1 for f in self.faults if f.get("severity") != "note")
+    self.caption(f"{label}: start  ({n} fault{'s' if n != 1 else ''} vs oracle)")
+    await asyncio.sleep(1.5)
+    last = ""
+    for i, ev in enumerate(self.events):
+      k = ev["kind"]
+      if k == "comment":
+        last = ev["text"][:110]
+        self.caption(f"{label} | {last}")
+        await asyncio.sleep(0.6)
+      elif k == "pick":
+        await self.pick(ev)
+      elif k == "drop":
+        await self.drop_tip()
+      elif k in ("aspirate", "dispense"):
+        vessels, mult = self.targets(ev)
+        await self.move_to(vessels[0], dz=5)
+        for v in vessels:
+          vol = ev["volume"] * mult
+          if k == "aspirate":
+            if v.tracker.get_used_volume() < vol:
+              v.tracker.set_volume(min(v.max_volume, vol))
+            v.tracker.remove_liquid(min(vol, v.tracker.get_used_volume()))
+          else:
+            v.tracker.add_liquid(min(vol, v.tracker.get_free_volume()))
+      elif k == "delay":
+        self.caption(f"{label} | {last}  [delay {ev['seconds']:.0f} s]")
+        await asyncio.sleep(0.4)
+      elif k in ("engage", "disengage", "temp"):
+        self.caption(f"{label} | " + {"engage": "magnet ENGAGED", "disengage": "magnet disengaged"}.get(k, f"temp {ev.get('celsius')} C"))
+        await asyncio.sleep(0.4)
+      for f in self.at.get(i, []):
+        for w in f["wells"]:
+          self.pin(f["slot"], w)
+        self.red(True)
+        self.caption(f"FAULT ({f['kind']}): {f['msg']}")
+        await asyncio.sleep(2.5)
+        self.red(False)
+        self.caption(f"{label} | {last}  [{self.pins} faulty well(s) pinned red]")
+    faults = [f for f in self.faults if f.get("severity") != "note"]
+    notes = [f for f in self.faults if f.get("severity") == "note"]
+    if faults:
+      self.red(True)
+      self.caption(f"{label}: {len(faults)} fault(s): " + " | ".join(f["msg"][:70] for f in faults)[:230])
+      await asyncio.sleep(4.0)
+      self.red(False)
+    if notes:
+      self.caption(f"{label}: notes vs authors' script: " + " | ".join(f["msg"] for f in notes))
+      await asyncio.sleep(3.0)
+    if not faults:
+      self.caption(f"{label}: matches the oracle, no faults")
+      await asyncio.sleep(3.0)
+
+
+async def main(events, faults_path, task, label, per_event, out_path):
+  replay_log.LogReplay = lambda log, task: FaultReplay(log, task, json.load(open(faults_path)))
+  orig_main = replay_log.main
+  # reuse replay_log.main's recording, adding a red-caption toggle once the page exists
+  import types
+  src = open(replay_log.__file__).read()
+  src = src.replace('rp.caption = lambda text:', 'rp.red = lambda on: loop.create_task(page.evaluate("o => { document.getElementById(\'cap\').style.background = o ? \'rgba(200,20,40,.92)\' : \'rgba(0,0,0,.75)\'; }", on))\n    rp.caption = lambda text:')
+  ns = {}
+  exec(compile(src.split('if __name__ == "__main__":')[0], replay_log.__file__, "exec"), ns)
+  ns["LogReplay"] = lambda log, task: FaultReplay(log, task, json.load(open(faults_path)))
+  await ns["main"](events, task, label, per_event, out_path, out_path + ".state.json")
+
+
+if __name__ == "__main__":
+  asyncio.run(main(*sys.argv[1:7]))
diff --git a/research/expansion/tools/replay_log.py b/research/expansion/tools/replay_log.py
new file mode 100644
index 0000000..64c15e9
--- /dev/null
+++ b/research/expansion/tools/replay_log.py
@@ -0,0 +1,211 @@
+"""Replay an Opentrons run log (from eval/runlog.py + comments) in PyLabRobot's 3D viewer.
+
+usage: replay_log.py <events.json> <task> <label> <seconds_per_event> <out.mp4> <final_state.json>
+The deck is rebuilt from the labware the protocol itself loaded; starting contents come from the
+task's fixed deck (by slot). Every aspirate/dispense/tip event is applied to the trackers in order.
+"""
+import asyncio, json, os, re, shutil, sys
+
+from replay3d import LABWARE, Replay, RNA_DECK, rna_ir, expand, Facility, Viewer3D
+from pylabrobot.resources import set_volume_tracking, set_tip_tracking, Coordinate, Resource
+from pylabrobot.resources.opentrons import OTDeck
+
+TASKS = os.path.expanduser("~/Desktop/Text2WetLab-harbor-results/tasks")
+ROWS = "ABCDEFGH"
+
+
+def slot_of(key):
+  return int(re.findall(r"on (\d+)$", key)[0])
+
+
+def initial_fill(task):
+  """[(slot, [wells] or None, volume or None)] from the task's fixed deck."""
+  if task.startswith("opentrons-rna-extraction"):
+    ir = rna_ir()
+    slot_by_label = {s["label"]: int(n) for n, s in RNA_DECK["slots"].items()}
+    return [(slot_by_label[c["container"]], c["wells"], c["volume_ul"]) for c in ir["initial_contents"]]
+  deck = json.load(open(f"{TASKS}/{task}/tests/deck.json"))
+  ir = json.load(open(f"{TASKS}/{task}/tests/ir.json"))
+  out = []
+  for c in ir["initial_contents"]:
+    cont = deck["containers"].get(c["container"], {"slot": None})
+    slot = cont["slot"]
+    if not isinstance(slot, int):
+      slot = int(re.findall(r"(\d+)$", str(slot))[0])
+    wells = expand(c["wells"]) if c["wells"] else [cont.get("well") or "A1"]
+    out.append((slot, wells, c["volume_ul"]))
+  return out
+
+
+class LogReplay(Replay):
+  def __init__(self, log, task):
+    set_volume_tracking(True)
+    set_tip_tracking(True)
+    self.facility = Facility(name="lab", size_x=800, size_y=700, size_z=400)
+    self.deck = OTDeck(with_trash=True)
+    self.facility.assign_child_resource(self.deck, location=Coordinate(0, 0, 0))
+    self.by_slot, self.key_to_slot = {}, {}
+    for key, load in log["labware"].items():
+      slot = slot_of(key)
+      self.key_to_slot[key] = slot
+      if slot in self.by_slot:
+        continue
+      lw = LABWARE[load](name=f"slot{slot}_{load[:20]}")
+      self.deck.assign_child_at_slot(lw, slot)
+      self.by_slot[slot] = lw
+    self.head = Resource(name="pipette", size_x=14, size_y=14, size_z=90, category="pipette")
+    self.facility.assign_child_resource(self.head, location=Coordinate(300, 300, 160))
+    self.events, self.task = log["events"], task
+    self.caption = lambda t: None
+    self.delay = 0.02
+    self.topped_up = 0
+    self.held = {}  # instrument -> volume in tip (for display only)
+
+  def resolve(self, labware_key):
+    key = labware_key
+    if key not in self.key_to_slot:  # run-log text vs str(labware) mismatch: match on slot
+      return self.by_slot[slot_of(key)]
+    return self.by_slot[self.key_to_slot[key]]
+
+  def targets(self, ev):
+    lw = self.resolve(ev["labware"])
+    if ev["channels"] == 8 and len(lw.get_all_items()) >= 96:
+      col = re.findall(r"\d+", ev["well"])[0]
+      return [self._vessel(lw, f"{r}{col}") for r in ROWS], 1
+    return [self._vessel(lw, ev["well"])], ev["channels"]
+
+  def racks_for(self, instrument):
+    size = re.findall(r"P(\d+)", instrument)
+    size = int(size[0]) if size else 300
+    want = {20: ("20ul",), 300: ("300ul", "200ul"), 1000: ("1000ul",)}.get(size, ("300ul",))
+    return [lw for lw in self.by_slot.values() if "tiprack" in lw.name and any(w in lw.name for w in want)]
+
+  async def pick(self, ev):
+    n = ev["channels"]
+    for rack in self.racks_for(ev["instrument"]):
+      for c in range(1, 13):
+        spots = [rack.get_item(f"{r}{c}") for r in ROWS]
+        free = [s for s in spots if s.tracker.has_tip]
+        if (n == 8 and len(free) == 8) or (n == 1 and free):
+          await self.move_to(free[0])
+          for s in (free if n == 8 else free[:1]):
+            s.tracker.remove_tip()
+          return
+    racks = self.racks_for(ev["instrument"])  # out of tips: the operator refills
+    for rack in racks:
+      for s in rack.get_all_items():
+        if not s.tracker.has_tip:
+          s.tracker.add_tip(s.make_tip())
+
+  def fill(self):
+    for slot, wells, vol in initial_fill(self.task):
+      lw = self.by_slot.get(slot)
+      if lw is None:
+        continue
+      for w in wells:
+        v = self._vessel(lw, w)
+        v.tracker.set_volume(min(v.max_volume, vol if vol is not None else v.max_volume * 0.8))
+
+  def final_state(self):
+    out = {}
+    for slot, lw in self.by_slot.items():
+      if "tiprack" in lw.name:
+        continue
+      for v in lw.get_all_children():
+        if hasattr(v, "tracker") and hasattr(v.tracker, "get_used_volume"):
+          vol = round(v.tracker.get_used_volume(), 2)
+          if vol:
+            out[f"{slot}:{v.name.split('_')[-1] if 'tube' not in v.name else v.name.split('_')[-2]}"] = vol
+    return out
+
+  async def run(self, label):
+    self.fill()
+    self.caption(f"{label}: start")
+    await asyncio.sleep(1.5)
+    last_comment = ""
+    for i, ev in enumerate(self.events):
+      k = ev["kind"]
+      if k == "comment":
+        last_comment = ev["text"][:110]
+        self.caption(f"{label} | {last_comment}")
+        await asyncio.sleep(0.6)
+      elif k == "pick":
+        await self.pick(ev)
+      elif k == "drop":
+        await self.drop_tip()
+      elif k in ("aspirate", "dispense"):
+        vessels, mult = self.targets(ev)
+        await self.move_to(vessels[0], dz=5)
+        for v in vessels:
+          vol = ev["volume"] * mult
+          if k == "aspirate":
+            have = v.tracker.get_used_volume()
+            if have < vol:
+              self.topped_up += 1
+              v.tracker.set_volume(min(v.max_volume, vol))
+            v.tracker.remove_liquid(min(vol, v.tracker.get_used_volume()))
+          else:
+            v.tracker.add_liquid(min(vol, v.tracker.get_free_volume()))
+      elif k == "delay":
+        self.caption(f"{label} | {last_comment}  [delay {ev['seconds']:.0f} s]")
+        await asyncio.sleep(0.4)
+      elif k in ("engage", "disengage", "temp"):
+        what = {"engage": "magnet ENGAGED", "disengage": "magnet disengaged"}.get(k, f"temp {ev.get('celsius')} C")
+        self.caption(f"{label} | {what}")
+        await asyncio.sleep(0.4)
+    self.caption(f"{label}: finished ({len(self.events)} robot events)")
+    await asyncio.sleep(3.0)
+
+
+async def main(events_path, task, label, per_event, out_path, state_path):
+  log = json.load(open(events_path))
+  rp = LogReplay(log, task)
+  rp.delay = float(per_event)
+  viewer = Viewer3D(rp.facility, open_browser=False, name=label)
+  await viewer.start()
+  from playwright.async_api import async_playwright
+  tmp = out_path + ".rec"
+  shutil.rmtree(tmp, ignore_errors=True)
+  async with async_playwright() as p:
+    browser = await p.chromium.launch(headless=True, args=["--use-angle=metal", "--enable-gpu", "--ignore-gpu-blocklist"])
+    ctx = await browser.new_context(viewport={"width": 1280, "height": 720}, record_video_dir=tmp,
+                                    record_video_size={"width": 1280, "height": 720})
+    page = await ctx.new_page()
+    await page.goto(viewer.url.replace("/#", "/?view=iso#"))
+    await viewer.wait_for_browser(timeout=60)
+    for _ in range(120):
+      if await page.evaluate("() => (window.plrViewer?.resources() || []).length > 0"):
+        break
+      await asyncio.sleep(0.25)
+    for btn in ("#toolbar-right-toggle", "#toolbar-left-toggle"):
+      try:
+        await page.click(btn, timeout=2000)
+      except Exception:
+        pass
+    await page.add_style_tag(content="#stats-panel,#scale-bar,#zoom-controls,#home-button,#navbar-device-tools{display:none!important}")
+    await asyncio.sleep(1.0)
+    await page.evaluate("n => plrViewer.focus(n, 'iso')", getattr(rp, "focus_name", "ot2_deck"))
+    await asyncio.sleep(0.5)
+    await page.keyboard.press("Escape")
+    await page.evaluate("""() => { const d = document.createElement('div'); d.id = 'cap';
+      d.style.cssText = 'position:fixed;left:12px;right:12px;bottom:12px;padding:10px 14px;' +
+        'background:rgba(0,0,0,.75);color:#fff;font:600 22px system-ui;border-radius:8px;z-index:99999';
+      document.body.appendChild(d); }""")
+    loop = asyncio.get_running_loop()
+    rp.caption = lambda text: loop.create_task(
+      page.evaluate("t => { document.getElementById('cap').textContent = t; }", text))
+    await asyncio.sleep(0.5)
+    await rp.run(label)
+    video = page.video
+    await ctx.close()
+    await browser.close()
+    src = await video.path()
+  os.system(f'ffmpeg -loglevel error -y -i "{src}" -c:v libx264 -pix_fmt yuv420p -crf 23 "{out_path}"')
+  shutil.rmtree(tmp, ignore_errors=True)
+  await viewer.stop()
+  json.dump({"final": rp.final_state(), "topped_up": rp.topped_up}, open(state_path, "w"))
+  print("wrote", out_path, "topped_up", rp.topped_up)
+
+
+if __name__ == "__main__":
+  asyncio.run(main(*sys.argv[1:7]))
diff --git a/research/expansion/verification.jsonl b/research/expansion/verification.jsonl
new file mode 100644
index 0000000..f6fa133
--- /dev/null
+++ b/research/expansion/verification.jsonl
@@ -0,0 +1,25 @@
+{"id": "ant-cloning", "code_url": "https://github.com/ljm176/ANTCloning", "code_license": "none", "status": "partly_verified", "protocols_found": 10, "ran": 10, "passed": 7, "custom_labware_dirs": 0, "results": [{"ok": true, "commands": 174, "error": null, "file": "Alternates/Step3_Gibson.py"}, {"ok": true, "commands": 874, "error": null, "file": "Plating_24_Wells.py"}, {"ok": false, "commands": 0, "error": "TabError: inconsistent use of tabs and spaces in indentation", "file": "Plating_No_Dilution48Wells.py", "category": "other"}, {"ok": true, "commands": 90, "error": null, "file": "Plating_No_Dilution96WP.py"}, {"ok": true, "commands": 480, "error": null, "file": "Plating_nodilution.py"}, {"ok": true, "commands": 184, "error": null, "file": "Step 1_PCRSetup.py"}, {"ok": true, "commands": 53, "error": null, "file": "Step 2_Dilution and Digestion.py"}, {"ok": true, "commands": 294, "error": null, "file": "Step 3_OEPCR.py"}, {"ok": false, "commands": 0, "error": "IndentationError: unexpected indent", "file": "Step 4_Transformation.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: IndexError [line 75]: list index out of range", "file": "Step 5_Plating.py", "category": "other"}]}
+{"id": "beckham-enzyme-pipeline", "code_url": "https://github.com/beckham-lab/opentrons", "code_license": "none (no LICENSE file)", "status": "partly_verified", "protocols_found": 15, "ran": 15, "passed": 2, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 52]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/OT-2/Custom Labware/twist_96_wellplate_400ul_P20multitest/twist_96_wellplate_400ul.json'", "file": "1-Transformation/Transformation_cherrypicking/2024-03-18_Transformation_cherrypicking_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "2e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/beckham-enzyme-pipeline/1-Transformation/Transformation_cherrypicking/Generate_transformation_cherrypicking_protocol.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "1-Transformation/Transformation_cherrypicking/Generate_transformation_cherrypicking_protocol.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 53]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/OT-2/Custom Labware/twist_96_wellplate_400ul_P20multitest/twist_96_wellplate_400ul.json'", "file": "1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 41]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "2-Inoculation/Inculation_swap_rows_for_multichannel/Inoculation_swap_rows_1x96_to_4x24_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "6017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/beckham-enzyme-pipeline/2-Inoculation/Inoculation_cherrypicking/Generate_inoculation_cherrypicking_protocol.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "2-Inoculation/Inoculation_cherrypicking/Generate_inoculation_cherrypicking_protocol.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 33]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/opentrons/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "2-Inoculation/Inoculation_platetoplate/Inoculation_1x96_to_4x24_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 40]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "3-Lysis/Lysis_1-plate_aspiration/Lysis_1-plate_aspiration_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 44]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul_on_homebuilt_magmod.json'", "file": "3-Lysis/Lysis_4-plate_aspiration/Lysis_4-plate_aspiration_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 37]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "3-Lysis/Lysis_buffer_addition/Lysis_buffer_addition_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 32]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "4-Transfer/Transfer_plate-to-plate/Transfer_plate-to-plate_4x24_to_1x96_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 40]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 40]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2_old.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 40]: [Errno 2] No such file or directory: '/Users/bnortonb/Documents/Automation_paper/Protocol_code/Custom_labware/thomsoninstrument_24_wellplate_10400ul.json'", "file": "4-Transfer/Transfer_row_swap/Transfer_rowswap_4x24_to_1x96_OT2_test_plateCandD.py", "category": "labware/definition"}, {"ok": true, "commands": 4995, "error": null, "file": "5-Purification/Purification_pipetting_only/Purification_pipetting_only_OT2.py"}, {"ok": true, "commands": 919, "error": null, "file": "5-Purification/Purification_with_shaker/Purification_with_shaker_OT2.py"}]}
+{"id": "blots-ot2", "code_url": "https://github.com/eyaplab/BLOTS-OT2", "code_license": "none", "status": "failed", "protocols_found": 1, "ran": 1, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.24 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "BLOTS-OT2_code.py", "category": "api version"}]}
+{"id": "cayman-his-elisa", "code_url": "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow", "code_license": "MIT", "status": "failed", "protocols_found": 4, "ran": 4, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "scripts/ot2_p1000single_elisa_sample_loading_final.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "scripts/ot2_p1000single_elisa_sample_loading_waste_chute.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "scripts/ot2_p300multi_elisa_wash_substrate.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "tests/ot2_tip_drop_waste_chute_test.py", "category": "api version"}]}
+{"id": "culturomics-isolation", "code_url": "https://github.com/microenvgen/Culturomics", "code_license": "none", "status": "partly_verified", "protocols_found": 11, "ran": 11, "passed": 2, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "Library preparation/First_PCR.py", "category": "api version"}, {"ok": true, "commands": 2053, "error": null, "file": "Library preparation/MicrovolumeDNAextraction.py"}, {"ok": true, "commands": 2003, "error": null, "file": "Library preparation/OmegaMagBindPCRpurificationMultichannel.py"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "Library preparation/Second_PCR.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "Library preparation/pool_plate_to_screw_cap_by_volume.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 54]: Unable to find a labware", "file": "Library preparation/prepare_MagneticBeadsPlate_highVol.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 54]: Unable to find a labware", "file": "Library preparation/prepare_MagneticBeadsPlate_lowVol.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 47]: Unable to find a labware", "file": "culturomics/c1_Appropriate_Dilution.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 71]: Unable to find a labware", "file": "culturomics/c3_Diluted_Growth.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "culturomics/c5_Well_Selection_part_1.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 48]: Unable to find a labware", "file": "culturomics/c5_Well_Selection_part_2.py", "category": "labware/definition"}]}
+{"id": "damplab-moclo-transformation", "code_url": "https://github.com/DAMPLAB/OT2-MoClo-Transformation-Ecoli", "code_license": "BSD-3-Clause", "status": "no_protocol_found", "protocols_found": 0, "ran": 0, "passed": 0, "custom_labware_dirs": 0, "results": []}
+{"id": "ester-library-synthesis", "code_url": "https://github.com/rz-flask/concise-ester-library-synthesis", "code_license": "MIT", "status": "failed", "protocols_found": 3, "ran": 3, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 15]: Unable to find a labware", "file": "substrate_screen_acids.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 22]: Unable to find a labware", "file": "substrate_screen_quench.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 14]: Unable to find a labware", "file": "substrate_screen_solvent_katsalt_KI.py", "category": "labware/definition"}]}
+{"id": "exfab-qiaseq-flex", "code_url": "https://github.com/exfab/Opentrons_Flex_ExFAB", "code_license": "GPL-3.0", "status": "verified", "protocols_found": 1, "ran": 1, "passed": 1, "custom_labware_dirs": 0, "results": [{"ok": true, "commands": 2897, "error": null, "file": "QIASeq FX 48x 6_24_25.py"}]}
+{"id": "flat-agar-celegans-ot2", "code_url": "https://github.com/Arcadia-Science/menisquish-flat-agar", "code_license": "MIT", "status": "failed", "protocols_found": 3, "ran": 3, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 2, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.28 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "opentrons/bowie_celegans_bleach_sync_var-col_v1.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "opentrons/hopsy_p20multi_op50_agar_spotting_centrifuge_v4.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.20 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "opentrons/hopsy_p20multi_worm_plating_centrifuge_v4.py", "category": "api version"}]}
+{"id": "formulations-prep-shampoo", "code_url": "https://github.com/sustainable-processes/formulations-prep", "code_license": "none", "status": "failed", "protocols_found": 1, "ran": 1, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "OpentronsProtocol_FormulationSamples.py", "category": "missing python package"}]}
+{"id": "gfp-codon-burden-ot2", "code_url": "https://github.com/alexismhill3/gfp_deoptimization_burden", "code_license": "MIT", "status": "partly_verified", "protocols_found": 15, "ran": 15, "passed": 7, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/low_temp_day_1/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/low_temp_day_1/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/low_temp_day_1/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/low_temp_day_2/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/low_temp_day_2/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/low_temp_day_2/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/low_temp_day_3/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/low_temp_day_3/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/low_temp_day_3/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/percent_day_1/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/percent_day_1/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/percent_day_1/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/percent_day_2/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/percent_day_2/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/percent_day_2/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/percent_day_3/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/percent_day_3/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 541, "error": null, "file": "wet_scripting/percent_day_3/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/percent_day_4/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/percent_day_4/base_protocol_multichannel.py", "category": "api version"}, {"ok": true, "commands": 416, "error": null, "file": "wet_scripting/percent_day_4/complete_protocol.py"}, {"ok": false, "commands": 0, "error": "/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/gfp-codon-burden-ot2/wet_scripting/percent_day_5/base_protocol_multichannel.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "wet_scripting/percent_day_5/base_protocol_multichannel.py", "category": "api version"}]}
+{"id": "greenaway-halogenation", "code_url": "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals", "code_license": "BSD-3-Clause", "status": "failed", "protocols_found": 9, "ran": 9, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 21]: Unable to find a labware", "file": "opentrons_dispense_code/nmr_sample_prep/nmr_sample_preparation.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 20]: Unable to find a labware", "file": "opentrons_dispense_code/nmr_sample_prep/nmr_sample_transfer.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 23]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_1(stage1_screening).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 21]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_2(stage2_0to6_chlor).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 23]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_3(stage2_0to10_nis_nbs).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 22]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_4(stage2_repeats_and_high_acidity).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 21]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_5(stage2_additional_repeats).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 21]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_6(stage2_single_halogenation_screen).py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 21]: Unable to find a labware", "file": "opentrons_dispense_code/reaction_setup/protocol_7(automated_scaleup).py", "category": "labware/definition"}]}
+{"id": "greenaway-mocs", "code_url": "https://github.com/GreenawayLab/development-automated-workflow-mocs", "code_license": "none", "status": "failed", "protocols_found": 5, "ran": 5, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 372]: Unable to find a labware", "file": "Opentrons_Protocols/Solvent_benchmark_acetonitrile_automated_screen.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 166]: Unable to find a labware", "file": "Opentrons_Protocols/Solvent_benchmark_acetonitrile_guest_assay.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 512]: Unable to find a labware", "file": "Opentrons_Protocols/automated_host_guest_assay_opentron_script.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 1586]: Unable to find a labware", "file": "Opentrons_Protocols/automated_screen_refined_opentron_script.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 533]: Unable to find a labware", "file": "Opentrons_Protocols/automated_synthesis_opentron_script.py", "category": "labware/definition"}]}
+{"id": "greenaway-pocs", "code_url": "https://github.com/GreenawayLab/Streamlining-Automated-Discovery-POCs", "code_license": "none", "status": "failed", "protocols_found": 6, "ran": 6, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 246]: [Errno 2] No such file or directory: '/root/Opentrons_Code/HRMS_transfer/substance_locations.json'", "file": "Opentrons_Protocols/HRMS_transfer/opentron_script.py", "category": "missing input file"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 246]: [Errno 2] No such file or directory: '/root/Opentrons_Code/NMR_transfer/substance_locations.json'", "file": "Opentrons_Protocols/NMR_transfer/opentron_script.py", "category": "missing input file"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 243]: [Errno 2] No such file or directory: '/root/Opentrons_Code/Plate1_example/substance_locations.json'", "file": "Opentrons_Protocols/Plate_example/opentron_script.py", "category": "missing input file"}, {"ok": false, "commands": 0, "error": "vel not declared in /private/tmp/claude-501/-Users-nialloleary/36017c47-22e1-459a-91a2-0b4a5634f844/scratchpad/verify/downloads/greenaway-pocs/Opentrons_Protocols/simulate.py. You must specify the target API version in the apiLevel key of the metadata dict. For instance, metadata={\"apiLevel\": \"2.0\"}", "file": "Opentrons_Protocols/simulate.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 244]: [Errno 2] No such file or directory: '/root/Opentrons_Code/solvent_topup_CDCl3/substance_locations.json'", "file": "Opentrons_Protocols/solvent_topup_CDCl3/opentron_script.py", "category": "missing input file"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 244]: [Errno 2] No such file or directory: '/root/Opentrons_Code/Solvent_TopUp_MeOHDCM/substance_locations.json'", "file": "Opentrons_Protocols/solvent_topup_MeOHDCM/opentron_script.py", "category": "missing input file"}]}
+{"id": "hyrad-adna-capture", "code_url": "https://github.com/TomaszSuchan/opentrons-hyRAD", "code_license": "none", "status": "verified", "protocols_found": 1, "ran": 1, "passed": 1, "custom_labware_dirs": 0, "results": [{"ok": true, "commands": 449, "error": null, "file": "hyRAD.ot2.py"}]}
+{"id": "jubiotech-ot2-autoclone", "code_url": "https://github.com/JuBiotech/OT-2-autoclone", "code_license": "AGPL-3.0", "status": "partly_verified", "protocols_found": 7, "ran": 7, "passed": 2, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 16]: Unable to find a labware", "file": "scripts/distributing_cells_on_agar_plates.py", "category": "labware/definition"}, {"ok": true, "commands": 14, "error": null, "file": "scripts/golden_gate_assembly.py"}, {"ok": true, "commands": 206, "error": null, "file": "scripts/golden_gate_assembly_mixing.py"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 16]: Unable to find a labware", "file": "scripts/heat-shock_transformation.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 15]: Unable to find a labware", "file": "scripts/heat-shock_transformation_mixing.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 15]: Unable to find a labware", "file": "scripts/plasmid_purification.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 15]: Unable to find a labware", "file": "scripts/restriction_digestion.py", "category": "labware/definition"}]}
+{"id": "lucks-cellfree-biosensor", "code_url": "https://github.com/LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024", "code_license": "none", "status": "failed", "protocols_found": 1, "ran": 1, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 19]: Unable to find a labware", "file": "Opentrons_Code/Figure_2_Sensor_Build.py", "category": "labware/definition"}]}
+{"id": "lysostaphin-turbidity", "code_url": "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025", "code_license": "AGPL-3.0", "status": "failed", "protocols_found": 1, "ran": 1, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: FileNotFoundError [line 28]: Unable to find a labware", "file": "code/Turbidity_assay_OT_8samples.py", "category": "labware/definition"}]}
+{"id": "massspecpreppy", "code_url": "https://github.com/stemicha/MassSpecPreppy", "code_license": "GPL-3.0", "status": "partly_verified", "protocols_found": 10, "ran": 10, "passed": 3, "custom_labware_dirs": 0, "results": [{"ok": true, "commands": 1827, "error": null, "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay.py"}, {"ok": true, "commands": 1348, "error": null, "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay_take3_HS.py"}, {"ok": true, "commands": 414, "error": null, "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay_take3_slow_retract.py"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well_without_red_alk.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_mix.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_sequential.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_EvoTip_loading.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_Trypsin_Mix_stock_concentration'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_vial_elution.py", "category": "other"}, {"ok": false, "commands": 0, "error": "opentrons.protocols.execution.errors.ExceptionInProtocolError: KeyError [line 17]: 'LysC_ratio'", "file": "OT2_protocols_template/Mass_Spec_Preppy__OT2_part4_post_EvoTip_loading.py", "category": "other"}]}
+{"id": "msd-biochem-assays-ot2", "code_url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays", "code_license": "Apache-2.0", "status": "verified", "protocols_found": 2, "ran": 2, "passed": 2, "custom_labware_dirs": 0, "results": [{"ok": true, "commands": 614, "error": null, "file": "Bradford_standard_curve.py"}, {"ok": true, "commands": 590, "error": null, "file": "PicoGreen_standard_curve_YW_validated.py"}]}
+{"id": "plant-phenotyping-ot2", "code_url": "https://github.com/Synthetic-Automated-Systems/automated_phenotyping_system", "code_license": "MIT", "status": "failed", "protocols_found": 2, "ran": 2, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'paho'", "file": "Code/OT2Code-FillPlates.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'paho'", "file": "Code/OT2Code.py", "category": "missing python package"}]}
+{"id": "roboctab", "code_url": "https://github.com/tomstamour/RoboCTAB", "code_license": "none", "status": "failed", "protocols_found": 2, "ran": 2, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 2, "error": "opentrons.protocol_reader.file_identifier.FileIdentificationError: API version 2.22 is not supported by this robot software. Please either reduce your requested API version or update your robot.", "file": "RoboCTAB_Flex.py", "category": "api version"}, {"ok": false, "commands": 0, "error": "ProtocolCommandFailedError [line 791]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): PythonException: FileNotFoundError: Labware \"vwrbox_96_tiprack_300ul\" not found with version 1 in namespace \"opentrons\".", "file": "RoboCTAB_OT2.py", "category": "labware/definition"}]}
+{"id": "roche-pipetting-performance-ot2", "code_url": "https://github.com/arthur-theuer/pipetting-performance", "code_license": "GPL-3.0", "status": "failed", "protocols_found": 2, "ran": 2, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "ProtocolCommandFailedError [line 64]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): PythonException: FileNotFoundError: Labware \"axygen_4_reservoir_70ul\" not found with version 1 in namespace \"opentrons\".", "file": "templates/opentrons/OT2_pipetting_performance_p20.py", "category": "labware/definition"}, {"ok": false, "commands": 0, "error": "ProtocolCommandFailedError [line 64]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): PythonException: FileNotFoundError: Labware \"axygen_4_reservoir_70ul\" not found with version 1 in namespace \"opentrons\".", "file": "templates/opentrons/OT2_pipetting_performance_p300.py", "category": "labware/definition"}]}
+{"id": "sapp-dmx-protein-design", "code_url": "https://github.com/bwicky/SAPP_DMX", "code_license": "MIT", "status": "failed", "protocols_found": 1, "ran": 1, "passed": 0, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "SyntaxError: invalid syntax", "file": "SAPP/SEC_pool_and_norm_v3.py", "category": "syntax"}]}
+{"id": "tidytron", "code_url": "https://github.com/PlantSynBioLab/TidyTron", "code_license": "Apache-2.0", "status": "partly_verified", "protocols_found": 15, "ran": 15, "passed": 3, "custom_labware_dirs": 0, "results": [{"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/DNAcleaning optimization.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/DNAcleaning.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/fig1A_B_p10_tip.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/fig1C_10ul_tip_cleaning_optimization.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/fig1D_96rack_variation_10ul_tip_cleaningproject.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/integrated_tipclean_plateclean_HOT_multi.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/integrated_tipclean_plateclean_RT_multi.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/optimization_scripts/plate_clean_optimization.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/p10/p10_DNAclean_neutralizers.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/p10/p10_DNAclean_neutralizers_multichan.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/p10/p10_DNAclean_no_neuts.py", "category": "missing python package"}, {"ok": false, "commands": 0, "error": "ModuleNotFoundError: No module named 'pandas'", "file": "scripts/p10/p10_DNAclean_no_neuts_multichan.py", "category": "missing python package"}, {"ok": true, "commands": 30, "error": null, "file": "scripts/p10/p10_Ecoliclean_1-1.py"}, {"ok": true, "commands": 120, "error": null, "file": "scripts/p10/p10_Ecoliclean_1-1_multichan.py"}, {"ok": true, "commands": 45, "error": null, "file": "scripts/p10/p10_Ecoliclean_1-2-1.py"}]}
diff --git a/research/expansion/web_candidates.jsonl b/research/expansion/web_candidates.jsonl
new file mode 100644
index 0000000..143a121
--- /dev/null
+++ b/research/expansion/web_candidates.jsonl
@@ -0,0 +1,60 @@
+{"id": "tidytron", "title": "TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 robots", "doi": "10.1016/j.slast.2023.08.007", "paper_url": "https://doi.org/10.1016/j.slast.2023.08.007", "year": 2024, "venue": "SLAS Technology", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/PlantSynBioLab/TidyTron", "code_files": ["scripts/optimization_scripts/DNAcleaning.py", "scripts/optimization_scripts/fig1C_10ul_tip_cleaning_optimization.py", "scripts/*.py (37 OT-2 scripts total)"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plasticware wash-and-reuse / tip and plate cleaning", "results_evidence": "Carryover after wash validated by qPCR/transformation and fluorescence assays showing no detectable cross-contamination vs fresh plasticware.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Open paper text (CC BY-NC-ND), Apache-2.0 repo with 37 standalone OT-2 API v2 scripts that should simulate as-is; wash/reuse figures give measured outcomes.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "beckham-enzyme-pipeline", "title": "Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline", "doi": "10.1038/s41598-024-64938-0", "paper_url": "https://www.nature.com/articles/s41598-024-64938-0", "year": 2024, "venue": "Scientific Reports", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/beckham-lab/opentrons", "code_files": ["1-Transformation/Transformation_cherrypicking/2024-03-18_Transformation_cherrypicking_OT2.py", "1-Transformation/Transformation_platetoplate/transformation_platetoplate_OT2.py", "2-Inoculation/*.py", "(21 OT-2 scripts total)"], "code_license": "none (no LICENSE file)", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "E. coli transformation, inoculation, expression, lysis, enzyme assay", "results_evidence": "Robot-assisted pipeline screened enzyme variant libraries; activity/expression measured and compared with manual handling.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper plus modular per-step OT-2 v2 scripts; only blocker is the unlicensed repo (cannot vendor, can still reference).", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "jubiotech-ot2-autoclone", "title": "Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation", "doi": "10.1007/s00253-022-12017-7", "paper_url": "https://doi.org/10.1007/s00253-022-12017-7", "year": 2022, "venue": "Applied Microbiology and Biotechnology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/JuBiotech/OT-2-autoclone", "code_files": ["scripts/golden_gate_assembly.py", "scripts/heat-shock_transformation.py", "scripts/restriction_digestion.py", "scripts/plasmid_purification.py", "scripts/distributing_cells_on_agar_plates.py"], "code_license": "AGPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "Golden Gate assembly, heat-shock transformation, plasmid prep, plating", "results_evidence": "Automated strain construction produced verified C. glutamicum secretion strains characterised in microbioreactor cultivations.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Open paper, one script per protocol step, each self-contained; AGPL-3.0 means reference-only (same constraint as APEX).", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "roboctab", "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping", "doi": "10.3390/plants14152263", "paper_url": "https://www.mdpi.com/2223-7747/14/15/2263", "year": 2025, "venue": "Plants (MDPI)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/tomstamour/RoboCTAB", "code_files": ["RoboCTAB_OT2.py", "RoboCTAB_Flex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "CTAB plant DNA extraction", "results_evidence": "DNA yield/purity and genotyping call rates from robot-extracted samples compared with manual CTAB extraction.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper; two complete protocols (OT-2 and Flex variants) give a natural easy/hard pair; repo unlicensed.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "blots-ot2", "title": "Bacterial Lysis Observation Over Time Assay (BLOTS) for High-Throughput Isolation and Screening", "doi": "10.1002/cpz1.70454", "paper_url": "https://doi.org/10.1002/cpz1.70454", "year": 2026, "venue": "Current Protocols", "open_access_license": "CC BY-NC 4.0", "code_url": "https://github.com/eyaplab/BLOTS-OT2", "code_files": ["BLOTS-OT2_code.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "384-well assay plate assembly / lysis kinetics screening", "results_evidence": "Assay plates assembled by the robot yielded time-resolved lysis curves used to recover and sequence isolates.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Current Protocols article is a step-by-step protocol (ideal NL input) with a single matching OT-2 script; licence of code unstated.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "hyrad-adna-capture", "title": "Performance and automation of ancient DNA capture with RNA hyRAD probes", "doi": "10.1111/1755-0998.13518", "paper_url": "https://doi.org/10.1111/1755-0998.13518", "year": 2022, "venue": "Molecular Ecology Resources", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/TomaszSuchan/opentrons-hyRAD", "code_files": ["hyRAD.ot2.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "hybridization capture + magnetic bead washes (magnetic module, thermocycler)", "results_evidence": "Capture efficiency and on-target read fractions for automated vs manual hybridization reported for ancient DNA libraries.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Single self-contained module-driven script; good hard task (magnetic module + temperature steps). Paper is ND-licensed so text can be linked not redistributed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "massspecpreppy", "title": "MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics", "doi": "10.1002/pmic.202300294", "paper_url": "https://doi.org/10.1002/pmic.202300294", "year": 2023, "venue": "PROTEOMICS", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/stemicha/MassSpecPreppy", "code_files": ["OT2_protocols_template/Mass_Spec_Preppy__OT2_BCAassay.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part1_sample_preparation_in_96well.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part2_SP3_in_96well_enzyme_mix.py", "OT2_protocols_template/Mass_Spec_Preppy__OT2_part3_Ev*.py"], "code_license": "GPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "BCA assay, reduction/alkylation, SP3 digestion, Evotip loading", "results_evidence": "BCA recovery 101.3% (SD 7.8) for the automated workflow vs 96.3% manual; 94.5% of protein groups passed thresholds for OT-2 digestion.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "GPL-3.0 templates, one file per workflow stage, quantitative wet-lab comparison in the paper; templates are parameterised by the Shiny app so some placeholder filling is needed.", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "lucks-cellfree-biosensor", "title": "Semi-automated production of cell-free biosensors", "doi": "10.1101/2024.10.13.618078", "paper_url": "https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1", "year": 2024, "venue": "bioRxiv", "open_access_license": "bioRxiv (CC licence per preprint page)", "code_url": "https://github.com/LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024", "code_files": ["Opentrons_Code/Figure_2_Sensor_Build.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free reaction assembly (384-well biosensor build)", "results_evidence": "A full 384-well plate of fluoride-sensing cell-free reactions assembled robotically matched expected colorimetric/fluorescent detection performance.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "One script maps to one figure, open preprint text, viscous cell-free liquid class makes it a good hard task; repo unlicensed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "greenaway-halogenation", "title": "An automated platform for tailored late-stage halogenation of pharmaceuticals", "doi": "10.26434/chemrxiv.15000393", "paper_url": "https://chemrxiv.org/engage/chemrxiv/article-details/15000393", "year": 2025, "venue": "ChemRxiv (preprint)", "open_access_license": "ChemRxiv CC BY (per posting)", "code_url": "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals", "code_files": ["opentrons_dispense_code/reaction_setup/protocol_1(stage1_screening).py", "opentrons_dispense_code/reaction_setup/protocol_2(stage2_0to6_chlor).py", "opentrons_dispense_code/nmr_sample_prep/nmr_sample_preparation.py", "(9 OT-2 scripts total)"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "reaction array setup, quench, NMR/LC-MS sample prep", "results_evidence": "Screening arrays dispensed by OT-2 gave halogenation conversions/selectivities measured by NMR and LC-MS across substrate panels.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "BSD-3 code, several independent stage scripts, chemistry (non-bio) diversity for the benchmark; must confirm final journal version.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "greenaway-mocs", "title": "Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages", "doi": "10.1002/anie.202424270", "paper_url": "https://doi.org/10.1002/anie.202424270", "year": 2025, "venue": "Angewandte Chemie Int. Ed.", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/GreenawayLab/development-automated-workflow-mocs", "code_files": ["Opentrons_Protocols/automated_synthesis_opentron_script.py", "Opentrons_Protocols/automated_screen_refined_opentron_script.py", "Opentrons_Protocols/automated_host_guest_assay_opentron_script.py", "Opentrons_Protocols/Solvent_benchmark_acetonitrile_automated_screen.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "solution-phase screening array + host-guest assay", "results_evidence": "Automated screen identified assembled cages confirmed by MS/NMR and host-guest binding measured across the array.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper, five discrete OT-2 scripts; repo carries no licence so reference-only.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "greenaway-pocs", "title": "Streamlining the automated discovery of porous organic cages", "doi": "10.1039/d3sc06133g", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc06133g", "year": 2024, "venue": "Chemical Science", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/GreenawayLab/Streamlining-Automated-Discovery-POCs", "code_files": ["Opentrons_Protocols/Plate_example/opentron_script.py", "Opentrons_Protocols/NMR_transfer/opentron_script.py", "Opentrons_Protocols/HRMS_transfer/opentron_script.py", "Opentrons_Protocols/simulate.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cage synthesis plate + analytical transfer protocols", "results_evidence": "Automated workflow produced porous organic cages characterised by HRMS/NMR, with hit rates reported vs manual discovery.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper and a repo that even ships simulate.py (so scripts are known to run in opentrons_simulate); unlicensed repo.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "ester-library-synthesis", "title": "Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction", "doi": "10.1039/d2cc05670d", "paper_url": "https://doi.org/10.1039/d2cc05670d", "year": 2023, "venue": "Chemical Communications", "open_access_license": "unclear (preprint CC BY-NC-ND on ChemRxiv 10.26434/chemrxiv-2022-9grb8)", "code_url": "https://github.com/rz-flask/concise-ester-library-synthesis", "code_files": ["substrate_screen_acids.py", "substrate_screen_quench.py", "substrate_screen_solvent_katsalt_KI.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "96-well library synthesis, quench, solvent/salt screen", "results_evidence": "96-well esterification library synthesised on OT-2 with yields/conversions measured by LC-MS.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "MIT code with custom labware JSON included; journal text may be paywalled but the ChemRxiv version is open.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "culturomics-isolation", "title": "Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex communities", "doi": "10.1002/imo2.70037", "paper_url": "https://doi.org/10.1002/imo2.70037", "year": 2025, "venue": "iMetaOmics", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/microenvgen/Culturomics", "code_files": ["Library preparation/First_PCR.py", "Library preparation/Second_PCR.py", "Library preparation/MicrovolumeDNAextraction.py", "Library preparation/OmegaMagBindPCRpurificationMultichannel.py", "Library preparation/pool_plate_to_screw_cap_by_volume.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "microvolume DNA extraction, two-step amplicon PCR, bead purification, pooling", "results_evidence": "Isolates recovered and phylogenetically identified from automated plates; sequencing success rates reported vs manual pipeline.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper with 11 modular OT-2 scripts, each a clean single-step task; repo has no licence.", "est_tasks": 8, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "damplab-moclo-transformation", "title": "A linear programming-based strategy to save pipette tips in automated DNA assembly (with DAMP Lab MoClo/transformation workflow)", "doi": "10.1093/synbio/ysac004", "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac004/6542944", "year": 2022, "venue": "Synthetic Biology (OUP)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/DAMPLAB/OT2-MoClo-Transformation-Ecoli", "code_files": ["moclo_transformation/data/moclo_template.py", "moclo_transformation/data/moclo_transform_template.py", "moclo_transformation/data/transform_template.py"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "MoClo Golden Gate assembly + E. coli transformation + plating", "results_evidence": "Tip-saving assembly strategy evaluated on OT-2 runs; assembly/transformation success measured against standard tip usage.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "BSD-3 templates, open paper; templates are parameterised so labware/volume filling is needed before simulation.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "lap-format-repository", "title": "The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology", "doi": "10.1021/acssynbio.3c00397", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.3c00397", "year": 2023, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/Biocomputation-CBGP/LAPrepository", "code_files": ["LAPEntries/**/ScriptsFinal/*.py (37 OT-2 entry scripts)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "library of standardised protocols (colony selection, PCR setup, media distribution, plate merging)", "results_evidence": "Each LAP entry documents wet-lab execution/validation records on OT-2 at the host biofoundry.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Large multi-protocol repo (same code base as the existing lap-transposon-genotyping source) with no licence; the LAP format paper itself is new to the corpus and each entry could become a task after per-entry validation.", "duplicate_of_existing": "lap-transposon-genotyping", "est_tasks": 10, "source_agent": "web"}
+{"id": "agentex-genetic-codes", "title": "Automated prototyping of genetic codes", "doi": "10.1038/s41586-026-10949-y", "paper_url": "https://doi.org/10.1038/s41586-026-10949-y", "year": 2026, "venue": "Nature", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/FelixRadford/AGENTEX", "code_files": ["AGENTEX reactions/Reactions/mixing.py", "Nucleic_acid_purifications/RNA/Step 1/Purification.py", "Nucleic_acid_purifications/RNA/Step 2/mixing.py", "Nucleic_acid_purifications/RNA/Step 3/Purification.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "in vitro translation reaction assembly, RNA purification", "results_evidence": "Automated prototyping produced and characterised reassigned genetic codes with mass-spec/translation readouts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Repo states Opentrons API 2.13 and has stage scripts, but the paper is ND-licensed and the repo unlicensed; scripts are tied to bespoke labware.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "sapp-dmx-protein-design", "title": "Accelerating protein design by scaling experimental characterization", "doi": "10.1038/s41467-026-76740-9", "paper_url": "https://doi.org/10.1038/s41467-026-76740-9", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/bwicky/SAPP_DMX", "code_files": ["SAPP/SEC_pool_and_norm_v3.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SEC fraction pooling and normalisation for protein characterisation", "results_evidence": "High-throughput expression/characterisation of designed proteins; thousands of designs assayed with the automated pipeline.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper, MIT single-purpose script (pool and normalise) \u2014 a clean medium task.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "openblend-media", "title": "Modular development enables rapid design of media for alternative hosts", "doi": "10.1002/bit.27947", "paper_url": "https://doi.org/10.1002/bit.27947", "year": 2022, "venue": "Biotechnology and Bioengineering", "open_access_license": "unclear (likely subscription)", "code_url": "https://github.com/abiedermann/openblend_public", "code_files": ["run_plate_prep.py", "openblend_plates.py", "plate_builder.py", "cal_protocol.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "combinatorial media blending into microplates", "results_evidence": "Blended media designs were tested in growth experiments for alternative microbial hosts, with growth rates reported per formulation.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "MIT code with a calibration protocol and plate-prep generator, but the paper text is probably not open, and the protocol is generated from an Excel template.", "est_tasks": 3, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "evotron-evolver-sampling", "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback", "doi": "10.1038/s41467-022-32392-z", "paper_url": "https://www.nature.com/articles/s41467-022-32392-z", "year": 2022, "venue": "Nature Communications", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/santkumar/evotron", "code_files": ["ot2/protocol_code/main_protocol.py", "ot2/calibration/get_xyz_location.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated sampling from eVOLVER bioreactors into plates", "results_evidence": "Closed-loop optogenetic control held co-culture ratios at setpoints, measured by cytometry/OD from robot-sampled timepoints.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "CC BY paper and a real sampling protocol, but hardware-coupled (custom needle, eVOLVER) and unlicensed, so simulation needs labware stubs.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "formulations-prep-shampoo", "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset", "doi": "10.1038/s41597-024-03573-w", "paper_url": "https://www.nature.com/articles/s41597-024-03573-w", "year": 2024, "venue": "Scientific Data", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/sustainable-processes/formulations-prep", "code_files": ["OpentronsProtocol_FormulationSamples.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscous liquid formulation preparation with gravimetric verification", "results_evidence": "Gravimetric analysis of robot-prepared formulations and downstream property measurements form the published dataset.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY data descriptor plus one OT-2 script; viscous-liquid handling parameters make a good hard variant. Repo unlicensed.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "tape-organoid-barcoding", "title": "Cell-type-specific signaling networks in heterocellular organoids (TOBis barcoding / robotic organoid extraction)", "doi": "10.1038/s41592-020-0737-8", "paper_url": "https://doi.org/10.1038/s41592-020-0737-8", "year": 2020, "venue": "Nature Methods", "open_access_license": "unclear (subscription)", "code_url": "https://github.com/TAPE-Lab/OT-2_Code", "code_files": ["TOBis_Barcoding/Barcode_Production/126_Plex_Production_Protocol.py", "TOBis_Barcoding/Barcode_Aliquoting/126_Plex_Aliquoting/126_Plex_Aliquoting_Barcodes_1_to_96_using_PCR_plates.py", "REPO/REPO_126_plex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "mass-cytometry barcode production/aliquoting, organoid extraction", "results_evidence": "TOBis barcoded organoids profiled by mass cytometry; signalling networks resolved per cell type.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Seven complete OT-2 protocols, but the paper is subscription-only and the repo has no licence, so paper text must be sourced elsewhere.", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "exposomics-384-flex", "title": "Opentrons Flex 384-well protein-precipitation sample preparation for nontargeted exposomics", "doi": null, "paper_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols", "year": 2025, "venue": "repository only (associated manuscript not located)", "open_access_license": null, "code_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols", "code_files": ["protocols/step1_solvent_addition_and_sample_aliquoting.py", "protocols/step2_dilution_and_supernatant_transfer.py"], "code_license": "MIT", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "protein precipitation / dilution in 384-well format for LC-HRMS", "results_evidence": "README reports up to 288 biological samples plus QC per plate feeding multiple LC-HRMS assays, but no peer-reviewed results found.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT Flex protocols with custom labware (rare and valuable), but no paper located yet, so the paper->code triple is incomplete.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "exfab-qiaseq-flex", "title": "Automated QIAseq FX DNA Library Preparation on the Opentrons Flex", "doi": "10.17504/protocols.io.n2bvjer3pgk5", "paper_url": "https://dx.doi.org/10.17504/protocols.io.n2bvjer3pgk5", "year": 2025, "venue": "protocols.io (ExFAB Biofoundry)", "open_access_license": "CC BY 4.0 (protocols.io)", "code_url": "https://github.com/exfab/Opentrons_Flex_ExFAB", "code_files": ["QIASeq FX 48x 6_24_25.py"], "code_license": "GPL-3.0", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "NGS library preparation (fragmentation, adapter ligation, bead cleanup, PCR)", "results_evidence": "Protocol entry reports libraries prepared for Illumina short-read sequencing of bee gut samples (sequencing-ready yields).", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "A protocols.io DOI with CC BY text is an ideal NL input, GPL-3.0 Flex script matches it one-to-one; Flex coverage is thin in the corpus.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "cayman-his-elisa", "title": "An Opentrons OT-2 workflow for the Cayman His-tag detection ELISA kit", "doi": "10.17504/protocols.io.n92ld4x3nl5b", "paper_url": "https://dx.doi.org/10.17504/protocols.io.n92ld4x3nl5b", "year": 2026, "venue": "protocols.io (Arcadia Science)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow", "code_files": ["scripts/ot2_p1000single_elisa_sample_loading_final.py", "scripts/ot2_p300multi_elisa_wash_substrate.py", "scripts/ot2_p1000single_elisa_sample_loading_waste_chute.py", "tests/ot2_tip_drop_waste_chute_test.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "ELISA sample/standard loading, plate washing, substrate addition", "results_evidence": "Standard curves and His-tag quantification generated from the automated ELISA runs in the Arcadia protocol record.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY protocols.io text, MIT scripts including a hardware test; a clean easy/hard pair (loading vs wash+substrate).", "est_tasks": 4, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "cfrna-pipeline", "title": "An inexpensive semi-automated sample processing pipeline for cell-free RNA (extraction)", "doi": "10.1038/s41596-023-00855-2", "paper_url": "https://doi.org/10.1038/s41596-023-00855-2", "year": 2023, "venue": "Nature Protocols (preprint: 10.1101/2020.08.18.256545)", "open_access_license": "preprint CC BY-NC-ND 4.0; journal version subscription", "code_url": "https://github.com/miramou/cfRNA_pipeline_automation", "code_files": ["Opentrons/scripts/48_format/1_add_slurry_lysis_to_plate.py", "Opentrons/scripts/48_format/3_transfer_etoh_centrifuge_remove_sup_add_etoh.py", "Opentrons/scripts/48_format/5_norgen_add_wash_buffer_elute.py", "Opentrons/scripts/48_format/6_zymo_clean_conc.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell-free RNA extraction and cleanup", "results_evidence": "RNA yields and sequencing library quality from the semi-automated pipeline compared with manual extraction.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Six numbered OT-2 steps (good task series) but code is unlicensed and the open text is the earlier preprint, not the Nature Protocols version.", "est_tasks": 5, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "plant-phenotyping-ot2", "title": "Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience", "doi": "10.1002/aisy.202500624", "paper_url": "https://doi.org/10.1002/aisy.202500624", "year": 2026, "venue": "Advanced Intelligent Systems", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Synthetic-Automated-Systems/automated_phenotyping_system", "code_files": ["Code/OT2Code.py", "Code/OT2Code-FillPlates.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "plate filling and treatment dosing for plant phenotyping", "results_evidence": "Automated phenotyping screen measured growth responses used to select stress-resilient conditions.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "CC BY paper and MIT scripts; two scripts give an easy (fill plates) and harder (full protocol) pair.", "est_tasks": 3, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "imperial-colony-picker", "title": "Automated colony picker add-on for the OT-2 (Imperial SSB MRes; cited by Slowpoke)", "doi": null, "paper_url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker", "year": 2022, "venue": "project report / cited in ACS Synth Biol 2026", "open_access_license": null, "code_url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker", "code_files": ["Client/colony_pcr_reagent_prep_protocol.py", "Client/colony_pcr_resuspension_protocol.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "colony PCR reagent prep and colony resuspension", "results_evidence": "Vision-guided colony picking demonstrated on OT-2; results reported only in the project write-up and via the Slowpoke citation.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Two clean OT-2 scripts closely related to the existing colony-PCR tasks, but no standalone peer-reviewed paper and no licence.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "spot-assay-ot2", "title": "Automated yeast spot assay on Opentrons OT-2 (bioinfo-tsukuba)", "doi": null, "paper_url": "https://github.com/bioinfo-tsukuba/ot2_spot_assay", "year": 2024, "venue": "repository (paper referenced in README, not yet identified)", "open_access_license": null, "code_url": "https://github.com/bioinfo-tsukuba/ot2_spot_assay", "code_files": ["ot2_execute/compiler/compile_predispense.py", "ot2_execute/compiler/compile_after_plate_reader.py", "ot2_execute/compiler/compile_after_plate_reader_for_paper.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "serial dilution and spotting with plate-reader feedback", "results_evidence": "README states the workflow executes automatic spot assays with Byonoy absorbance readings feeding the dispensing plan.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Protocols are generated by compilers rather than being standalone .py, and the paper is unidentified; same lab as the existing pipetting-speed-ot2 source.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "msd-biochemical-assays", "title": "Opentrons OT-2 biochemical assay scripts (Merck/MSD, Bradford and PicoGreen standard curves)", "doi": null, "paper_url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays", "year": 2023, "venue": "company \"papers\" repo (associated publication not located)", "open_access_license": null, "code_url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays", "code_files": ["Bradford_standard_curve.py", "PicoGreen_standard_curve_YW_validated.py"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "standard-curve assays (Bradford protein, PicoGreen dsDNA)", "results_evidence": "Filename and README indicate a validated PicoGreen standard curve run on the OT-2; no published figures located.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Apache-2.0 and simple enough to simulate immediately, but no linked paper or reported results, so it fails the triple requirement.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "llm-rdf-synthesis", "title": "An automatic end-to-end chemical synthesis development platform powered by large language models", "doi": "10.1038/s41467-024-54457-x", "paper_url": "https://www.nature.com/articles/s41467-024-54457-x", "year": 2024, "venue": "Nature Communications", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/Ruan-Yixiang/LLM-RDF", "code_files": ["Backend Files/backend/input_screen.py"], "code_license": "MIT (per README badge)", "robot_platform": "other", "api": "other", "protocol_category": "LLM-driven reaction development and robotic execution", "results_evidence": "End-to-end synthesis campaigns executed with reported yields and optimised conditions.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Strong paper+code pairing but the robot layer is not Opentrons/PLR, so it is more a comparison system than a task source.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "icfree-cfps", "title": "An AI-driven workflow for the accelerated optimization of cell-free protein synthesis", "doi": "10.1016/j.isci.2025.113599", "paper_url": "https://doi.org/10.1016/j.isci.2025.113599", "year": 2025, "venue": "iScience", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/brsynth/icfree-ml", "code_files": ["(no Opentrons protocol .py; generates Echo/liquid-handler instruction CSVs)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "cell-free reaction composition DoE and instruction generation", "results_evidence": "Iterative ML rounds improved cell-free protein yields measured on plate reader across generated compositions.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the output is an instruction CSV for an acoustic dispenser, so a task would need a translation layer rather than an Opentrons script.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "myra-cfe-platform", "title": "A liquid handling platform for standardized quantification of cell-free enzymatic activity", "doi": "10.1093/synbio/ysag010", "paper_url": "https://academic.oup.com/synbio/article/doi/10.1093/synbio/ysag010", "year": 2026, "venue": "Synthetic Biology (OUP)", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Mo42-mb/Myra_automation", "code_files": ["(R script generates python for BMS Myra; no Opentrons protocol)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "cell-free enzymatic activity assay setup", "results_evidence": "Standardised enzymatic activity quantification reproducible across operators/platforms reported in the paper.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "CC BY paper with generated-protocol code for a BMS Myra; useful for cross-platform generalisation tasks but not directly simulatable.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "duckbot-jubilee", "title": "The Duckbot: A system for automated imaging and manipulation of duckweed", "doi": "10.1371/journal.pone.0296717", "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0296717", "year": 2024, "venue": "PLOS ONE", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/machineagency/duckbot", "code_files": ["(Jupyter notebooks driving science_jubilee; no Opentrons .py)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "duckweed plate manipulation, media exchange, imaging", "results_evidence": "Automated growth assays measured duckweed area/growth across treatments.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the Jubilee/science_jubilee API is a third platform; valuable for platform breadth, needs a new runner.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "helleckes-catib-screening", "title": "High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization", "doi": "10.1186/s12934-024-02319-y", "paper_url": "https://doi.org/10.1186/s12934-024-02319-y", "year": 2024, "venue": "Microbial Cell Factories", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023", "code_files": ["(analysis-only python: catibts/models.py, catibts/parsing.py; robot methods not in repo)"], "code_license": "GPL-3.0", "robot_platform": "other", "api": "other", "protocol_category": "automated CatIB expression screening with Bayesian optimisation", "results_evidence": "Screening campaign identified improved CatIB variants with activity measurements across rounds.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "Repo holds analysis code and raw data only; the liquid-handler methods (Tecan/Hamilton) are not published as Python.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "proteoautonet", "title": "ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning", "doi": "10.1038/s41467-026-68484-3", "paper_url": "https://doi.org/10.1038/s41467-026-68484-3", "year": 2026, "venue": "Nature Communications", "open_access_license": "CC BY 4.0 (to confirm)", "code_url": "https://github.com/guomics-lab/ProteoAutoNet", "code_files": ["(11 analysis python files; no liquid-handler protocol script found)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "automated proteomics sample handling + ML analysis", "results_evidence": "Co-elution networks derived from robot-processed samples validated against known complexes.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "Only ML/analysis code is released; no robot protocol code.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "polymerization-planner", "title": "Automation-Assisted Photoinduced Atom Transfer Radical Polymerization", "doi": "10.1021/acspolymersau.5c00067", "paper_url": "https://doi.org/10.1021/acspolymersau.5c00067", "year": 2026, "venue": "ACS Polymers Au", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/GormleyLab/polymerization_planner", "code_files": ["polymerization_planner/runner.py", "polymerization_planner/atrp/calculator.py", "polymerization_planner/pet_raft/calculator.py"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "polymerisation recipe planning for automated dispensing", "results_evidence": "Polymerisations run from planner recipes characterised by GPC (conversion, dispersity).", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Open paper and MIT code, but the package only computes recipes; the dispensing layer (custom handler) is separate.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "sdl-guide-gormley", "title": "A user's guide to your first self-driving liquid handling lab", "doi": "10.1039/d5dd00525f", "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2026/dd/d5dd00525f", "year": 2026, "venue": "Digital Discovery", "open_access_license": "CC BY 3.0", "code_url": "https://github.com/GormleyLab/SDLGuide", "code_files": ["(GUI/driver python for ACRO + Integra pipette; no Opentrons protocol)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "self-driving lab enzyme assay optimisation", "results_evidence": "Closed-loop campaign optimised enzyme assay conditions with plate-reader readouts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Great tutorial-style open text and MIT code, but a bespoke handler API; useful as a non-Opentrons generalisation target.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "pipette-show", "title": "Pipette Show: An Open Source Web Application to Support Pipetting into Microplates", "doi": "10.1021/acssynbio.1c00494", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.1c00494", "year": 2022, "venue": "ACS Synthetic Biology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Global-Biofoundries-Alliance/pipette-show", "code_files": ["(web app; no robot protocol .py)"], "code_license": "MIT", "robot_platform": "other", "api": "other", "protocol_category": "manual pipetting guidance", "results_evidence": "Error rates for manual plate filling with vs without the app.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "No robot code; manual-pipetting aid only.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "opentrons-accs-dup", "title": "Open-source cell culture automation system with integrated cell counting for passaging microplate cultures", "doi": "10.1093/pnasnexus/pgaf385", "paper_url": "https://doi.org/10.1093/pnasnexus/pgaf385", "year": 2025, "venue": "PNAS Nexus", "open_access_license": "CC BY-NC-ND 4.0", "code_url": "https://github.com/czbiohub-sf/accs-protocol-software-pub", "code_files": ["cal_dummy_scripts/cal_cell_splitting.py", "cal_dummy_scripts/cal_96to8x12.py", "accs-protocols/accs_npf/resources/sim_proxy_script/run.py"], "code_license": "BSD-3-Clause", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "cell culture passaging / cell counting", "results_evidence": "Automated passaging maintained cell cultures over weeks with counting accuracy benchmarked against manual counts.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already in the corpus as opencell-automation, but this second BSD-3 repo (protocol framework, calibration scripts, simulation proxy) was not ingested and could yield runnable tasks.", "duplicate_of_existing": "opencell-automation", "est_tasks": 3, "source_agent": "web"}
+{"id": "moeller-library-dup", "title": "Moeller Lab Opentrons protocol library (Zymo magbead extraction, Hackflex, Quantifluor)", "doi": "10.1186/s13059-022-02777-w", "paper_url": "https://doi.org/10.1186/s13059-022-02777-w", "year": 2022, "venue": "Genome Biology", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/tanaes/Moeller_Opentrons_protocol_library", "code_files": ["Extraction/Zymo_fecal-soil_magbead/Zymo_fecal-soil_magbead_B-extraction.py", "Library_Prep/Hackflex/hackflex.py", "Quantification/Quantifluor_DNA_quant/Quantifluor_DNA_four-plates.py", "Transfers/tubes_to_96well.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "magnetic-bead DNA extraction, Hackflex library prep, DNA quantification", "results_evidence": "Hackflex libraries and extractions benchmarked by sequencing yield/quality in the companion paper.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "MIT library with nine OT-2 scripts beyond the Hackflex one already tracked; extraction and quantification protocols are new task material.", "duplicate_of_existing": "moeller-hackflex", "est_tasks": 5, "source_agent": "web"}
+{"id": "maggielam-digestion-dup", "title": "Shotgun proteomics sample processing automated by an open-source lab robot (standard digestion scripts)", "doi": "10.3791/63092", "paper_url": "https://www.jove.com/t/63092", "year": 2021, "venue": "JoVE", "open_access_license": "unclear (JoVE subscription)", "code_url": "https://github.com/MaggieLam-Lab/StandardDigestion-Opentrons", "code_files": ["digestion_scripts/SP3_digestion.py", "digestion_scripts/NoSP3_digestion.py", "digestion_scripts/SP3_peptide_cleanup.py", "misc_scripts/BCA_protocol.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "proteomics digestion, SP3 cleanup, BCA assay", "results_evidence": "Peptide identifications/CVs for automated vs manual digestion reported in the JoVE article.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already represented by shotgun-proteomics-jove; MIT scripts are usable but the JoVE text is not open.", "duplicate_of_existing": "shotgun-proteomics-jove", "est_tasks": 3, "source_agent": "web"}
+{"id": "apex-guide-dup", "title": "Opentrons OT-2 Automated Protein Expression and Purification Guide (APEX companion repo)", "doi": "10.1021/acssynbio.5c00189", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.5c00189", "year": 2025, "venue": "ACS Synthetic Biology", "open_access_license": "unclear (journal version)", "code_url": "https://github.com/btx11/opentrons-apex-protein-guide", "code_files": ["(guide/reimplementation of APEX OT-2 steps)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protein expression and purification", "results_evidence": "APEX validated by expressing and purifying proteins with yields reported in the paper.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Duplicate of the existing apex source; note that the journal version (ACS Synth Biol 2025) is newer than the bioRxiv entry on file.", "duplicate_of_existing": "apex", "est_tasks": 0, "source_agent": "web"}
+{"id": "opensampler-dup", "title": "Modification of a low-cost pipetting robot for nanoliter liquid handling and autosampling for LC-MS", "doi": "10.1002/jssc.70379", "paper_url": "https://doi.org/10.1002/jssc.70379", "year": 2026, "venue": "Journal of Separation Science", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/RTKlab-BYU/OpenSampler", "code_files": ["(OpenSampler/OpenLC control python)"], "code_license": "none", "robot_platform": "other", "api": "other", "protocol_category": "nanoliter autosampling for LC-MS", "results_evidence": "Injection precision and chromatographic performance measured for the modified robot.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already tracked as pipetting-robot-nanoliter; control software is not an Opentrons protocol.", "duplicate_of_existing": "pipetting-robot-nanoliter", "est_tasks": 0, "source_agent": "web"}
+{"id": "proxy-viscometer-dup", "title": "Opentrons for automated and high-throughput viscometry (supplementary protocol files)", "doi": "10.1039/d2dd00126h", "paper_url": "https://doi.org/10.1039/d2dd00126h", "year": 2023, "venue": "Digital Discovery", "open_access_license": "CC BY 4.0", "code_url": "https://github.com/Kedar-Materials-by-Design-Lab/Opentrons-ProxyViscometer", "code_files": ["(protocol files for proxy viscometer; see also beatricesoh/OTProxyViscometer)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "viscosity measurement by timed aspiration", "results_evidence": "Measured viscosities correlated with reference rheometer values.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Duplicate of proxy-viscometer; a second mirror repo (beatricesoh/OTProxyViscometer) exists with the same content.", "duplicate_of_existing": "proxy-viscometer", "est_tasks": 0, "source_agent": "web"}
+{"id": "uc2-platereader-dup", "title": "UC2 Opentrons imaging unit / automated immunostaining (OT-2 + UC2 microscope)", "doi": null, "paper_url": "https://www.protocols.io/view/uc2-automated-immunostaining-protocol-using-the-op-bw8dphs6", "year": 2022, "venue": "protocols.io + openUC2 docs", "open_access_license": "CC BY 4.0 (protocols.io)", "code_url": "https://github.com/beniroquai/Opentrons-Microscope-Platereader", "code_files": ["IMJOY/main_opentrons.py"], "code_license": "NOASSERTION", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "automated immunostaining with in-situ imaging", "results_evidence": "Immunostained plates imaged on the UC2 microscope with staining quality shown in the protocol record.", "wet_lab_validated": true, "readiness": "partial", "readiness_reason": "Already covered by uc2-hi2; the protocols.io immunostaining entry is a CC BY NL source that could still be paired with the control script.", "duplicate_of_existing": "uc2-hi2", "est_tasks": 2, "source_agent": "web"}
+{"id": "biomationscripter", "title": "BiomationScripter: Python library for scripting bio-automation protocols", "doi": null, "paper_url": "https://biomationscripterlib.readthedocs.io", "year": 2022, "venue": "software (associated paper not located)", "open_access_license": null, "code_url": "https://github.com/intbio-ncl/BiomationScripterLib", "code_files": ["BiomationScripter/OTProto/*.py (20 Opentrons-aware files incl. labware test protocols)"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "protocol-generation library (templates for PCR, dilution, transformation)", "results_evidence": "No wet-lab results tied to a publication found.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT library whose OTProto templates could seed tasks, but no paper and protocols are generated rather than literal scripts.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "dtu-synbio-automation", "title": "DTU Synbio lab automation protocol collection", "doi": null, "paper_url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation", "code_files": ["protocols/opentrons/library_examples/*.py", "protocols/opentrons/Course_Introduction_to_automation/*.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "teaching/library protocols (agar plating, liquid-class optimisation, parameterised transfers)", "results_evidence": "No published results; teaching and internal-use repository.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT and clean enough to simulate, and useful as extra solution exemplars, but no paper so it is not a triple.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "damplab-sars-assay", "title": "DAMP Lab OT-2 diagnostic assay scripts (bead-based RNA extraction + multiplex RT-qPCR setup)", "doi": null, "paper_url": "https://github.com/DAMPLAB/OT2-SARS-CoV2", "year": 2020, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/DAMPLAB/OT2-SARS-CoV2", "code_files": ["rna_extraction_magmax/rna_extraction_magmax.py", "qPCR_taqpath_multiplex/qPCR_taqpath_multiplex.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "magnetic-bead nucleic acid extraction, qPCR plate setup", "results_evidence": "No peer-reviewed results in the repo; kit instructions are the reference.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Two complete scripts in a protocol family already represented by covid19clinic/hulp sources, but no paper and no licence.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "newcastle-neg-opentrons", "title": "Newcastle Network Ecology Group OT-2 protocol and labware collection", "doi": null, "paper_url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons", "year": 2022, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons", "code_files": ["Labware/api_v2/test_*.py", "Protocols/*.py (51 Opentrons-aware files; mix of API v1 and v2)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "mixed lab protocols and custom labware definitions", "results_evidence": "No linked publication found.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "No paper, unlicensed, and many scripts are API v1 labware tests.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "endylab-opentrons", "title": "Endy Lab Opentrons protocol collection", "doi": null, "paper_url": "https://github.com/EndyLab/opentrons", "year": 2018, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/EndyLab/opentrons", "code_files": ["protocols/OT2/pcr.py", "protocols/OT2/primer-dilute.py", "protocols/dilution-series.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "PCR setup, dilution series, calibration", "results_evidence": "No linked publication.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "Mostly legacy API v1, no paper, no licence.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "xchem-opentrons", "title": "XChem Opentrons reaction liquid-handling toolkit", "doi": null, "paper_url": "https://github.com/xchem/opentrons", "year": 2019, "venue": "repository only (XChem crystallography pipeline papers do not release these scripts)", "open_access_license": null, "code_url": "https://github.com/xchem/opentrons", "code_files": ["examples/**/*.py (60 Opentrons-aware files, API v1 era)"], "code_license": "Apache-2.0", "robot_platform": "ot2", "api": "opentrons_v1", "protocol_category": "reaction dispensing arrays for crystallographic screening", "results_evidence": "No single paper ties these scripts to reported results.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "Apache-2.0 but API v1 generated scripts and no paper pairing.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "pozzo-ot2-doe", "title": "Pozzo group OT-2 design-of-experiments protocols", "doi": null, "paper_url": "https://github.com/pozzo-research-group/OT2Protocols", "year": 2021, "venue": "repository only (group has related SDL papers)", "open_access_license": null, "code_url": "https://github.com/pozzo-research-group/OT2Protocols", "code_files": ["ot2protocol/app_protocols/DES_combined_protocol.py", "PlanPrepareProcess_OT2/Modules/OT2Commands.py"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "formulation DoE sample preparation", "results_evidence": "Results appear in separate group publications, not this repo.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT and simulatable, but the paper pairing must be established before it is a triple.", "est_tasks": 1, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "myrplate-flex-casting", "title": "myrPlate engineered connective tissue casting on Opentrons Flex", "doi": null, "paper_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15", "code_files": ["myrPlate_tissue_casting_8Ch1ml_Fast_V15-ECTsFinal.py", "myrPlate-V15(aspiration).py", "myrPlate-V15(dispensing).py"], "code_license": "MIT", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "collagen/cell suspension casting into 48-well tissue plates", "results_evidence": "README describes casting engineered connective tissues; no publication located.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "MIT Flex scripts with viscous cell-laden gel handling (valuable hard task) but no paper yet.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "flex-genomics-di-omics", "title": "Opentrons Flex whole-genome / methylation / TIP-seq workflows (di-omics)", "doi": null, "paper_url": "https://github.com/di-omics/ot-flex-automation", "year": 2026, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/di-omics/ot-flex-automation", "code_files": ["protocols/whole_genome_seq_flex.py", "protocols/methylation_sequencing_flex.py", "protocols/tipseq_epigenome_flex.py", "bench/wgs_preparation_water_test_flex.py"], "code_license": "none", "robot_platform": "flex", "api": "opentrons_v2", "protocol_category": "NGS library prep on Flex with off-deck handoffs", "results_evidence": "README tracks validation status per protocol but no publication.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "Rich Flex protocol set with explicit validation status, but unlicensed and unpublished.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "kedar-balance-integration", "title": "Opentrons OT-2 mass-balance integration (application note supplement)", "doi": null, "paper_url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance", "year": 2022, "venue": "Opentrons application note", "open_access_license": null, "code_url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance", "code_files": ["OT-2_BalanceAutomation.ipynb (notebook, no .py)"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "gravimetric calibration with external balance", "results_evidence": "Gravimetric accuracy of dispensed volumes reported in the application note.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "Notebook-only, external-hardware dependent, no peer-reviewed paper.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "retro-10x-scrnaseq", "title": "OT-2 10x scRNA-seq library prep with multiplexing (Retro Biosciences)", "doi": null, "paper_url": "https://github.com/retrobiosciences/opentrons-10x", "year": 2023, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/retrobiosciences/opentrons-10x", "code_files": ["multi_8sample.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "single-cell library prep with magnetic bead steps", "results_evidence": "README warns the protocol is difficult to run reliably; no published results.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "No paper, no licence, and the authors flag reliability problems.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "sp3-magbead-protocol-repo", "title": "Automated magnetic bead-based digestion protocols for Opentrons OT-2 (proteomics CNB-CBM)", "doi": null, "paper_url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol", "year": 2025, "venue": "repository only", "open_access_license": null, "code_url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol", "code_files": ["(no .py in repo; protocol documentation only)"], "code_license": "MIT", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "SP3 bead digestion", "results_evidence": "None published.", "wet_lab_validated": false, "readiness": "no", "readiness_reason": "No Python protocol files present despite the MIT licence and OT-2 framing.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "worm-food-preference", "title": "C. elegans food preference protocol (bacteria and worm spotting on OT-2)", "doi": "10.1242/jeb.01955", "paper_url": "https://github.com/slhogle/c_elegans_food_preference_protocol", "year": 2023, "venue": "repository (protocol adapted from J Exp Biol 2006)", "open_access_license": "source paper subscription", "code_url": "https://github.com/slhogle/c_elegans_food_preference_protocol", "code_files": ["02_spot_bacteria.py", "03_spot_worms.py"], "code_license": "GPL-3.0", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "spotting bacteria and worms onto agar plates", "results_evidence": "Protocol reproduces a published behavioural assay; no new results in the repo.", "wet_lab_validated": false, "readiness": "partial", "readiness_reason": "GPL-3.0 and two tidy scripts; the referenced paper predates the automation, so the triple is weak.", "est_tasks": 2, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "ant-cloning", "title": "Automated cloning by natural transformation (ANT) OT-2 workflow", "doi": "10.1021/acssynbio.0c00240", "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.0c00240", "year": 2020, "venue": "ACS Synthetic Biology", "open_access_license": "unclear (journal)", "code_url": "https://github.com/ljm176/ANTCloning", "code_files": ["Step 1_PCRSetup.py", "Step 2_Dilution and Digestion.py", "Step 3_OEPCR.py", "Step 4_Transformation.py", "Step 5_Plating.py"], "code_license": "none", "robot_platform": "ot2", "api": "opentrons_v2", "protocol_category": "PCR, digestion, overlap-extension PCR, natural transformation, plating", "results_evidence": "Cloning efficiency and correct-assembly rates for automated natural transformation reported in the paper.", "wet_lab_validated": true, "readiness": "ready", "readiness_reason": "Five numbered end-to-end scripts explicitly tied to a named publication; repo unlicensed and the ACS text may need an author copy.", "est_tasks": 6, "source_agent": "web", "duplicate_of_existing": null}
+{"id": "opentrons-physicalai-hf", "title": "Opentrons/PhysicalAI (Hugging Face dataset of Flex teleoperation episodes)", "doi": null, "paper_url": "https://huggingface.co/datasets/Opentrons/PhysicalAI", "year": 2026, "venue": "Hugging Face dataset (Opentrons)", "open_access_license": "unstated on dataset card", "code_url": "https://huggingface.co/datasets/Opentrons/PhysicalAI", "code_files": ["(HDF5 episodes + GIFs, e.g. flex_to_biotek/inference/*.hdf5; no protocol .py)"], "code_license": "unstated", "robot_platform": "flex", "api": "other", "protocol_category": "Flex plate-handoff manipulation episodes (imitation learning data)", "results_evidence": "Inference session summaries record on-robot execution of plate handoffs to a BioTek reader.", "wet_lab_validated": true, "readiness": "no", "readiness_reason": "No protocol code or paper; relevant as embodiment data rather than a paper->code task, and the licence is unstated.", "est_tasks": 0, "source_agent": "web", "duplicate_of_existing": null}
diff --git a/research/expansion/web_notes.md b/research/expansion/web_notes.md
new file mode 100644
index 0000000..ff02778
--- /dev/null
+++ b/research/expansion/web_notes.md
@@ -0,0 +1,107 @@
+# Web expansion sweep — notes (source_agent: web, 2026-10-11/12)
+
+Goal: find new (paper, public robot code, reported wet-lab results) triples for Text2WetLab, deduplicated
+against the 48 papers in `docs/task-sources.md` and the folders under `sources/`.
+
+## Searches run
+
+Literature indexes
+- Europe PMC REST search: `("opentrons" OR "pylabrobot" OR "pyhamilton") AND ("github.com" OR "zenodo")`
+  → 251 records (2016–2026); full-text XML pulled for 204 of them, then GitHub/Zenodo links and
+  Opentrons-mention counts extracted per paper (ranked table in the scratch run; top ~120 inspected by hand).
+- Crossref `query.bibliographic` lookups to resolve DOIs, venues and licences for 15 titles found only
+  via repo READMEs (halogenation platform, MassSpecPreppy, C. glutamicum autoclone, Culturomics,
+  esterification library, plant phenotyping, LAP format, enzyme-discovery pipeline, ELISA protocols.io entry, …).
+- Targeted web searches: Opentrons/Flex protocol papers 2023–2026; PyLabRobot/Hamilton validated protocols;
+  SLAS Technology / HardwareX / ACS Synth Biol / PLOS ONE Opentrons code-availability statements;
+  self-driving-lab + OT-2 + Bayesian optimisation; protocol-to-code benchmarks and datasets.
+  (Web-search quota was exhausted late in the run; Crossref + Europe PMC + GitHub APIs covered the rest.)
+
+Code indexes
+- GitHub code search (`search/code`) for `apiLevel` co-occurring with doi / biorxiv / "et al" /
+  publication / cite, plus `opentrons doi.org`, `pylabrobot doi`, `protocol_api zenodo` → 245 hits, mostly noise,
+  ~15 usable repos.
+- GitHub repo search: `topic:opentrons`, `topic:opentrons-ot2`, `topic:liquid-handling`, `topic:opentrons-flex`,
+  name/readme searches for opentrons+paper/manuscript/biorxiv/zenodo → 398 + 469 rows, filtered to ~70 relevant repos.
+- Hugging Face dataset API searches: opentrons, protocol-code, lab automation, pylabrobot, bioprot,
+  protocolqa, labbench, bioplanner, "wet lab protocol".
+
+Verification (per candidate repo): `gh api repos/OWNER/REPO` for existence/licence/default branch,
+`git/trees/<branch>?recursive=1` for the full file list, and raw content checks on up to 60 `.py` files for
+`from opentrons` / `import opentrons` / `apiLevel` / `protocol_api` / `pylabrobot`. ~45 repos were verified this
+way (a GitHub secondary rate limit forced the last five to be checked via the unauthenticated API).
+
+## Counts
+
+| | |
+|---|---|
+| Candidates screened and recorded | 60 |
+| Repos verified to exist (API) | 45 (all 45 existed; 0 dead links) |
+| Repos with confirmed Opentrons/PLR `.py` (import or `apiLevel`) | 31 |
+| readiness = ready | 21 |
+| readiness = partial | 29 |
+| readiness = no | 10 |
+| New (not in the 48-paper corpus) | 52 |
+| Marked `duplicate_of_existing` | 8 (opencell-automation, moeller-hackflex, shotgun-proteomics-jove, apex, pipetting-robot-nanoliter, proxy-viscometer, uc2-hi2, lap-transposon-genotyping) |
+| Sum of `est_tasks` | 159 (≈118 from the `ready` + strong `partial` rows) |
+| Platform mix | ot2 40, flex 4, other 16 (Jubilee, ACRO/Integra, BMS Myra, acoustic dispenser, analysis-only) |
+
+Licence notes: 13 candidate repos carry a permissive licence (MIT/Apache-2.0/BSD-3), 4 are copyleft
+(GPL-3.0, AGPL-3.0), and 21 have no licence file at all (reference-only, cannot be vendored — same constraint
+the corpus already applies to APEX and HULP). Paper licences: 24 of the new candidates are CC BY or CC BY-NC,
+8 are CC BY-NC-ND (link-only), and 6 are subscription/unclear.
+
+## Existing datasets/benchmarks we could absorb or compare against
+
+| Dataset / benchmark | Content & size | Robot code? | Licence |
+|---|---|---|---|
+| **BioProBench** (arXiv 2505.07889, ICML 2026; `github.com/YuyangSunshine/bioprobench`, HF `BioProBench`) | 22,413 human-written protocols → 523,784 task instances across 5 tasks (QA, step ordering, error correction, generation, reasoning) | No — natural-language protocol reasoning only | CC BY-NC 4.0 (repo shows NOASSERTION) |
+| **BioProt / BioPlanner** (EMNLP 2023, arXiv 2310.10632; `github.com/bioplanner/bioplanner`) | 100 protocols.io protocols with pseudocode + function-library annotations; 5 python eval/prompt files | Pseudocode, not robot API code | no LICENSE file in repo |
+| **LAB-Bench** (`futurehouse/lab-bench`) | 1,967 items total; relevant subsets ProtocolQA 108, CloningScenarios 33 | No | CC BY-SA 4.0 |
+| **LAB-Bench 2** (`EdisonScientific/labbench2`, arXiv 2604.09554) | successor set incl. `protocolqa2` config (size endpoint unavailable at time of check) | No | CC BY-SA 4.0 |
+| **AEGIS** (arXiv 2607.15620) | 24 OT-2 protocols across 5 assay families, plus validation benchmark and monitoring model weights; live OT-2 demo | Yes — OT-2 Python protocols, stated MIT | MIT (per paper; repo URL not given in the abstract page) |
+| **ProtoPilot** (arXiv 2606.31763) | 294 tasks derived from 98 gold-standard protocols; reports Opentrons code-gate pass rates (88.2% vs 32.4% baseline) and wet-lab checks | Generated Opentrons code; release not stated | not stated |
+| **ProtoAct / BioP2E** (arXiv 2608.01690) | 22 cell-culture protocols → 258 monitoring conditions, 910 executable subtasks, 962 grounded action calls | Embodied action calls (manipulator), not liquid-handler Python | not stated |
+| **ProtoCode** (SLAS Technology 29(3), 2024) | LLM pipeline turning published PCR protocols into machine-readable thermocycler files; web server only, no dataset dump | Thermocycler files, not Opentrons | web service, licence unstated |
+| **BioCoder** (arXiv 2308.16458) | 2,269 bioinformatics coding problems | No robot code | open (repo) |
+| **Opentrons/PhysicalAI** (HF) | Flex teleoperation/inference episodes (HDF5 + GIFs) for plate handoffs to a plate reader | Embodiment data, no protocol `.py` | unstated |
+| **Opentrons/Protocols** (`github.com/Opentrons/Protocols`) | Public protocol library source; large, but entries are vendor/kit protocols and rarely cite a paper — low triple yield, useful as solution-style exemplars | Yes, OT-2/Flex Python | no LICENSE file |
+
+Take-away: nothing in this list pairs a *published paper* with *runnable liquid-handler code* and *wet-lab results*
+the way Text2WetLab does. AEGIS (24 OT-2 protocols, MIT) is the closest and the best absorb/compare target;
+BioProBench and LAB-Bench ProtocolQA are text-only and belong in a related-work comparison, not an absorb.
+
+## Top 15 candidates
+
+1. **tidytron** — SLAS Technol 2024, Apache-2.0 repo, 37 OT-2 scripts, wash-and-reuse validated by carryover assays. Highest ready-to-task density found.
+2. **beckham-enzyme-pipeline** — Sci Rep 2024 (CC BY), 21 modular OT-2 scripts covering transformation → inoculation → assay; repo unlicensed.
+3. **massspecpreppy** — Proteomics 2023, GPL-3.0, one script per stage (BCA, digestion, SP3, Evotip) with quantitative manual-vs-robot comparison (101.3% vs 96.3% BCA recovery).
+4. **jubiotech-ot2-autoclone** — Appl Microbiol Biotechnol 2022 (CC BY), AGPL-3.0, seven one-protocol-per-file scripts (Golden Gate, heat-shock, digest, plasmid prep, plating).
+5. **culturomics-isolation** — iMetaOmics 2025 (CC BY), 11 single-step OT-2 scripts (microvolume extraction, two-step PCR, bead purification, pooling).
+6. **ant-cloning** — ACS Synth Biol 2020, five numbered end-to-end scripts (PCR → digestion → OE-PCR → transformation → plating) explicitly tied to the paper.
+7. **roboctab** — Plants 2025 (CC BY) with *both* OT-2 and Flex versions of one CTAB extraction: a natural easy/hard pair and rare Flex coverage.
+8. **cayman-his-elisa** — protocols.io CC BY text + MIT repo with loading, wash/substrate and a hardware test script (Arcadia Science).
+9. **greenaway-halogenation** — BSD-3-Clause, nine OT-2 scripts across screening stages plus NMR prep; chemistry breadth for the benchmark.
+10. **greenaway-pocs** — Chem Sci 2024 (CC BY), repo even ships `simulate.py`, so the scripts are known to pass `opentrons_simulate`.
+11. **exfab-qiaseq-flex** — protocols.io CC BY NGS protocol with a matching GPL-3.0 Flex script, one-to-one.
+12. **lucks-cellfree-biosensor** — open preprint, script maps to a single figure (384-well cell-free build); good viscous-liquid hard task.
+13. **hyrad-adna-capture** — Mol Ecol Resour 2022, one self-contained script driving magnetic + temperature modules.
+14. **damplab-moclo-transformation** — Synth Biol 2022 (CC BY) + BSD-3 MoClo/transformation templates; closest licence-clean analogue to the existing APEX tasks.
+15. **lap-format-repository** — ACS Synth Biol 2023 LAP paper (new to the corpus) over the already-known LAPrepository code: ~37 validated entry scripts, each a candidate task once licence is clarified.
+
+Runners-up worth a second look: `sapp-dmx-protein-design` (Nat Commun 2026, MIT, SEC pooling),
+`blots-ot2` (Current Protocols 2026 — protocol-journal text is ideal NL input), `greenaway-mocs`,
+`formulations-prep-shampoo` (viscous handling), `plant-phenotyping-ot2`, `moeller-library-dup`
+(9 MIT scripts beyond the Hackflex one already tracked), `opentrons-accs-dup` (BSD-3 framework repo not yet ingested).
+
+## Gaps / follow-ups
+
+- Flex and PyLabRobot coverage is still thin: only 4 Flex candidates (roboctab, exfab-qiaseq-flex,
+  exposomics-384-flex, flex-genomics-di-omics) and no new PyLabRobot paper+code+results triple beyond the
+  PyLabRobot paper itself (already in corpus via chory/olh forks).
+- Hamilton/Tecan papers mostly release analysis code only (helleckes-catib-screening, proteoautonet) —
+  the robot methods stay in vendor formats.
+- Three repos need a paper identified before they count as triples: `exposomics-384-flex`,
+  `spot-assay-ot2`, `biomationscripter`.
+- AEGIS's own OT-2 protocol set (MIT) should be located and screened next; its repo URL was not in the
+  abstract page.
diff --git a/scripts/ingest.py b/scripts/ingest.py
index 9c196bf..337a3ec 100644
--- a/scripts/ingest.py
+++ b/scripts/ingest.py
@@ -174,38 +174,172 @@ def analyse_clone(path):
     return {"py_files": len(py), "opentrons_py_files": len(ot), "api_levels": sorted(api), "robot_mentions": sorted(robots)}
 
 
-def ingest_code(url, slug):
-    host, owner, name = repo_of(url)
-    rec = {"url": url, "host": host, "status": "manual"}
-    if host != "github.com" or not owner:
-        rec["status"] = "non-github: needs manual download"
-        return rec
-    meta = gh_json(f"repos/{owner}/{name}")
-    if meta is None:
-        rec["status"] = "not found (404 or private)"
-        return rec
-    lic = (meta.get("license") or {}).get("spdx_id")
-    rec.update({"repo": f"{owner}/{name}", "default_branch": meta["default_branch"], "size_kb": meta["size"], "archived": meta["archived"],
-                "licence": lic if lic and lic != "NOASSERTION" else ("unclear" if lic else "none"),
-                "redistributable": "yes" if lic in {"MIT", "Apache-2.0", "BSD-2-Clause", "BSD-3-Clause", "ISC", "Unlicense", "CC0-1.0"} else "no"})
-    if meta["size"] > MAX_REPO_KB:
-        rec["status"] = f"skipped: {meta['size'] // 1024} MB exceeds the clone limit"
-        return rec
-    dest = CACHE / "code" / slug / f"{owner}__{name}"
+PERMISSIVE = {"MIT", "Apache-2.0", "BSD-2-Clause", "BSD-3-Clause", "ISC", "Unlicense", "CC0-1.0"}
+SPARSE = ["*.py", "*.ipynb", "*.json", "*.yaml", "*.yml", "*.toml", "*.cfg", "*.md", "*.rst", "*.txt", "*.csv", "*.xdl", "*.xml",
+          "LICENSE*", "LICENCE*", "COPYING*"]
+ARCHIVE_EXT = (".zip", ".tar.gz", ".tgz", ".tar")
+
+
+def licence_from_text(root):
+    """SPDX-ish id from a LICENSE/COPYING file, for hosts that do not report one."""
+    for f in sorted(root.rglob("*")):
+        if f.is_file() and re.match(r"(licen[cs]e|copying)", f.name, re.I) and ".git" not in f.parts:
+            t = f.read_text(errors="replace")[:4000]
+            for pat, spdx in [(r"MIT License|Permission is hereby granted, free of charge", "MIT"), (r"Apache License,? Version 2", "Apache-2.0"),
+                              (r"GNU AFFERO GENERAL PUBLIC LICENSE", "AGPL-3.0"), (r"GNU LESSER GENERAL PUBLIC", "LGPL-3.0"),
+                              (r"GNU GENERAL PUBLIC LICENSE\s+Version 3", "GPL-3.0"), (r"GNU GENERAL PUBLIC LICENSE\s+Version 2", "GPL-2.0"),
+                              (r"Redistribution and use in source and binary forms", "BSD-3-Clause"), (r"Creative Commons Attribution 4", "CC-BY-4.0"),
+                              (r"CC0|Creative Commons Zero", "CC0-1.0"), (r"unlicense\.org", "Unlicense")]:
+                if re.search(pat, t, re.I):
+                    return spdx
+            return "unclear"
+    return "none"
+
+
+def git_clone(remote, dest, partial):
+    """Shallow clone; a partial clone (sparse checkout of code, configs and docs) for repositories over the size limit."""
     if dest.exists():
         shutil.rmtree(dest)
     dest.parent.mkdir(parents=True, exist_ok=True)
-    r = subprocess.run(["git", "clone", "-q", "--depth", "1", f"https://github.com/{owner}/{name}", str(dest)], capture_output=True, text=True)
+    if not partial:
+        r = subprocess.run(["git", "clone", "-q", "--depth", "1", remote, str(dest)], capture_output=True, text=True, timeout=900)
+        return r.returncode == 0, r.stderr
+    r = subprocess.run(["git", "clone", "-q", "--depth", "1", "--filter=blob:none", "--no-checkout", remote, str(dest)],
+                       capture_output=True, text=True, timeout=900)
     if r.returncode:
-        rec["status"] = "clone failed: " + r.stderr.strip()[-100:]
-        return rec
-    rec["commit"] = subprocess.run(["git", "-C", str(dest), "rev-parse", "HEAD"], capture_output=True, text=True).stdout.strip()
+        return False, r.stderr
+    subprocess.run(["git", "-C", str(dest), "sparse-checkout", "set", "--no-cone", *SPARSE], capture_output=True, text=True)
+    r = subprocess.run(["git", "-C", str(dest), "checkout", "-q"], capture_output=True, text=True, timeout=900)
+    return r.returncode == 0, r.stderr
+
+
+def download_files(files, dest):
+    """files: [(name, url, size_bytes)]. Downloads up to MAX_REPO_KB in total and unpacks archives."""
+    if dest.exists():
+        shutil.rmtree(dest)
+    dest.mkdir(parents=True, exist_ok=True)
+    total, got, skipped = 0, [], []
+    with httpx.Client(headers=HEADERS, timeout=600, follow_redirects=True) as http:
+        for name, url, size in sorted(files, key=lambda f: (not f[0].lower().endswith(ARCHIVE_EXT + (".py",)), f[2] or 0)):
+            if (size or 0) + total > MAX_REPO_KB * 1024:
+                skipped.append(name)
+                continue
+            r = get(http, url)
+            if r is None or r.status_code != 200:
+                skipped.append(name)
+                continue
+            out = dest / pathlib.Path(name).name
+            out.write_bytes(r.content)
+            total += len(r.content)
+            got.append(name)
+            if out.name.lower().endswith(ARCHIVE_EXT):
+                try:
+                    shutil.unpack_archive(str(out), str(dest / (out.name + "_x")))
+                except Exception:
+                    pass
+    return got, skipped, total
+
+
+def zenodo_id(url):
+    m = re.search(r"zenodo\.(\d+)|zenodo\.org/(?:record|records)/(\d+)", url)
+    return (m.group(1) or m.group(2)) if m else None
+
+
+def osf_id(url):
+    m = re.search(r"osf\.io/([a-z0-9]{5})", url)
+    return m.group(1) if m else None
+
+
+def osf_files(node):
+    """Walk an OSF node's osfstorage and list (path, download url, size)."""
+    out, stack = [], [f"https://api.osf.io/v2/nodes/{node}/files/osfstorage/"]
+    with httpx.Client(headers=HEADERS, timeout=60, follow_redirects=True) as http:
+        while stack and len(out) < 2000:
+            r = get(http, stack.pop())
+            if r is None or r.status_code != 200:
+                continue
+            j = r.json()
+            for d in j.get("data", []):
+                a = d["attributes"]
+                if a["kind"] == "folder":
+                    stack.append(d["relationships"]["files"]["links"]["related"]["href"])
+                else:
+                    out.append((a["materialized_path"].lstrip("/"), d["links"]["download"], a.get("size") or 0))
+            if j.get("links", {}).get("next"):
+                stack.append(j["links"]["next"])
+    return out
+
+
+def finish(rec, dest):
     rec.update(analyse_clone(dest))
-    rec["status"] = "cloned"
     rec["cache_path"] = str(dest).replace(str(pathlib.Path.home()), "~")
+    if rec.get("licence") in (None, "", "none", "unclear"):
+        rec["licence"] = licence_from_text(dest)
+    rec["redistributable"] = "yes" if rec["licence"] in PERMISSIVE else "no"
     return rec
 
 
+def ingest_code(url, slug):
+    rec = {"url": url, "status": "manual"}
+    if not re.match(r"https?://", url or ""):
+        rec["status"] = "no public code"
+        return rec
+    host, owner, name = repo_of(url)
+    rec["host"] = host
+    if "zenodo" in url and zenodo_id(url):
+        zid = zenodo_id(url)
+        with httpx.Client(headers=HEADERS, timeout=60, follow_redirects=True) as http:
+            r = get(http, f"https://zenodo.org/api/records/{zid}")
+        if r is None or r.status_code != 200:
+            rec["status"] = "zenodo record not found"
+            return rec
+        meta = r.json()
+        files = [(f["key"], f["links"]["self"], f.get("size") or 0) for f in meta.get("files", [])]
+        dest = CACHE / "code" / slug / f"zenodo-{zid}"
+        got, skipped, total = download_files(files, dest)
+        rec.update({"repo": f"zenodo:{zid}", "licence": ((meta.get("metadata") or {}).get("license") or {}).get("id") or "",
+                    "files": len(files), "files_downloaded": len(got), "files_skipped_size": skipped, "size_kb": total // 1024})
+        rec["status"] = "downloaded" if got else "zenodo: no files within the size limit"
+        return finish(rec, dest) if got else rec
+    if "osf.io" in host and osf_id(url):
+        node = osf_id(url)
+        files = osf_files(node)
+        dest = CACHE / "code" / slug / f"osf-{node}"
+        got, skipped, total = download_files(files, dest)
+        rec.update({"repo": f"osf:{node}", "files": len(files), "files_downloaded": len(got), "files_skipped_size": skipped, "size_kb": total // 1024})
+        rec["status"] = "downloaded" if got else "osf: no files downloaded"
+        return finish(rec, dest) if got else rec
+    if host in ("huggingface.co", "www.protocols.io", "protocols.io"):
+        rec["status"] = "not code: " + ("dataset" if host == "huggingface.co" else "protocol text")
+        return rec
+    if host == "github.com" and owner and not name:
+        rec["status"] = "organisation link: name the repository with --code-url"
+        return rec
+    if not owner:
+        rec["status"] = "non-git link: needs manual download"
+        return rec
+    if host == "github.com":
+        meta = gh_json(f"repos/{owner}/{name}")
+        if meta is None:
+            rec["status"] = "not found (404 or private)"
+            return rec
+        lic = (meta.get("license") or {}).get("spdx_id")
+        rec.update({"repo": f"{owner}/{name}", "default_branch": meta["default_branch"], "size_kb": meta["size"], "archived": meta["archived"],
+                    "licence": lic if lic and lic != "NOASSERTION" else ("unclear" if lic else "none")})
+        partial = meta["size"] > MAX_REPO_KB
+    else:  # GitLab and other git hosts: owner/group path may be nested, so clone the URL as given
+        rec["repo"] = urlparse(url).path.strip("/").removesuffix(".git")
+        partial = True
+    dest = CACHE / "code" / slug / f"{owner}__{(name or 'repo')}"
+    ok, err = git_clone(url.removesuffix("/") if host != "github.com" else f"https://github.com/{owner}/{name}", dest, partial)
+    if not ok:
+        rec["status"] = "clone failed: " + err.strip()[-100:]
+        return rec
+    rec["commit"] = subprocess.run(["git", "-C", str(dest), "rev-parse", "HEAD"], capture_output=True, text=True).stdout.strip()
+    rec["status"] = "cloned (partial: code, configs and docs only)" if partial else "cloned"
+    return finish(rec, dest)
+
+
 # ---------------------------------------------------------------- merging with a previous record
 def stricter(new, old):
     """A previous explicit "no" always wins; any other stored value ("unknown" just means nothing was known yet)
@@ -229,8 +363,9 @@ def merge_prev(rec, prev):
     merged = []
     for c in rec.get("code", []):
         o = old_code.get(c.get("url"))
-        if o and (o.get("host") != "github.com" or o.get("status") == "downloaded"):
-            c = o                                   # hand-managed non-GitHub archive: never overwritten
+        fetched = str(c.get("status", "")).startswith(("cloned", "downloaded"))
+        if o and (o.get("status") == "downloaded" and not o.get("files_downloaded") or (o.get("host") != "github.com" and not fetched)):
+            c = o                                   # hand-managed archive, or a non-GitHub link this run could not fetch: kept
         elif o:
             keep = stricter(c.get("redistributable"), o.get("redistributable"))
             if keep == "no" and c.get("redistributable") != "no" and o.get("licence"):
diff --git a/scripts/ingest_experimental.py b/scripts/ingest_experimental.py
new file mode 100644
index 0000000..96fa1dd
--- /dev/null
+++ b/scripts/ingest_experimental.py
@@ -0,0 +1,102 @@
+"""
+Ingest the experimental expansion candidates (research/expansion/merged_candidates.jsonl) with scripts/ingest.py.
+
+    python scripts/ingest_experimental.py [--registry-only] [--only ID ...] [--force]
+
+Experimental sources live apart from the curated corpus so its counts and scripts are unchanged:
+sources/experimental/sources.json is their registry and sources/experimental/<id>/record.json their records
+(scripts that glob sources/*/record.json or read sources/sources.json do not see them). Each record is tagged
+"experimental": true with the search that found it and its readiness, structure level and simulator status.
+PDFs and clones go to the same cache outside the repo as ingest.py ($INGEST_CACHE). Never spends API credit.
+Resumable: a candidate with a record is skipped unless --force, so it can be re-run after a dropped connection.
+"""
+import argparse
+import json
+import pathlib
+import subprocess
+import sys
+
+ROOT = pathlib.Path(__file__).resolve().parent.parent
+EXP = ROOT / "research/expansion"
+DEST = ROOT / "sources/experimental"
+# Code links the searches got wrong, resolved by hand (2026-10-13): an organisation link or a renamed repository.
+CODE_FIXES = {
+    "archemist": "https://github.com/cooper-group-uol-robotics/archemist",
+    "takahashi-turbidostat": "https://github.com/Flexostat/Flexostat-interface",
+    "synthetic-cells-robotics": "https://github.com/IdoGalil/syn-cells-classification",
+}
+FETCHED = ("cloned", "downloaded", "not code", "no public code")
+
+
+def candidates():
+    rows = [json.loads(l) for l in (EXP / "merged_candidates.jsonl").read_text().splitlines() if l.strip()]
+    ver = {}
+    if (EXP / "verification.jsonl").exists():
+        ver = {r["id"]: r for r in (json.loads(l) for l in (EXP / "verification.jsonl").read_text().splitlines() if l.strip())}
+    out = []
+    for r in rows:
+        if r.get("duplicate_of_existing"):
+            continue
+        doi = (r.get("doi") or "").strip().removeprefix("https://doi.org/").removeprefix("doi:") or None
+        if not doi and not r.get("code_url"):
+            continue
+        out.append({
+            "slug": r["id"], "dois": [doi] if doi else [], "title": r.get("title") or "", "paper_url": r.get("paper_url"),
+            "known_code": [CODE_FIXES.get(r["id"]) or r["code_url"]] if r.get("code_url") else [], "found_by": r.get("found_by", []),
+            "readiness": r.get("readiness"), "robot_platform": r.get("robot_platform") or r.get("task_type"),
+            "code_licence": r.get("code_license"), "simulator": (ver.get(r["id"]) or {}).get("status", "not run"),
+            "origin": ["expansion search 2026-10-12 (experimental)"],
+        })
+    return out
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("--registry-only", action="store_true")
+    ap.add_argument("--only", nargs="*")
+    ap.add_argument("--force", action="store_true")
+    ap.add_argument("--refetch-code", action="store_true",
+                    help="re-run only candidates whose code was not fetched, keeping their PDF (no PDF re-download)")
+    a = ap.parse_args()
+    cands = candidates()
+    DEST.mkdir(parents=True, exist_ok=True)
+    (DEST / "sources.json").write_text(json.dumps(cands, indent=1, ensure_ascii=False) + "\n")
+    print(f"registry: {len(cands)} experimental sources -> {DEST.relative_to(ROOT)}/sources.json")
+    if a.registry_only:
+        return
+    for c in cands:
+        if a.only and c["slug"] not in a.only:
+            continue
+        rec_path = DEST / c["slug"] / "record.json"
+        if a.refetch_code:
+            if not rec_path.exists():
+                continue
+            old = json.loads(rec_path.read_text())
+            if all(str(x.get("status", "")).startswith(FETCHED) for x in old.get("code", [])) and c["slug"] not in CODE_FIXES:
+                continue
+            old["code"] = [x for x in old.get("code", []) if str(x.get("status", "")).startswith(FETCHED)]
+            rec_path.write_text(json.dumps(old, indent=1, ensure_ascii=False, sort_keys=True) + "\n")
+        elif rec_path.exists() and not a.force:
+            continue
+        cmd = [sys.executable, str(ROOT / "scripts/ingest.py"), f"experimental/{c['slug']}", "--title", c["title"]]
+        for d in c["dois"]:
+            cmd += ["--doi", d]
+        for u in c["known_code"]:
+            cmd += ["--code-url", u]
+        if not c["dois"] or a.refetch_code:
+            cmd += ["--no-pdf"]
+        try:
+            p = subprocess.run(cmd, capture_output=True, text=True, timeout=900)
+            print((p.stdout.strip().splitlines() or [p.stderr.strip()[-300:]])[-1], flush=True)
+        except subprocess.TimeoutExpired:
+            print(f"experimental/{c['slug']}: timed out (re-run to resume)", flush=True)
+            continue
+        if rec_path.exists():
+            rec = json.loads(rec_path.read_text())
+            rec.update({"experimental": True, "origin": c["origin"], "found_by": c["found_by"], "readiness": c["readiness"],
+                        "robot_platform": c["robot_platform"], "simulator": c["simulator"]})
+            rec_path.write_text(json.dumps(rec, indent=1, ensure_ascii=False, sort_keys=True) + "\n")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/sources/experimental/a-lab-2023/record.json b/sources/experimental/a-lab-2023/record.json
new file mode 100644
index 0000000..e94c466
--- /dev/null
+++ b/sources/experimental/a-lab-2023/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/a-lab-2023/njszym__ARROWS",
+   "commit": "cb630e944315c8ac19f5b9a3c9d8984be93258a6",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 13,
+   "redistributable": "no",
+   "repo": "njszym/ARROWS",
+   "robot_mentions": [],
+   "size_kb": 9371,
+   "status": "cloned",
+   "url": "https://github.com/njszym/ARROWS"
+  }
+ ],
+ "doi_primary": "10.1038/s41586-023-06734-w",
+ "dois": [
+  "10.1038/s41586-023-06734-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 15,
+  "source": "europepmc:PMC10700133"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 10411037,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "574b5523f857b544ffdf4eff00dd742977636ba90bb09798d413237724542f7e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10700133?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10700133.1/PMC10700133.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10700133.1/PMC10700133.1.pdf"
+ },
+ "pmcid": "PMC10700133",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/a-lab-2023",
+ "title": "An autonomous laboratory for the accelerated synthesis of novel materials (A-Lab)",
+ "year": "2023"
+}
diff --git a/sources/experimental/ac-training-lab/record.json b/sources/experimental/ac-training-lab/record.json
new file mode 100644
index 0000000..db6d937
--- /dev/null
+++ b/sources/experimental/ac-training-lab/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.16"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ac-training-lab/AccelerationConsortium__ac-training-lab",
+   "commit": "ffbbb0132cbcdd11ae2bdcd43e459ca8af23374d",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 5,
+   "py_files": 176,
+   "redistributable": "yes",
+   "repo": "AccelerationConsortium/ac-training-lab",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 173824,
+   "status": "cloned",
+   "url": "https://github.com/AccelerationConsortium/ac-training-lab"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/ac-training-lab",
+ "title": "Acceleration Consortium Training Lab (remote-access SDL modules incl. Hello-World, sample transfer)",
+ "year": ""
+}
diff --git a/sources/experimental/ada-thin-films/record.json b/sources/experimental/ada-thin-films/record.json
new file mode 100644
index 0000000..45b2951
--- /dev/null
+++ b/sources/experimental/ada-thin-films/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ada-thin-films/berlinguette__ada",
+   "commit": "9a88c8d020e5bcd32c69092f349b56acb0adadf2",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 49,
+   "redistributable": "yes",
+   "repo": "berlinguette/ada",
+   "robot_mentions": [],
+   "size_kb": 654854,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/berlinguette/ada"
+  }
+ ],
+ "doi_primary": "10.1126/sciadv.aaz8867",
+ "dois": [
+  "10.1126/sciadv.aaz8867"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 22,
+  "source": "europepmc:PMC7220369"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 708811,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "2a19ea229d3fed824cb40a2fe84165ad2d3cff937079c1708a4f086af7c7e321",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7220369?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7220369.1/PMC7220369.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7220369.1/PMC7220369.1.pdf"
+ },
+ "pmcid": "PMC7220369",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/ada-thin-films",
+ "title": "Self-driving laboratory for accelerated discovery of thin-film materials (Ada)",
+ "year": "2020"
+}
diff --git a/sources/experimental/adept-framework/record.json b/sources/experimental/adept-framework/record.json
new file mode 100644
index 0000000..266292c
--- /dev/null
+++ b/sources/experimental/adept-framework/record.json
@@ -0,0 +1,58 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "none found"
+  }
+ ],
+ "doi_primary": "10.1038/s42004-026-01932-9",
+ "dois": [
+  "10.1038/s42004-026-01932-9"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 41,
+  "source": "europepmc:PMC12923569"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 6380237,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "ba0afd45e467d6457cd1d073f8cd86343357f1881ab3ef0a98294fcf8817a23e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12923569?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12923569.1/PMC12923569.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12923569.1/PMC12923569.1.pdf"
+ },
+ "pmcid": "PMC12923569",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/adept-framework",
+ "title": "The ADePT framework for assessing autonomous laboratory robotics",
+ "year": "2026"
+}
diff --git a/sources/experimental/afion-plasmonic/record.json b/sources/experimental/afion-plasmonic/record.json
new file mode 100644
index 0000000..8ce2a0f
--- /dev/null
+++ b/sources/experimental/afion-plasmonic/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/afion-plasmonic/Taylorwutianyi__AFION-LAB",
+   "commit": "0e98561118e008d5d7c2179c5032df776e40c5ab",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 20,
+   "redistributable": "no",
+   "repo": "Taylorwutianyi/AFION-LAB",
+   "robot_mentions": [],
+   "size_kb": 2777,
+   "status": "cloned",
+   "url": "https://github.com/Taylorwutianyi/AFION-LAB"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-025-56788-9",
+ "dois": [
+  "10.1038/s41467-025-56788-9"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 34,
+  "source": "europepmc:PMC11807174"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 2583740,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "5e43ec6737805fa1f685b9bd73850f220d862019b4eb9eb995f0edf8ca4877c7",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11807174?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11807174.1/PMC11807174.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11807174.1/PMC11807174.1.pdf"
+ },
+ "pmcid": "PMC11807174",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/afion-plasmonic",
+ "title": "Self-driving lab for the photochemical synthesis of plasmonic nanoparticles (AFION)",
+ "year": "2025"
+}
diff --git a/sources/experimental/agentex-genetic-codes/record.json b/sources/experimental/agentex-genetic-codes/record.json
new file mode 100644
index 0000000..66962e8
--- /dev/null
+++ b/sources/experimental/agentex-genetic-codes/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/agentex-genetic-codes/FelixRadford__AGENTEX",
+   "commit": "7a5bf4bd612fc6824f3e3c7e7592882f770930f2",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 4,
+   "py_files": 5,
+   "redistributable": "no",
+   "repo": "FelixRadford/AGENTEX",
+   "robot_mentions": [],
+   "size_kb": 53,
+   "status": "cloned",
+   "url": "https://github.com/FelixRadford/AGENTEX"
+  }
+ ],
+ "doi_primary": "10.1038/s41586-026-10949-y",
+ "dois": [
+  "10.1038/s41586-026-10949-y"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 15,
+  "sections": 45,
+  "source": "europepmc:PMC13645668"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 18098299,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "879e2f842d01f9b14e0bb765bf3eb9a5e7bf6fba512d71373072fb430f6e1fa5",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://europepmc.org/articles/PMC13645668?pdf=render"
+   }
+  ],
+  "url": "https://europepmc.org/articles/PMC13645668?pdf=render"
+ },
+ "pmcid": "PMC13645668",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/agentex-genetic-codes",
+ "title": "Automated prototyping of genetic codes",
+ "year": "2026"
+}
diff --git a/sources/experimental/ahtech-electrochem/record.json b/sources/experimental/ahtech-electrochem/record.json
new file mode 100644
index 0000000..d03b363
--- /dev/null
+++ b/sources/experimental/ahtech-electrochem/record.json
@@ -0,0 +1,73 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ahtech-electrochem/Liu-Lab-JHU__AHTech",
+   "commit": "d70696e49a2aded3436bdbd9c9b4a7652f20d1a4",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 4,
+   "py_files": 10,
+   "redistributable": "yes",
+   "repo": "Liu-Lab-JHU/AHTech",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 2299,
+   "status": "cloned",
+   "url": "https://github.com/Liu-Lab-JHU/AHTech"
+  }
+ ],
+ "doi_primary": "10.1126/sciadv.adu4391",
+ "dois": [
+  "10.1126/sciadv.adu4391"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 22,
+  "source": "europepmc:PMC13109943"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 1833045,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "3eaf7524dbe6c555d5223a9cd321078063f8e3c9adb9964dac6a0ff41d6a63d5",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13109943?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13109943.1/PMC13109943.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13109943.1/PMC13109943.1.pdf"
+ },
+ "pmcid": "PMC13109943",
+ "readiness": "partial",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/ahtech-electrochem",
+ "title": "A high-throughput experimentation platform for data-driven discovery in electrochemistry (AHTech)",
+ "year": "2025"
+}
diff --git a/sources/experimental/ai-chemist-ustc/record.json b/sources/experimental/ai-chemist-ustc/record.json
new file mode 100644
index 0000000..8a26c4b
--- /dev/null
+++ b/sources/experimental/ai-chemist-ustc/record.json
@@ -0,0 +1,58 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "none found"
+  }
+ ],
+ "doi_primary": "10.1093/nsr/nwac190",
+ "dois": [
+  "10.1093/nsr/nwac190"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 16,
+  "source": "europepmc:PMC9674120"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1633381,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "577858778bcd1ef236658ce7c093fc667694985bea08fe32f0f02bbbd193834b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9674120?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9674120.1/PMC9674120.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9674120.1/PMC9674120.1.pdf"
+ },
+ "pmcid": "PMC9674120",
+ "readiness": "no",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/ai-chemist-ustc",
+ "title": "An all-round AI-Chemist with a scientific mind",
+ "year": "2022"
+}
diff --git a/sources/experimental/ai4pd-flex-protein-purification/record.json b/sources/experimental/ai4pd-flex-protein-purification/record.json
new file mode 100644
index 0000000..fcf122c
--- /dev/null
+++ b/sources/experimental/ai4pd-flex-protein-purification/record.json
@@ -0,0 +1,46 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.18",
+    "2.20",
+    "2.21"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ai4pd-flex-protein-purification/AI4PDLab__Opentrons_Flex_Protocols",
+   "commit": "aba0edcab77168ead2e8319e68f872c3bfef9399",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 7,
+   "py_files": 7,
+   "redistributable": "yes",
+   "repo": "AI4PDLab/Opentrons_Flex_Protocols",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 28,
+   "status": "cloned",
+   "url": "https://github.com/AI4PDLab/Opentrons_Flex_Protocols"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/ai4pd-flex-protein-purification",
+ "title": "Opentrons Flex protein purification and molecular biology scripts (AI4PD Lab)",
+ "year": ""
+}
diff --git a/sources/experimental/alabos-alab/record.json b/sources/experimental/alabos-alab/record.json
new file mode 100644
index 0000000..02faca2
--- /dev/null
+++ b/sources/experimental/alabos-alab/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/alabos-alab/CederGroupHub__alab_management",
+   "commit": "a81d607957f4a02a56961c8c6cb95d3f61ddb5be",
+   "default_branch": "main_gpss",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 137,
+   "redistributable": "yes",
+   "repo": "CederGroupHub/alab_management",
+   "robot_mentions": [],
+   "size_kb": 61227,
+   "status": "cloned",
+   "url": "https://github.com/CederGroupHub/alab_management"
+  }
+ ],
+ "dois": [
+  "10.1039/d4dd00129j"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d4dd00129j:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://pubs.rsc.org/en/content/articlepdf/2024/DD/D4DD00129J"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "scheduling",
+ "simulator": "not run",
+ "slug": "experimental/alabos-alab",
+ "title": "AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories (A-Lab)",
+ "year": ""
+}
diff --git a/sources/experimental/aliquot-niaid/record.json b/sources/experimental/aliquot-niaid/record.json
new file mode 100644
index 0000000..d00857f
--- /dev/null
+++ b/sources/experimental/aliquot-niaid/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.26",
+    "2.27"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/aliquot-niaid/QVEU__ALIQUOT",
+   "commit": "9a5cb78eb7f34135c3a808320e7392cde29990a2",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 13,
+   "py_files": 13,
+   "redistributable": "no",
+   "repo": "QVEU/ALIQUOT",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 286,
+   "status": "cloned",
+   "url": "https://github.com/QVEU/ALIQUOT"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/aliquot-niaid",
+ "title": "ALIQUOT: Automated Liquid handling Infection Quantification Using OpenTrons (NIH/NIAID QVEU)",
+ "year": ""
+}
diff --git a/sources/experimental/aml-drug-synergy-pyhamilton/record.json b/sources/experimental/aml-drug-synergy-pyhamilton/record.json
new file mode 100644
index 0000000..e1e0ae3
--- /dev/null
+++ b/sources/experimental/aml-drug-synergy-pyhamilton/record.json
@@ -0,0 +1,84 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/aml-drug-synergy-pyhamilton/stefangolas__drug_dilutions",
+   "commit": "e3fa6548642ef7c1647744f947db5dfd68f4db31",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "stefangolas/drug_dilutions",
+   "robot_mentions": [],
+   "size_kb": 698,
+   "status": "cloned",
+   "url": "https://github.com/stefangolas/drug_dilutions"
+  }
+ ],
+ "doi_primary": "10.1016/j.slasd.2023.04.004",
+ "dois": [
+  "10.1016/j.slasd.2023.04.004"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slasd.2023.04.004:\n  europepmc: Server error '500 ' for url 'h",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10449086?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10449086.1/PMC10449086.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10449086.2/PMC10449086.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10449086.3/PMC10449086.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC10449086&blobtype=pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC10449086",
+ "readiness": "partial",
+ "robot_platform": "hamilton",
+ "simulator": "not run",
+ "slug": "experimental/aml-drug-synergy-pyhamilton",
+ "title": "High-throughput approaches to uncover synergistic drug combinations in leukemia",
+ "year": "2023"
+}
diff --git a/sources/experimental/amplicon-seq-bisanz/record.json b/sources/experimental/amplicon-seq-bisanz/record.json
new file mode 100644
index 0000000..f8fa59b
--- /dev/null
+++ b/sources/experimental/amplicon-seq-bisanz/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.7"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/amplicon-seq-bisanz/jbisanz__AmpliconSeq",
+   "commit": "fd7cf6412a4538e9de07aa7a49d350b7537a81ca",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 5,
+   "py_files": 5,
+   "redistributable": "no",
+   "repo": "jbisanz/AmpliconSeq",
+   "robot_mentions": [],
+   "size_kb": 3965,
+   "status": "cloned",
+   "url": "https://github.com/jbisanz/AmpliconSeq"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/amplicon-seq-bisanz",
+ "title": "AmpliconSeq (16S amplicon library OT-2 scripts, Bisanz lab)",
+ "year": ""
+}
diff --git a/sources/experimental/angelovangel-ot2-ngs/record.json b/sources/experimental/angelovangel-ot2-ngs/record.json
new file mode 100644
index 0000000..69d31b5
--- /dev/null
+++ b/sources/experimental/angelovangel-ot2-ngs/record.json
@@ -0,0 +1,50 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13",
+    "2.15",
+    "2.16",
+    "2.18",
+    "2.21",
+    "2.8"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/angelovangel-ot2-ngs/angelovangel__opentrons",
+   "commit": "87040ecefa76c39bf3f6f80e7d605ad667d00fdd",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 22,
+   "py_files": 24,
+   "redistributable": "no",
+   "repo": "angelovangel/opentrons",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 1067,
+   "status": "cloned",
+   "url": "https://github.com/angelovangel/opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/angelovangel-ot2-ngs",
+ "title": "angelovangel/opentrons (KAUST Bioscience core NGS/Sanger OT-2 + Flex protocols)",
+ "year": ""
+}
diff --git a/sources/experimental/ant-cloning/record.json b/sources/experimental/ant-cloning/record.json
new file mode 100644
index 0000000..77eca44
--- /dev/null
+++ b/sources/experimental/ant-cloning/record.json
@@ -0,0 +1,56 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.2"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ant-cloning/ljm176__ANTCloning",
+   "commit": "e33484f3f365afed54da1cdd0e1dc1a89d3d980a",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 10,
+   "py_files": 10,
+   "redistributable": "no",
+   "repo": "ljm176/ANTCloning",
+   "robot_mentions": [],
+   "size_kb": 313,
+   "status": "cloned",
+   "url": "https://github.com/ljm176/ANTCloning"
+  }
+ ],
+ "doi_primary": "10.1021/acssynbio.0c00240",
+ "dois": [
+  "10.1021/acssynbio.0c00240"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/acssynbio.0c00240:\n  europepmc: no Europe PMC full text for this",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/ant-cloning",
+ "title": "Automated cloning by natural transformation (ANT) OT-2 workflow",
+ "year": "2020"
+}
diff --git a/sources/experimental/aquarium/record.json b/sources/experimental/aquarium/record.json
new file mode 100644
index 0000000..d469966
--- /dev/null
+++ b/sources/experimental/aquarium/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/aquarium/aquariumbio__aquarium",
+   "commit": "325c06d426d6633ec4b3bebd4e2359473b0b5133",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "aquariumbio/aquarium",
+   "robot_mentions": [],
+   "size_kb": 34662,
+   "status": "cloned",
+   "url": "https://github.com/aquariumbio/aquarium"
+  }
+ ],
+ "doi_primary": "10.1093/synbio/ysad005",
+ "dois": [
+  "10.1093/synbio/ysad005"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 44,
+  "source": "europepmc:PMC10105856"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 2252664,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "939c0df4dabc75e565f10c018a7c1ca832d22f75f1c7f45695272c9662602595",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10105856?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10105856.1/PMC10105856.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10105856.1/PMC10105856.1.pdf"
+ },
+ "pmcid": "PMC10105856",
+ "readiness": "partial",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/aquarium",
+ "title": "Aquarium laboratory operating system (UW BIOFAB) - used in SD2 robustness studies",
+ "year": "2023"
+}
diff --git a/sources/experimental/archemist/record.json b/sources/experimental/archemist/record.json
new file mode 100644
index 0000000..fcb8a8f
--- /dev/null
+++ b/sources/experimental/archemist/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/archemist/cooper-group-uol-robotics__archemist",
+   "commit": "52cbf816dbb42097417c00a8b6c0c7860ae7a388",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 221,
+   "redistributable": "yes",
+   "repo": "cooper-group-uol-robotics/archemist",
+   "robot_mentions": [],
+   "size_kb": 99391,
+   "status": "cloned",
+   "url": "https://github.com/cooper-group-uol-robotics/archemist"
+  }
+ ],
+ "dois": [
+  "10.1109/ICRA46639.2022.9811996"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1109/ICRA46639.2022.9811996:\n  europepmc: no Europe PMC full text for",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/archemist",
+ "title": "ARChemist: Autonomous Robotic Chemistry System Architecture (Fakhruldeen et al.)",
+ "year": ""
+}
diff --git a/sources/experimental/artic-normalisation-esr/record.json b/sources/experimental/artic-normalisation-esr/record.json
new file mode 100644
index 0000000..4153408
--- /dev/null
+++ b/sources/experimental/artic-normalisation-esr/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.2",
+    "2.3"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/artic-normalisation-esr/ESR-NZ__opentrons_protocols",
+   "commit": "ab3354c88ed1b1bbfb3403e626a76c89cc57a783",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 11,
+   "py_files": 11,
+   "redistributable": "no",
+   "repo": "ESR-NZ/opentrons_protocols",
+   "robot_mentions": [],
+   "size_kb": 260,
+   "status": "cloned",
+   "url": "https://github.com/ESR-NZ/opentrons_protocols"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/artic-normalisation-esr",
+ "title": "ESR-NZ ARTIC normalisation/end-repair/barcoding (OT-2)",
+ "year": ""
+}
diff --git a/sources/experimental/aurora-materials/record.json b/sources/experimental/aurora-materials/record.json
new file mode 100644
index 0000000..9a15169
--- /dev/null
+++ b/sources/experimental/aurora-materials/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/aurora-materials/PalmSens__MethodSCRIPT_Examples",
+   "commit": "1aa78fc195e34cb03acd08ec96ee887a76fa3150",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 14,
+   "redistributable": "no",
+   "repo": "PalmSens/MethodSCRIPT_Examples",
+   "robot_mentions": [],
+   "size_kb": 20834,
+   "status": "cloned",
+   "url": "https://github.com/PalmSens/MethodSCRIPT_Examples"
+  }
+ ],
+ "doi_primary": "10.1021/acsami.5c02605",
+ "dois": [
+  "10.1021/acsami.5c02605"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 15,
+  "source": "europepmc:PMC12067375"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 7008228,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "60f8512cdd9190f01176d0ec0b8a914c02612d4ea3fa9f44422ffb2f2b49b8e7",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12067375?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12067375.1/PMC12067375.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12067375.1/PMC12067375.1.pdf"
+ },
+ "pmcid": "PMC12067375",
+ "readiness": "no",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/aurora-materials",
+ "title": "AURORA - An Automatic Robotic Platform for Materials Discovery",
+ "year": "2025"
+}
diff --git a/sources/experimental/auto-sp-proteomics/record.json b/sources/experimental/auto-sp-proteomics/record.json
new file mode 100644
index 0000000..4c2a324
--- /dev/null
+++ b/sources/experimental/auto-sp-proteomics/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/acs.analchem.5c00886",
+ "dois": [
+  "10.1021/acs.analchem.5c00886"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/acs.analchem.5c00886:\n  europepmc: Server error '500 ' for url '",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 4974278,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "71141a31956c1571a2712e2596d00908311e85232a54a551a89efcea7174ba9b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12355475?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12355475.1/PMC12355475.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12355475.1/PMC12355475.1.pdf"
+ },
+ "pmcid": "PMC12355475",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/auto-sp-proteomics",
+ "title": "AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications",
+ "year": "2025"
+}
diff --git a/sources/experimental/autopots-proteome/record.json b/sources/experimental/autopots-proteome/record.json
new file mode 100644
index 0000000..1f31f34
--- /dev/null
+++ b/sources/experimental/autopots-proteome/record.json
@@ -0,0 +1,66 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/acs.analchem.0c04240",
+ "dois": [
+  "10.1021/acs.analchem.0c04240"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/acs.analchem.0c04240:\n  europepmc: Server error '500 ' for url '",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8140400?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8140400.1/PMC8140400.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8140400.2/PMC8140400.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8140400.3/PMC8140400.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8140400&blobtype=pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC8140400",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/autopots-proteome",
+ "title": "Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling",
+ "year": "2021"
+}
diff --git a/sources/experimental/autoprotocol-dnada/record.json b/sources/experimental/autoprotocol-dnada/record.json
new file mode 100644
index 0000000..4c39c3c
--- /dev/null
+++ b/sources/experimental/autoprotocol-dnada/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/autoprotocol-dnada/JBEI__dnada",
+   "commit": "ec9022c83b9da58f832246c42d56be9d03db7d58",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 0,
+   "py_files": 208,
+   "redistributable": "yes",
+   "repo": "JBEI/dnada",
+   "robot_mentions": [],
+   "size_kb": 1471,
+   "status": "cloned",
+   "url": "https://github.com/JBEI/dnada"
+  }
+ ],
+ "doi_primary": "10.1021/acssynbio.3c00292",
+ "dois": [
+  "10.1021/acssynbio.3c00292"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 7,
+  "source": "europepmc:PMC10729297"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3259528,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "fe49de7b3b3408f62d4f8b56ec8f9656fd0838c02881fb10819e1f7552885133",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10729297?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10729297.1/PMC10729297.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10729297.1/PMC10729297.1.pdf"
+ },
+ "pmcid": "PMC10729297",
+ "readiness": "ready",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/autoprotocol-dnada",
+ "title": "Automated Platform for the Plasmid Construction Process (DNAda -> Autoprotocol)",
+ "year": "2023"
+}
diff --git a/sources/experimental/autoprotocol-python/record.json b/sources/experimental/autoprotocol-python/record.json
new file mode 100644
index 0000000..5d52a39
--- /dev/null
+++ b/sources/experimental/autoprotocol-python/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/autoprotocol-python/autoprotocol__autoprotocol-python",
+   "commit": "4795408f8a814fc7e3e70d54ada64da5ca125161",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 46,
+   "redistributable": "no",
+   "repo": "autoprotocol/autoprotocol-python",
+   "robot_mentions": [],
+   "size_kb": 4471,
+   "status": "cloned",
+   "url": "https://github.com/autoprotocol/autoprotocol-python"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/autoprotocol-python",
+ "title": "Autoprotocol-python (Strateos/Transcriptic protocol IR)",
+ "year": ""
+}
diff --git a/sources/experimental/autorelacs/record.json b/sources/experimental/autorelacs/record.json
new file mode 100644
index 0000000..c4a1fb2
--- /dev/null
+++ b/sources/experimental/autorelacs/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/autorelacs/FrancescoFerrari88__AutoRELACS",
+   "commit": "a305feb5f5e9252de960b66e3072719c0c7c0e35",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "FrancescoFerrari88/AutoRELACS",
+   "robot_mentions": [],
+   "size_kb": 8079,
+   "status": "cloned",
+   "url": "https://github.com/FrancescoFerrari88/AutoRELACS"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-020-69443-8",
+ "dois": [
+  "10.1038/s41598-020-69443-8"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 20,
+  "source": "europepmc:PMC7381599"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1879327,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "eb2124f30194d3bf533842c8c673290500f66baf12e6dc521a8905def095b364",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7381599?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7381599.1/PMC7381599.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7381599.1/PMC7381599.1.pdf"
+ },
+ "pmcid": "PMC7381599",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/autorelacs",
+ "title": "AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq",
+ "year": "2020"
+}
diff --git a/sources/experimental/baybe/record.json b/sources/experimental/baybe/record.json
new file mode 100644
index 0000000..b3905ee
--- /dev/null
+++ b/sources/experimental/baybe/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/baybe/emdgroup__baybe",
+   "commit": "640f84804925b8995ffbeee620cb715a2b9db71f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 0,
+   "py_files": 350,
+   "redistributable": "yes",
+   "repo": "emdgroup/baybe",
+   "robot_mentions": [],
+   "size_kb": 164634,
+   "status": "cloned",
+   "url": "https://github.com/emdgroup/baybe"
+  }
+ ],
+ "dois": [
+  "10.1039/D5DD00050E"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/D5DD00050E:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/baybe",
+ "title": "BayBE: Bayesian Back End for design of experiments",
+ "year": ""
+}
diff --git a/sources/experimental/bead-digestion-ann/record.json b/sources/experimental/bead-digestion-ann/record.json
new file mode 100644
index 0000000..8997156
--- /dev/null
+++ b/sources/experimental/bead-digestion-ann/record.json
@@ -0,0 +1,35 @@
+{
+ "code": [],
+ "doi_primary": "10.1016/j.talanta.2024.125988",
+ "dois": [
+  "10.1016/j.talanta.2024.125988"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.talanta.2024.125988:\n  europepmc: no Europe PMC full text for ",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "licence": "cc by-nc",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/bead-digestion-ann",
+ "title": "Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network",
+ "year": "2024"
+}
diff --git a/sources/experimental/bean-kasp-anthracnose/record.json b/sources/experimental/bean-kasp-anthracnose/record.json
new file mode 100644
index 0000000..8fe83ee
--- /dev/null
+++ b/sources/experimental/bean-kasp-anthracnose/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/bean-kasp-anthracnose/McGillHaricots__peas-andlove",
+   "commit": "43d4beb8c4a0437c938fc37dbf57a4a769cfc6c1",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 22,
+   "redistributable": "no",
+   "repo": "McGillHaricots/peas-andlove",
+   "robot_mentions": [],
+   "size_kb": 951155,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/McGillHaricots/peas-andlove"
+  }
+ ],
+ "doi_primary": "10.1186/s13007-023-01071-5",
+ "dois": [
+  "10.1186/s13007-023-01071-5"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 32,
+  "source": "europepmc:PMC10546687"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1262229,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "ea8a956c58941db322d9eb447e6f955ead3a152638d8caddc6946b4d907e3629",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10546687?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10546687.1/PMC10546687.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10546687.1/PMC10546687.1.pdf"
+ },
+ "pmcid": "PMC10546687",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/bean-kasp-anthracnose",
+ "title": "Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR",
+ "year": "2023"
+}
diff --git a/sources/experimental/bear-mechanics/record.json b/sources/experimental/bear-mechanics/record.json
new file mode 100644
index 0000000..e4392da
--- /dev/null
+++ b/sources/experimental/bear-mechanics/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/bear-mechanics/KelseyEng__BEAR_ADTS",
+   "commit": "621d294e2df6b7c7156f0f72dab4ec39c168fd0f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "Unlicense",
+   "opentrons_py_files": 0,
+   "py_files": 6,
+   "redistributable": "yes",
+   "repo": "KelseyEng/BEAR_ADTS",
+   "robot_mentions": [],
+   "size_kb": 87474,
+   "status": "cloned",
+   "url": "https://github.com/KelseyEng/BEAR_ADTS"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-024-48534-4",
+ "dois": [
+  "10.1038/s41467-024-48534-4"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 16,
+  "source": "europepmc:PMC11109101"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 49219137,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "cd45627e4cfc40ccbb0aacd381375f1f0f56793194b675238e1543605ad83a3e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11109101?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11109101.1/PMC11109101.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11109101.1/PMC11109101.1.pdf"
+ },
+ "pmcid": "PMC11109101",
+ "readiness": "partial",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/bear-mechanics",
+ "title": "Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership (BEAR)",
+ "year": "2024"
+}
diff --git a/sources/experimental/beckham-enzyme-pipeline/record.json b/sources/experimental/beckham-enzyme-pipeline/record.json
new file mode 100644
index 0000000..49b8285
--- /dev/null
+++ b/sources/experimental/beckham-enzyme-pipeline/record.json
@@ -0,0 +1,76 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/beckham-enzyme-pipeline/beckham-lab__opentrons",
+   "commit": "f4afa187b3cff913097e1a51ce90a28172090777",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 21,
+   "py_files": 22,
+   "redistributable": "no",
+   "repo": "beckham-lab/opentrons",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 18507,
+   "status": "cloned",
+   "url": "https://github.com/beckham-lab/opentrons"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-024-64938-0",
+ "dois": [
+  "10.1038/s41598-024-64938-0"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 34,
+  "source": "europepmc:PMC11196671"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2278683,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "b3f5b1bd3773e6834d91c032b8443135422adb59f2ed48f6aa262d04dfe3dc87",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11196671?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11196671.1/PMC11196671.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11196671.1/PMC11196671.1.pdf"
+ },
+ "pmcid": "PMC11196671",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/beckham-enzyme-pipeline",
+ "title": "Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline",
+ "year": "2024"
+}
diff --git a/sources/experimental/bio-spec-hardwarex/record.json b/sources/experimental/bio-spec-hardwarex/record.json
new file mode 100644
index 0000000..11abfed
--- /dev/null
+++ b/sources/experimental/bio-spec-hardwarex/record.json
@@ -0,0 +1,58 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "see paper repository (OSF/Zenodo, not verified)"
+  }
+ ],
+ "doi_primary": "10.1016/j.ohx.2025.e00670",
+ "dois": [
+  "10.1016/j.ohx.2025.e00670"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 35,
+  "sections": 31,
+  "source": "europepmc:PMC12341735"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 6896920,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "cc2d271dde2fa2536700a4969c11852dce17f78b8b162f299a762891cc3c466a",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12341735?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12341735.1/PMC12341735.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12341735.1/PMC12341735.1.pdf"
+ },
+ "pmcid": "PMC12341735",
+ "readiness": "no",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/bio-spec-hardwarex",
+ "title": "BIO-SPEC: An open-source bench-top parallel bioreactor system",
+ "year": "2025"
+}
diff --git a/sources/experimental/bioclonebot/record.json b/sources/experimental/bioclonebot/record.json
new file mode 100644
index 0000000..830e031
--- /dev/null
+++ b/sources/experimental/bioclonebot/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/bioclonebot/osf-qdp7v",
+   "files": 161,
+   "files_downloaded": 161,
+   "files_skipped_size": [],
+   "host": "osf.io",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "osf:qdp7v",
+   "robot_mentions": [],
+   "size_kb": 151344,
+   "status": "downloaded",
+   "url": "https://osf.io/qdp7v"
+  }
+ ],
+ "doi_primary": "10.1016/j.ohx.2024.e00516",
+ "dois": [
+  "10.1016/j.ohx.2024.e00516"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 13,
+  "sections": 30,
+  "source": "europepmc:PMC10955647"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 4653630,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "af51b52306905d75c0933f551e52d9fe2dcddeb39affccb4dd87ac94d539587c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10955647?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10955647.1/PMC10955647.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10955647.1/PMC10955647.1.pdf"
+ },
+ "pmcid": "PMC10955647",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/bioclonebot",
+ "title": "BioCloneBot: A versatile, low-cost, and open-source automated liquid handler",
+ "year": "2024"
+}
diff --git a/sources/experimental/biomationscripter/record.json b/sources/experimental/biomationscripter/record.json
new file mode 100644
index 0000000..565e69b
--- /dev/null
+++ b/sources/experimental/biomationscripter/record.json
@@ -0,0 +1,46 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.10",
+    "2.11"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/biomationscripter/intbio-ncl__BiomationScripterLib",
+   "commit": "2d6b0829f0812fa510a78aa9052ea92f45ce9866",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 19,
+   "py_files": 29,
+   "redistributable": "yes",
+   "repo": "intbio-ncl/BiomationScripterLib",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 4653,
+   "status": "cloned",
+   "url": "https://github.com/intbio-ncl/BiomationScripterLib"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/biomationscripter",
+ "title": "BiomationScripter: Python library for scripting bio-automation protocols",
+ "year": ""
+}
diff --git a/sources/experimental/blots-ot2/record.json b/sources/experimental/blots-ot2/record.json
new file mode 100644
index 0000000..0709bff
--- /dev/null
+++ b/sources/experimental/blots-ot2/record.json
@@ -0,0 +1,69 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.24"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/blots-ot2/eyaplab__BLOTS-OT2",
+   "commit": "58ade714bf217efad3fa84b33a55ce4b2f2447fb",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "eyaplab/BLOTS-OT2",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 13,
+   "status": "cloned",
+   "url": "https://github.com/eyaplab/BLOTS-OT2"
+  }
+ ],
+ "doi_primary": "10.1002/cpz1.70454",
+ "dois": [
+  "10.1002/cpz1.70454"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 131,
+  "source": "europepmc:PMC13528971"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 1359717,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "71997d9ea0452f5e71de19eab495b9d17ffbeb2c0582276d386700bd60559b28",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://europepmc.org/articles/PMC13528971?pdf=render"
+   }
+  ],
+  "url": "https://europepmc.org/articles/PMC13528971?pdf=render"
+ },
+ "pmcid": "PMC13528971",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/blots-ot2",
+ "title": "Bacterial Lysis Observation Over Time Assay (BLOTS) for High-Throughput Isolation and Screening",
+ "year": "2026"
+}
diff --git a/sources/experimental/brightfield-biofilm/record.json b/sources/experimental/brightfield-biofilm/record.json
new file mode 100644
index 0000000..3ca3ad1
--- /dev/null
+++ b/sources/experimental/brightfield-biofilm/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/brightfield-biofilm/BridgesLabCMU__Brightfield-biofilm-assay",
+   "commit": "c37c99e1515da05c10c263fccc018d8f3edee298",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "BridgesLabCMU/Brightfield-biofilm-assay",
+   "robot_mentions": [],
+   "size_kb": 45671,
+   "status": "cloned",
+   "url": "https://github.com/BridgesLabCMU/Brightfield-biofilm-assay"
+  }
+ ],
+ "doi_primary": "10.1128/mbio.00448-26",
+ "dois": [
+  "10.1128/mbio.00448-26"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 21,
+  "source": "europepmc:PMC13251385"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5865819,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "ac2d0c38174c4908124f87966502c9cbf2d2179f2da940f70f4af45523f25539",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13251385?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13251385.1/PMC13251385.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13251385.1/PMC13251385.1.pdf"
+ },
+ "pmcid": "PMC13251385",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/brightfield-biofilm",
+ "title": "Label-free microscopy enables high-throughput identification of genes controlling biofilm development",
+ "year": "2026"
+}
diff --git a/sources/experimental/catib-screening/record.json b/sources/experimental/catib-screening/record.json
new file mode 100644
index 0000000..77c0b92
--- /dev/null
+++ b/sources/experimental/catib-screening/record.json
@@ -0,0 +1,78 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/catib-screening/JuBiotech__Supplement-to-Helleckes-Kuesters-et-al.-2023",
+   "commit": "0e74f221ebf95e25e7de90233e765cdb769f2fec",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023",
+   "robot_mentions": [],
+   "size_kb": 47929,
+   "status": "cloned",
+   "url": "https://github.com/JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023"
+  }
+ ],
+ "doi_primary": "10.1186/s12934-024-02319-y",
+ "dois": [
+  "10.1186/s12934-024-02319-y"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 25,
+  "source": "europepmc:PMC10894497"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2782752,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "e8c1df16dbe6664a48d53d63e9c95de06137ad6f592b922038e1c98dd0f151e3",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://microbialcellfactories.biomedcentral.com/counter/pdf/10.1186/s12934-024-02319-y"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10894497?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10894497.1/PMC10894497.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10894497.1/PMC10894497.1.pdf"
+ },
+ "pmcid": "PMC10894497",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/catib-screening",
+ "title": "\"High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization\"",
+ "year": "2024"
+}
diff --git a/sources/experimental/cayman-his-elisa/record.json b/sources/experimental/cayman-his-elisa/record.json
new file mode 100644
index 0000000..60c0551
--- /dev/null
+++ b/sources/experimental/cayman-his-elisa/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.20"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/cayman-his-elisa/Arcadia-Science__cayman-his-elisa-opentrons-workflow",
+   "commit": "45b29bc29da2d3dca63f7820b2cce825c4d9f39b",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 4,
+   "py_files": 4,
+   "redistributable": "yes",
+   "repo": "Arcadia-Science/cayman-his-elisa-opentrons-workflow",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 36052,
+   "status": "cloned",
+   "url": "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow"
+  }
+ ],
+ "dois": [
+  "10.17504/protocols.io.n92ld4x3nl5b"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.17504/protocols.io.n92ld4x3nl5b:\n  europepmc: no Europe PMC full text",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/cayman-his-elisa",
+ "title": "An Opentrons OT-2 workflow for the Cayman His-tag detection ELISA kit",
+ "year": ""
+}
diff --git a/sources/experimental/cellfree-biosensor-ot2/record.json b/sources/experimental/cellfree-biosensor-ot2/record.json
new file mode 100644
index 0000000..bbc5197
--- /dev/null
+++ b/sources/experimental/cellfree-biosensor-ot2/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/acssynbio.4c00703",
+ "dois": [
+  "10.1021/acssynbio.4c00703"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/acssynbio.4c00703:\n  europepmc: no Europe PMC full text for this",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://pubs.acs.org/doi/pdf/10.1021/acssynbio.4c00703"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/cellfree-biosensor-ot2",
+ "title": "Semiautomated Production of Cell-Free Biosensors",
+ "year": "2025"
+}
diff --git a/sources/experimental/cfrna-pipeline/record.json b/sources/experimental/cfrna-pipeline/record.json
new file mode 100644
index 0000000..d5d63ba
--- /dev/null
+++ b/sources/experimental/cfrna-pipeline/record.json
@@ -0,0 +1,61 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/cfrna-pipeline/miramou__cfRNA_pipeline_automation",
+   "commit": "7682321f46e89310503f9f766e53f4b282b6fca3",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 6,
+   "py_files": 13,
+   "redistributable": "no",
+   "repo": "miramou/cfRNA_pipeline_automation",
+   "robot_mentions": [],
+   "size_kb": 1294,
+   "status": "cloned",
+   "url": "https://github.com/miramou/cfRNA_pipeline_automation"
+  }
+ ],
+ "doi_primary": "10.1038/s41596-023-00855-2",
+ "dois": [
+  "10.1038/s41596-023-00855-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41596-023-00855-2:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://www.nature.com/articles/s41596-023-00855-2.pdf"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/cfrna-pipeline",
+ "title": "An inexpensive semi-automated sample processing pipeline for cell-free RNA (extraction)",
+ "year": "2023"
+}
diff --git a/sources/experimental/chemcrow/record.json b/sources/experimental/chemcrow/record.json
new file mode 100644
index 0000000..523964a
--- /dev/null
+++ b/sources/experimental/chemcrow/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemcrow/ur-whitelab__chemcrow-public",
+   "commit": "e7ebd5193334ac1d8dea137b635721c7cb470d33",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 27,
+   "redistributable": "yes",
+   "repo": "ur-whitelab/chemcrow-public",
+   "robot_mentions": [],
+   "size_kb": 6059,
+   "status": "cloned",
+   "url": "https://github.com/ur-whitelab/chemcrow-public"
+  }
+ ],
+ "doi_primary": "10.1038/s42256-024-00832-8",
+ "dois": [
+  "10.1038/s42256-024-00832-8"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 53,
+  "source": "europepmc:PMC11116106"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2396611,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "3b97df0a3d4fa1c73cd7ad97b60ea129388ece2b6b505aefa30a809b67946993",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11116106?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11116106.1/PMC11116106.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11116106.1/PMC11116106.1.pdf"
+ },
+ "pmcid": "PMC11116106",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/chemcrow",
+ "title": "Augmenting large language models with chemistry tools (ChemCrow)",
+ "year": "2024"
+}
diff --git a/sources/experimental/chemos-2020/record.json b/sources/experimental/chemos-2020/record.json
new file mode 100644
index 0000000..8a73474
--- /dev/null
+++ b/sources/experimental/chemos-2020/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemos-2020/aspuru-guzik-group__ChemOS",
+   "commit": "50117f572e95e68dc4dccb624cedb28dbfc6e419",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 139,
+   "redistributable": "no",
+   "repo": "aspuru-guzik-group/ChemOS",
+   "robot_mentions": [],
+   "size_kb": 16918,
+   "status": "cloned",
+   "url": "https://github.com/aspuru-guzik-group/ChemOS"
+  }
+ ],
+ "doi_primary": "10.1371/journal.pone.0229862",
+ "dois": [
+  "10.1371/journal.pone.0229862"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 25,
+  "source": "europepmc:PMC7161969"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2305130,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "4af746456f8e4febd5c1ca4c49629d3940664948005a6ff07753e3632b504992",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 400,
+    "manual": false,
+    "ok": false,
+    "url": "https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pone.0229862/1/pone.0229862.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210215%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210215T065405Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7161969?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7161969.1/PMC7161969.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7161969.1/PMC7161969.1.pdf"
+ },
+ "pmcid": "PMC7161969",
+ "readiness": "partial",
+ "robot_platform": "scheduling",
+ "simulator": "not run",
+ "slug": "experimental/chemos-2020",
+ "title": "ChemOS: An orchestration software to democratize autonomous discovery",
+ "year": "2020"
+}
diff --git a/sources/experimental/chemos2-atlas/record.json b/sources/experimental/chemos2-atlas/record.json
new file mode 100644
index 0000000..f111da3
--- /dev/null
+++ b/sources/experimental/chemos2-atlas/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemos2-atlas/aspuru-guzik-group__atlas",
+   "commit": "ebb1f4f728107f759c48289c2faecfa3af19254f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 90,
+   "redistributable": "yes",
+   "repo": "aspuru-guzik-group/atlas",
+   "robot_mentions": [],
+   "size_kb": 28124,
+   "status": "cloned",
+   "url": "https://github.com/aspuru-guzik-group/atlas"
+  }
+ ],
+ "dois": [
+  "10.1039/D4DD00115J"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/D4DD00115J:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/chemos2-atlas",
+ "title": "Atlas: a brain for self-driving laboratories (BO library used in ChemOS 2.0 campaigns)",
+ "year": ""
+}
diff --git a/sources/experimental/chemputer-acra/record.json b/sources/experimental/chemputer-acra/record.json
new file mode 100644
index 0000000..e9ec764
--- /dev/null
+++ b/sources/experimental/chemputer-acra/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemputer-acra/croningp__acra",
+   "commit": "723b1e282ba00c5aed1a087ba92422a3bc3ead7d",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 41,
+   "redistributable": "yes",
+   "repo": "croningp/acra",
+   "robot_mentions": [],
+   "size_kb": 33637,
+   "status": "cloned",
+   "url": "https://github.com/croningp/acra"
+  }
+ ],
+ "doi_primary": "10.1038/s42004-026-01993-w",
+ "dois": [
+  "10.1038/s42004-026-01993-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 22,
+  "source": "europepmc:PMC13219472"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3308563,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "e6be067d784bcb490ec787e67ba2a7e2820f248ac47aeecc3d684e0108c92eb2",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13219472?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13219472.1/PMC13219472.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13219472.1/PMC13219472.1.pdf"
+ },
+ "pmcid": "PMC13219472",
+ "readiness": "ready",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/chemputer-acra",
+ "title": "Verification and execution of the scientific literature via chemputation augmented by large language models",
+ "year": "2026"
+}
diff --git a/sources/experimental/chemputer-blueprints/record.json b/sources/experimental/chemputer-blueprints/record.json
new file mode 100644
index 0000000..fde7673
--- /dev/null
+++ b/sources/experimental/chemputer-blueprints/record.json
@@ -0,0 +1,68 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemputer-blueprints/croningroup__chemputer",
+   "commit": "6d60e8da7218a589b9c8715a239956601b17cd07",
+   "host": "gitlab.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 155,
+   "redistributable": "no",
+   "repo": "croningroup/chemputer/xdl",
+   "robot_mentions": [],
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://gitlab.com/croningroup/chemputer/xdl"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-024-54238-6",
+ "dois": [
+  "10.1038/s41467-024-54238-6"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 5,
+  "source": "europepmc:PMC11599859"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1532400,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "fcb9a893490c1e20eb8986b38dbe56921b3c17fbdcfcc9d6922f45fc53c16743",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11599859?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11599859.1/PMC11599859.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11599859.1/PMC11599859.1.pdf"
+ },
+ "pmcid": "PMC11599859",
+ "readiness": "ready",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/chemputer-blueprints",
+ "title": "Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer",
+ "year": "2024"
+}
diff --git a/sources/experimental/chemputer-modules-acscs/record.json b/sources/experimental/chemputer-modules-acscs/record.json
new file mode 100644
index 0000000..e4d0c04
--- /dev/null
+++ b/sources/experimental/chemputer-modules-acscs/record.json
@@ -0,0 +1,60 @@
+{
+ "code": [
+  {
+   "host": "gitlab.com",
+   "repo": "croningroup/chemputer",
+   "status": "clone failed: fatal: could not read Username for 'https://gitlab.com': Device not configured",
+   "url": "https://gitlab.com/croningroup/chemputer"
+  }
+ ],
+ "doi_primary": "10.1021/acscentsci.3c00304",
+ "dois": [
+  "10.1021/acscentsci.3c00304"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 13,
+  "source": "europepmc:PMC10450877"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3494124,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "f7834bb2b305c7f571da0436ffa3d3f654dcda31aca18156ef31477d865cff45",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10450877?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10450877.1/PMC10450877.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10450877.1/PMC10450877.1.pdf"
+ },
+ "pmcid": "PMC10450877",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/chemputer-modules-acscs",
+ "title": "Robotic Modules for the Programmable Chemputation of Molecules and Materials",
+ "year": "2023"
+}
diff --git a/sources/experimental/chemputer-peptide/record.json b/sources/experimental/chemputer-peptide/record.json
new file mode 100644
index 0000000..61b26f4
--- /dev/null
+++ b/sources/experimental/chemputer-peptide/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chemputer-peptide/zenodo-15948769",
+   "files": 12,
+   "files_downloaded": 12,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "zenodo:15948769",
+   "robot_mentions": [],
+   "size_kb": 24,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.15948769"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-025-62344-2",
+ "dois": [
+  "10.1038/s41467-025-62344-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 28,
+  "source": "europepmc:PMC12334676"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3390053,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "f889b5e63fc5f705c75d1a325fc3f84b71c71a687368f1183538ff37aaa04d3d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12334676?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12334676.1/PMC12334676.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12334676.1/PMC12334676.1.pdf"
+ },
+ "pmcid": "PMC12334676",
+ "readiness": "ready",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/chemputer-peptide",
+ "title": "Universal peptide synthesis via solid-phase methods fused with chemputation",
+ "year": "2025"
+}
diff --git a/sources/experimental/chibio-2020/record.json b/sources/experimental/chibio-2020/record.json
new file mode 100644
index 0000000..b553b14
--- /dev/null
+++ b/sources/experimental/chibio-2020/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/chibio-2020/HarrisonSteel__ChiBio",
+   "commit": "c4e6950ac2b5a9c980aeb2d0a78ad793f5f896de",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "HarrisonSteel/ChiBio",
+   "robot_mentions": [],
+   "size_kb": 126,
+   "status": "cloned",
+   "url": "https://github.com/HarrisonSteel/ChiBio"
+  }
+ ],
+ "doi_primary": "10.1371/journal.pbio.3000794",
+ "dois": [
+  "10.1371/journal.pbio.3000794"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 24,
+  "source": "europepmc:PMC7419009"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1945541,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "b97d4c43984146a5debb2856505f8f423a467b2b54be22c7163f9ed85bfb488e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7419009?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7419009.1/PMC7419009.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7419009.1/PMC7419009.1.pdf"
+ },
+ "pmcid": "PMC7419009",
+ "readiness": "partial",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/chibio-2020",
+ "title": "In situ characterisation and manipulation of biological systems with Chi.Bio",
+ "year": "2020"
+}
diff --git a/sources/experimental/clairify-xdl/record.json b/sources/experimental/clairify-xdl/record.json
new file mode 100644
index 0000000..e462514
--- /dev/null
+++ b/sources/experimental/clairify-xdl/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/clairify-xdl/ac-rad__xdl-generation",
+   "commit": "1d75c294bf67e14bbacb049995f7defffb13984f",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 9,
+   "redistributable": "yes",
+   "repo": "ac-rad/xdl-generation",
+   "robot_mentions": [],
+   "size_kb": 1043,
+   "status": "cloned",
+   "url": "https://github.com/ac-rad/xdl-generation"
+  }
+ ],
+ "dois": [
+  "10.1007/s10514-023-10136-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1007/s10514-023-10136-2:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://link.springer.com/content/pdf/10.1007/s10514-023-10136-2.pdf"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/clairify-xdl",
+ "title": "Large language models for chemistry robotics (CLAIRify: NL -> XDL)",
+ "year": ""
+}
diff --git a/sources/experimental/clio-electrolytes/record.json b/sources/experimental/clio-electrolytes/record.json
new file mode 100644
index 0000000..90567de
--- /dev/null
+++ b/sources/experimental/clio-electrolytes/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/clio-electrolytes/BattModels__Clio-PythonAPI",
+   "commit": "4989db41fcb855ac7ab873d7c1fc5d2f555472a8",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "BattModels/Clio-PythonAPI",
+   "robot_mentions": [],
+   "size_kb": 13,
+   "status": "cloned",
+   "url": "https://github.com/BattModels/Clio-PythonAPI"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-022-32938-1",
+ "dois": [
+  "10.1038/s41467-022-32938-1"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 25,
+  "source": "europepmc:PMC9515088"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1134113,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "58de17d3f354b547599fecb4f2e8180c63d402e732bfec8184af7bc22b78a548",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9515088?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9515088.1/PMC9515088.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9515088.1/PMC9515088.1.pdf"
+ },
+ "pmcid": "PMC9515088",
+ "readiness": "partial",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/clio-electrolytes",
+ "title": "Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation (Clio)",
+ "year": "2022"
+}
diff --git a/sources/experimental/cloudlab-chiral-perovskite/record.json b/sources/experimental/cloudlab-chiral-perovskite/record.json
new file mode 100644
index 0000000..e12e516
--- /dev/null
+++ b/sources/experimental/cloudlab-chiral-perovskite/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "none found"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-020-15728-5",
+ "dois": [
+  "10.1038/s41467-020-15728-5"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 34,
+  "source": "europepmc:PMC7184584"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2396548,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "88aed5d49f7af2cfdaad05eaca91f143ea88463968dff4a50ff9103aa79a4fc4",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41467-020-15728-5.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41467-020-15728-5.pdf"
+ },
+ "pmcid": "PMC7184584",
+ "readiness": "no",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/cloudlab-chiral-perovskite",
+ "title": "Autonomous discovery of optically active chiral inorganic perovskite nanocrystals through an intelligent cloud lab",
+ "year": "2020"
+}
diff --git a/sources/experimental/combinatorial-barcode-dna/record.json b/sources/experimental/combinatorial-barcode-dna/record.json
new file mode 100644
index 0000000..558f9c2
--- /dev/null
+++ b/sources/experimental/combinatorial-barcode-dna/record.json
@@ -0,0 +1,73 @@
+{
+ "code": [
+  {
+   "files": 1,
+   "files_downloaded": 0,
+   "files_skipped_size": [
+    "combinatorial_barcode_scripts.zip"
+   ],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "repo": "zenodo:7415652",
+   "size_kb": 0,
+   "status": "zenodo: no files within the size limit",
+   "url": "https://doi.org/10.5281/zenodo.7415652"
+  }
+ ],
+ "doi_primary": "10.3390/ijms24032549",
+ "dois": [
+  "10.3390/ijms24032549"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 13,
+  "source": "europepmc:PMC9917336"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3180065,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "76dd497d584163f64e9a79322970e05671e5c9ed141738162e17fce0987d14a9",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://www.mdpi.com/1422-0067/24/3/2549/pdf?version=1674966322"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9917336?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9917336.1/PMC9917336.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9917336.1/PMC9917336.1.pdf"
+ },
+ "pmcid": "PMC9917336",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/combinatorial-barcode-dna",
+ "title": "Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications",
+ "year": "2023"
+}
diff --git a/sources/experimental/coscientist/record.json b/sources/experimental/coscientist/record.json
new file mode 100644
index 0000000..249ad6f
--- /dev/null
+++ b/sources/experimental/coscientist/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/coscientist/gomesgroup__coscientist",
+   "commit": "417e82b85743f88719ba7cf8838220fcb872e2ae",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 3,
+   "redistributable": "no",
+   "repo": "gomesgroup/coscientist",
+   "robot_mentions": [],
+   "size_kb": 835,
+   "status": "cloned",
+   "url": "https://github.com/gomesgroup/coscientist"
+  }
+ ],
+ "doi_primary": "10.1038/s41586-023-06792-0",
+ "dois": [
+  "10.1038/s41586-023-06792-0"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 9,
+  "sections": 14,
+  "source": "europepmc:PMC10733136"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 8869905,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "09cfaa1ccf4c951eebc347bab909e1e495d6701be38d3808c38016dff35dbd4e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10733136?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10733136.1/PMC10733136.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10733136.1/PMC10733136.1.pdf"
+ },
+ "pmcid": "PMC10733136",
+ "readiness": "partial",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/coscientist",
+ "title": "Autonomous chemical research with large language models (Coscientist)",
+ "year": "2023"
+}
diff --git a/sources/experimental/covid-fosh-review/record.json b/sources/experimental/covid-fosh-review/record.json
new file mode 100644
index 0000000..4186249
--- /dev/null
+++ b/sources/experimental/covid-fosh-review/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "host": "www.protocols.io",
+   "status": "not code: protocol text",
+   "url": "https://www.protocols.io/groups/opentrons-covid19-testing"
+  }
+ ],
+ "doi_primary": "10.3389/fmedt.2022.969203",
+ "dois": [
+  "10.3389/fmedt.2022.969203"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 26,
+  "source": "europepmc:PMC9521367"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1628684,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "eb3f959260faa3a485402086475f5c84f9b43ebff69b0ba223a3b6de0bdfb99c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9521367?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9521367.1/PMC9521367.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9521367.1/PMC9521367.1.pdf"
+ },
+ "pmcid": "PMC9521367",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/covid-fosh-review",
+ "title": "High-throughput and automated screening for COVID-19",
+ "year": "2022"
+}
diff --git a/sources/experimental/covid-mastermix-omix/record.json b/sources/experimental/covid-mastermix-omix/record.json
new file mode 100644
index 0000000..15f5379
--- /dev/null
+++ b/sources/experimental/covid-mastermix-omix/record.json
@@ -0,0 +1,79 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/covid-mastermix-omix/Donald-OMIX__Liquid_Handler_Methods",
+   "commit": "527879af02bea49f4818b53335e382f57aa7c95b",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "Donald-OMIX/Liquid_Handler_Methods",
+   "robot_mentions": [],
+   "size_kb": 131140,
+   "status": "cloned",
+   "url": "https://github.com/Donald-OMIX/Liquid_Handler_Methods"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2024.100195",
+ "dois": [
+  "10.1016/j.slast.2024.100195"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 12,
+  "sections": 26,
+  "source": "europepmc:PMC11639134"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "not_found",
+  "tried": [
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11639134.1/PMC11639134.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11639134.2/PMC11639134.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11639134.3/PMC11639134.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC11639134&blobtype=pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC11639134",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/covid-mastermix-omix",
+ "title": "Development and validation of automated methods for COVID-19 PCR Master Mix preparation",
+ "year": "2024"
+}
diff --git a/sources/experimental/culturomics-colony-picking/record.json b/sources/experimental/culturomics-colony-picking/record.json
new file mode 100644
index 0000000..1fab5b1
--- /dev/null
+++ b/sources/experimental/culturomics-colony-picking/record.json
@@ -0,0 +1,51 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "see paper code availability (not verified)"
+  }
+ ],
+ "doi_primary": "10.1038/s41587-023-01674-2",
+ "dois": [
+  "10.1038/s41587-023-01674-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41587-023-01674-2:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5994780,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "86011be4f29b88e3d02d6a95b04358152e2b984ad345a6f0fa7097351f557ecb",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41587-023-01674-2.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41587-023-01674-2.pdf"
+ },
+ "pmcid": "PMC10567565",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/culturomics-colony-picking",
+ "title": "High-throughput microbial culturomics using automation and machine learning (CAMII colony picker)",
+ "year": "2023"
+}
diff --git a/sources/experimental/culturomics-isolation/record.json b/sources/experimental/culturomics-isolation/record.json
new file mode 100644
index 0000000..15d6a28
--- /dev/null
+++ b/sources/experimental/culturomics-isolation/record.json
@@ -0,0 +1,75 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11",
+    "2.20",
+    "2.9"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/culturomics-isolation/microenvgen__Culturomics",
+   "commit": "9c4aefcbbcf7aba76dc1fa38c41e9fd118b26df9",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 11,
+   "py_files": 22,
+   "redistributable": "no",
+   "repo": "microenvgen/Culturomics",
+   "robot_mentions": [],
+   "size_kb": 812131,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/microenvgen/Culturomics"
+  }
+ ],
+ "doi_primary": "10.1002/imo2.70037",
+ "dois": [
+  "10.1002/imo2.70037"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 1,
+  "sections": 21,
+  "source": "europepmc:PMC12805989"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1554429,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "c5909ae05e267a411b35b0d1edd8acc5b22c4fc53580a86369e2cae31c210d6b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12805989?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12805989.1/PMC12805989.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12805989.1/PMC12805989.1.pdf"
+ },
+ "pmcid": "PMC12805989",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/culturomics-isolation",
+ "title": "Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex communities",
+ "year": "2025"
+}
diff --git a/sources/experimental/curcumin-formulation-sdl/record.json b/sources/experimental/curcumin-formulation-sdl/record.json
new file mode 100644
index 0000000..efe52d1
--- /dev/null
+++ b/sources/experimental/curcumin-formulation-sdl/record.json
@@ -0,0 +1,79 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/curcumin-formulation-sdl/shorthouse-lab__Ros_SDformulation",
+   "commit": "c044c8034e348193863b9dfffe3d53dcbc823183",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "shorthouse-lab/Ros_SDformulation",
+   "robot_mentions": [],
+   "size_kb": 1143,
+   "status": "cloned",
+   "url": "https://github.com/shorthouse-lab/Ros_SDformulation"
+  }
+ ],
+ "doi_primary": "10.1039/d5dd00171d",
+ "dois": [
+  "10.1039/d5dd00171d"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 26,
+  "source": "europepmc:PMC13576497"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "not_found",
+  "tried": [
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13576497.1/PMC13576497.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13576497.2/PMC13576497.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13576497.3/PMC13576497.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC13576497&blobtype=pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC13576497",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/curcumin-formulation-sdl",
+ "title": "Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator",
+ "year": "2025"
+}
diff --git a/sources/experimental/damplab-moclo-transformation/record.json b/sources/experimental/damplab-moclo-transformation/record.json
new file mode 100644
index 0000000..a091689
--- /dev/null
+++ b/sources/experimental/damplab-moclo-transformation/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/damplab-moclo-transformation/DAMPLAB__OT2-MoClo-Transformation-Ecoli",
+   "commit": "ce49b7eb891fb16be95a269e292ec02cb4fa294f",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 3,
+   "py_files": 4,
+   "redistributable": "yes",
+   "repo": "DAMPLAB/OT2-MoClo-Transformation-Ecoli",
+   "robot_mentions": [],
+   "size_kb": 844,
+   "status": "cloned",
+   "url": "https://github.com/DAMPLAB/OT2-MoClo-Transformation-Ecoli"
+  }
+ ],
+ "doi_primary": "10.1093/synbio/ysac004",
+ "dois": [
+  "10.1093/synbio/ysac004"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 20,
+  "source": "europepmc:PMC9074407"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 862094,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "12200b23dc0f0760ba661332f4aec09822be48e883a34e97096e604f495260da",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9074407?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9074407.1/PMC9074407.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9074407.1/PMC9074407.1.pdf"
+ },
+ "pmcid": "PMC9074407",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "no_protocol_found",
+ "slug": "experimental/damplab-moclo-transformation",
+ "title": "A linear programming-based strategy to save pipette tips in automated DNA assembly (with DAMP Lab MoClo/transformation workflow)",
+ "year": "2022"
+}
diff --git a/sources/experimental/damplab-taqpath-ot2/record.json b/sources/experimental/damplab-taqpath-ot2/record.json
new file mode 100644
index 0000000..55ced79
--- /dev/null
+++ b/sources/experimental/damplab-taqpath-ot2/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.7"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/damplab-taqpath-ot2/DAMPLAB__OT2-SARS-CoV2",
+   "commit": "f9a719cbf1db7ea2d827f3574225e317c75287a2",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "DAMPLAB/OT2-SARS-CoV2",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 448,
+   "status": "cloned",
+   "url": "https://github.com/DAMPLAB/OT2-SARS-CoV2"
+  }
+ ],
+ "dois": [
+  "10.17504/protocols.io.brhvm366"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.17504/protocols.io.brhvm366:\n  europepmc: no Europe PMC full text for",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/damplab-taqpath-ot2",
+ "title": "Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex RT-PCR (BU DAMP Lab)",
+ "year": ""
+}
diff --git a/sources/experimental/daxi-lightsheet/record.json b/sources/experimental/daxi-lightsheet/record.json
new file mode 100644
index 0000000..2739063
--- /dev/null
+++ b/sources/experimental/daxi-lightsheet/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/daxi-lightsheet/royerlab__daxi",
+   "commit": "294586d19a1f3f8c762602eeca8c1da8a1494537",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 9,
+   "redistributable": "no",
+   "repo": "royerlab/daxi",
+   "robot_mentions": [],
+   "size_kb": 32250,
+   "status": "cloned",
+   "url": "https://github.com/royerlab/daxi"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-022-01417-2",
+ "dois": [
+  "10.1038/s41592-022-01417-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 15,
+  "sections": 29,
+  "source": "europepmc:PMC9007742"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5955878,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "a1606df4738f0c465a1e4398564cbb758388deda62972aed177b54e19de5467b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41592-022-01417-2.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41592-022-01417-2.pdf"
+ },
+ "pmcid": "PMC9007742",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/daxi-lightsheet",
+ "title": "DaXi: high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy",
+ "year": "2022"
+}
diff --git a/sources/experimental/detectr-covid-ot2/record.json b/sources/experimental/detectr-covid-ot2/record.json
new file mode 100644
index 0000000..7b31602
--- /dev/null
+++ b/sources/experimental/detectr-covid-ot2/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/detectr-covid-ot2/tsdobbs__mammoth-COVID19-assay-OT2",
+   "commit": "447008ce24f6b1740fcbea040a5d0eb664f3b083",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "tsdobbs/mammoth-COVID19-assay-OT2",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 907,
+   "status": "cloned",
+   "url": "https://github.com/tsdobbs/mammoth-COVID19-assay-OT2"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/detectr-covid-ot2",
+ "title": "Mammoth DETECTR COVID-19 assay on OT-2",
+ "year": ""
+}
diff --git a/sources/experimental/diy-ot-linear-motion-qpcr/record.json b/sources/experimental/diy-ot-linear-motion-qpcr/record.json
new file mode 100644
index 0000000..c769fcf
--- /dev/null
+++ b/sources/experimental/diy-ot-linear-motion-qpcr/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [],
+ "doi_primary": "10.1038/s41598-020-70465-5",
+ "dois": [
+  "10.1038/s41598-020-70465-5"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 24,
+  "source": "europepmc:PMC7424513"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2825640,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "c8fefb18bd92d2db5059acd6487a5ece1e6bd4c78c53636ea53f480f20f891fa",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7424513?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7424513.1/PMC7424513.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7424513.1/PMC7424513.1.pdf"
+ },
+ "pmcid": "PMC7424513",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/diy-ot-linear-motion-qpcr",
+ "title": "Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting",
+ "year": "2020"
+}
diff --git a/sources/experimental/diy-stem-lhr/record.json b/sources/experimental/diy-stem-lhr/record.json
new file mode 100644
index 0000000..7c599bd
--- /dev/null
+++ b/sources/experimental/diy-stem-lhr/record.json
@@ -0,0 +1,47 @@
+{
+ "code": [],
+ "doi_primary": "10.1371/journal.pone.0275688",
+ "dois": [
+  "10.1371/journal.pone.0275688"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 17,
+  "source": "europepmc:PMC9645590"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3377066,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "fe97b9fcc18b186e6db6415b28810ed72245547f9537fd69b1f706140671ba23",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0275688&type=printable"
+   }
+  ],
+  "url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0275688&type=printable"
+ },
+ "pmcid": "PMC9645590",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/diy-stem-lhr",
+ "title": "DIY liquid handling robots for integrated STEM education and life science research",
+ "year": "2022"
+}
diff --git a/sources/experimental/dtu-synbio-automation/record.json b/sources/experimental/dtu-synbio-automation/record.json
new file mode 100644
index 0000000..61e1a92
--- /dev/null
+++ b/sources/experimental/dtu-synbio-automation/record.json
@@ -0,0 +1,48 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11",
+    "2.16",
+    "2.20",
+    "2.8"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/dtu-synbio-automation/DALSA-Lab__dtu_synbio_lab_automation",
+   "commit": "1e66a1762099709e9f8882133c22f253654bb686",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 10,
+   "py_files": 13,
+   "redistributable": "yes",
+   "repo": "DALSA-Lab/dtu_synbio_lab_automation",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 1385,
+   "status": "cloned",
+   "url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/dtu-synbio-automation",
+ "title": "DTU Synbio lab automation protocol collection",
+ "year": ""
+}
diff --git a/sources/experimental/duckbot-jubilee/record.json b/sources/experimental/duckbot-jubilee/record.json
new file mode 100644
index 0000000..18f5e2d
--- /dev/null
+++ b/sources/experimental/duckbot-jubilee/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/duckbot-jubilee/machineagency__duckbot",
+   "commit": "6890a8bda253a0efd5d902d203b014466ed959e2",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 1,
+   "redistributable": "yes",
+   "repo": "machineagency/duckbot",
+   "robot_mentions": [],
+   "size_kb": 415295,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/machineagency/duckbot"
+  }
+ ],
+ "doi_primary": "10.1371/journal.pone.0296717",
+ "dois": [
+  "10.1371/journal.pone.0296717"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 10,
+  "sections": 8,
+  "source": "europepmc:PMC10805289"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2681746,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "34fd9a7a9a96d47d94f37d90aef8da935126d8548ad0210bb9003cf59825ba39",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296717&type=printable"
+   }
+  ],
+  "url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296717&type=printable"
+ },
+ "pmcid": "PMC10805289",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/duckbot-jubilee",
+ "title": "The Duckbot: A system for automated imaging and manipulation of duckweed",
+ "year": "2024"
+}
diff --git a/sources/experimental/duckweed-hte/record.json b/sources/experimental/duckweed-hte/record.json
new file mode 100644
index 0000000..a2a535e
--- /dev/null
+++ b/sources/experimental/duckweed-hte/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/duckweed-hte/zenodo-8060938",
+   "files": 2,
+   "files_downloaded": 2,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "mit-license",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "zenodo:8060938",
+   "robot_mentions": [],
+   "size_kb": 4,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.8060938"
+  }
+ ],
+ "doi_primary": "10.1371/journal.pone.0287739",
+ "dois": [
+  "10.1371/journal.pone.0287739"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 16,
+  "source": "europepmc:PMC10361482"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2448845,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "09ed03667954c5c982b11b8d9fc3b844318920806e35facaa801cfd2f3987f71",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10361482?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10361482.1/PMC10361482.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10361482.1/PMC10361482.1.pdf"
+ },
+ "pmcid": "PMC10361482",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/duckweed-hte",
+ "title": "Accelerated high-throughput imaging and phenotyping system for small organisms",
+ "year": "2023"
+}
diff --git a/sources/experimental/ecoli-protein-expr-purif-ot2/record.json b/sources/experimental/ecoli-protein-expr-purif-ot2/record.json
new file mode 100644
index 0000000..10fb33b
--- /dev/null
+++ b/sources/experimental/ecoli-protein-expr-purif-ot2/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ecoli-protein-expr-purif-ot2/nortonbakerbc__opentrons",
+   "commit": "f4afa187b3cff913097e1a51ce90a28172090777",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 21,
+   "py_files": 22,
+   "redistributable": "no",
+   "repo": "nortonbakerbc/opentrons",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 18507,
+   "status": "cloned",
+   "url": "https://github.com/nortonbakerbc/opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ecoli-protein-expr-purif-ot2",
+ "title": "OT-2 assisted recombinant protein expression and purification in E. coli (Norton-Baker)",
+ "year": ""
+}
diff --git a/sources/experimental/eda-event-driven/record.json b/sources/experimental/eda-event-driven/record.json
new file mode 100644
index 0000000..2d27d38
--- /dev/null
+++ b/sources/experimental/eda-event-driven/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/eda-event-driven/wl-stepp__eda_plugin",
+   "commit": "94b042401ae774fbac381952203350f4b30bbe0a",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 44,
+   "redistributable": "yes",
+   "repo": "wl-stepp/eda_plugin",
+   "robot_mentions": [],
+   "size_kb": 126068,
+   "status": "cloned",
+   "url": "https://github.com/wl-stepp/eda_plugin"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-022-01589-x",
+ "dois": [
+  "10.1038/s41592-022-01589-x"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 34,
+  "source": "europepmc:PMC7613693"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 2362726,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "718d4199b0fb77aee8b43e4f2fae11318fd2ec7421b1168a14431cbefa5fe50a",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://www.nature.com/articles/s41592-022-01589-x.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7613693?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7613693.1/PMC7613693.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7613693.1/PMC7613693.1.pdf"
+ },
+ "pmcid": "PMC7613693",
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/eda-event-driven",
+ "title": "Event-driven acquisition for content-enriched microscopy",
+ "year": "2022"
+}
diff --git a/sources/experimental/egf-sequeduct/record.json b/sources/experimental/egf-sequeduct/record.json
new file mode 100644
index 0000000..cb65877
--- /dev/null
+++ b/sources/experimental/egf-sequeduct/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/egf-sequeduct/Edinburgh-Genome-Foundry__Sequeduct",
+   "commit": "d3544eae7a47bd3d16b1654fb75a5684d9ff8b55",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 12,
+   "redistributable": "no",
+   "repo": "Edinburgh-Genome-Foundry/Sequeduct",
+   "robot_mentions": [],
+   "size_kb": 221,
+   "status": "cloned",
+   "url": "https://github.com/Edinburgh-Genome-Foundry/Sequeduct"
+  }
+ ],
+ "doi_primary": "10.1021/acssynbio.3c00589",
+ "dois": [
+  "10.1021/acssynbio.3c00589"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 1,
+  "sections": 13,
+  "source": "europepmc:PMC10877595"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1640656,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "64e4d63396c4f533297104e526d880ea4d474d9e27f6df0fe6d34ce262769144",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10877595?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10877595.1/PMC10877595.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10877595.1/PMC10877595.1.pdf"
+ },
+ "pmcid": "PMC10877595",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/egf-sequeduct",
+ "title": "Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing",
+ "year": "2024"
+}
diff --git a/sources/experimental/endylab-opentrons/record.json b/sources/experimental/endylab-opentrons/record.json
new file mode 100644
index 0000000..9f2714f
--- /dev/null
+++ b/sources/experimental/endylab-opentrons/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/endylab-opentrons/EndyLab__opentrons",
+   "commit": "75d1789ad6ddef556a2c46e6608d5496f9f5ec7d",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 39,
+   "py_files": 60,
+   "redistributable": "no",
+   "repo": "EndyLab/opentrons",
+   "robot_mentions": [],
+   "size_kb": 139255,
+   "status": "cloned",
+   "url": "https://github.com/EndyLab/opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/endylab-opentrons",
+ "title": "Endy Lab Opentrons protocol collection",
+ "year": ""
+}
diff --git a/sources/experimental/ester-library-synthesis/record.json b/sources/experimental/ester-library-synthesis/record.json
new file mode 100644
index 0000000..ec353d6
--- /dev/null
+++ b/sources/experimental/ester-library-synthesis/record.json
@@ -0,0 +1,62 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ester-library-synthesis/rz-flask__concise-ester-library-synthesis",
+   "commit": "137e0592b396594c92ec09159c0ceeeea5c2d963",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 3,
+   "py_files": 3,
+   "redistributable": "yes",
+   "repo": "rz-flask/concise-ester-library-synthesis",
+   "robot_mentions": [],
+   "size_kb": 10,
+   "status": "cloned",
+   "url": "https://github.com/rz-flask/concise-ester-library-synthesis"
+  }
+ ],
+ "doi_primary": "10.1039/d2cc05670d",
+ "dois": [
+  "10.1039/d2cc05670d"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d2cc05670d:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://pubs.rsc.org/en/content/articlepdf/2023/CC/D2CC05670D"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/ester-library-synthesis",
+ "title": "Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction",
+ "year": "2023"
+}
diff --git a/sources/experimental/etsted/record.json b/sources/experimental/etsted/record.json
new file mode 100644
index 0000000..c62083c
--- /dev/null
+++ b/sources/experimental/etsted/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/etsted/jonatanalvelid__etSTED-widget",
+   "commit": "b7b2dc1ae8518881fc3aa053a43ebba125552489",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 15,
+   "redistributable": "no",
+   "repo": "jonatanalvelid/etSTED-widget",
+   "robot_mentions": [],
+   "size_kb": 211,
+   "status": "cloned",
+   "url": "https://github.com/jonatanalvelid/etSTED-widget"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-022-01588-y",
+ "dois": [
+  "10.1038/s41592-022-01588-y"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 13,
+  "sections": 44,
+  "source": "europepmc:PMC9550628"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 9704490,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "788218922d73bc627bb88b10ac88189e97386e9b010344fb24622b2c6124e24c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41592-022-01588-y.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41592-022-01588-y.pdf"
+ },
+ "pmcid": "PMC9550628",
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/etsted",
+ "title": "Event-triggered STED imaging",
+ "year": "2022"
+}
diff --git a/sources/experimental/evobot/record.json b/sources/experimental/evobot/record.json
new file mode 100644
index 0000000..e791153
--- /dev/null
+++ b/sources/experimental/evobot/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [],
+ "doi_primary": "10.1177/2472630316689285",
+ "dois": [
+  "10.1177/2472630316689285"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1177/2472630316689285:\n  europepmc: no Europe PMC full text for this ",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://journals.sagepub.com/doi/pdf/10.1177/2472630316689285"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/evobot",
+ "title": "New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot",
+ "year": "2017"
+}
diff --git a/sources/experimental/evogen-ot-library/record.json b/sources/experimental/evogen-ot-library/record.json
new file mode 100644
index 0000000..31fe148
--- /dev/null
+++ b/sources/experimental/evogen-ot-library/record.json
@@ -0,0 +1,47 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.12",
+    "2.2",
+    "2.7"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/evogen-ot-library/anttonalberdi__EvoGenOT",
+   "commit": "855fec9d2e47ca12b95e14dae3f43260caee4d75",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 77,
+   "py_files": 78,
+   "redistributable": "no",
+   "repo": "anttonalberdi/EvoGenOT",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 829,
+   "status": "cloned",
+   "url": "https://github.com/anttonalberdi/EvoGenOT"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/evogen-ot-library",
+ "title": "EvoGenOT (UCPH EvoGenomics Opentrons protocol library)",
+ "year": ""
+}
diff --git a/sources/experimental/evolver-2018/record.json b/sources/experimental/evolver-2018/record.json
new file mode 100644
index 0000000..7c1a0d2
--- /dev/null
+++ b/sources/experimental/evolver-2018/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/evolver-2018/FYNCH-BIO__dpu",
+   "commit": "ec41600bb20ae7fdecdcbce7bd9e6807e34e0f18",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 12,
+   "redistributable": "yes",
+   "repo": "FYNCH-BIO/dpu",
+   "robot_mentions": [],
+   "size_kb": 6260,
+   "status": "cloned",
+   "url": "https://github.com/FYNCH-BIO/dpu"
+  }
+ ],
+ "doi_primary": "10.1038/nbt.4151",
+ "dois": [
+  "10.1038/nbt.4151"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 17,
+  "source": "europepmc:PMC6035058"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 2792861,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "b6f4eeda994c515b46854d056ea62290bf5024cf3b5bd424467353336f1776b2",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC6035058?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6035058.1/PMC6035058.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6035058.1/PMC6035058.1.pdf"
+ },
+ "pmcid": "PMC6035058",
+ "readiness": "ready",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/evolver-2018",
+ "title": "Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER",
+ "year": "2018"
+}
diff --git a/sources/experimental/evolver-ddr-elife/record.json b/sources/experimental/evolver-ddr-elife/record.json
new file mode 100644
index 0000000..3b172b4
--- /dev/null
+++ b/sources/experimental/evolver-ddr-elife/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/evolver-ddr-elife/khalillab__DDR-eVOLVER-model",
+   "commit": "7019f031598169723a5828f3909eba1e199794d2",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "khalillab/DDR-eVOLVER-model",
+   "robot_mentions": [],
+   "size_kb": 47809,
+   "status": "cloned",
+   "url": "https://github.com/khalillab/DDR-eVOLVER-model"
+  }
+ ],
+ "doi_primary": "10.7554/eLife.67175",
+ "dois": [
+  "10.7554/eLife.67175"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 23,
+  "sections": 29,
+  "source": "europepmc:PMC8460265"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1986256,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "07ac37f06d53892dcbb44fa49d2fe7df78c8ff91b164269a946ae2e9306717df",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8460265?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8460265.1/PMC8460265.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8460265.1/PMC8460265.1.pdf"
+ },
+ "pmcid": "PMC8460265",
+ "readiness": "partial",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/evolver-ddr-elife",
+ "title": "Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community (eVOLVER)",
+ "year": "2021"
+}
diff --git a/sources/experimental/evotron-evolver-sampling/record.json b/sources/experimental/evotron-evolver-sampling/record.json
new file mode 100644
index 0000000..7d37d72
--- /dev/null
+++ b/sources/experimental/evotron-evolver-sampling/record.json
@@ -0,0 +1,70 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/evotron-evolver-sampling/santkumar__evotron",
+   "commit": "7bc0f1f36c8363dd0810ddb8be9856fa958d17e1",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "santkumar/evotron",
+   "robot_mentions": [],
+   "size_kb": 3093,
+   "status": "cloned",
+   "url": "https://github.com/santkumar/evotron"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-022-32392-z",
+ "dois": [
+  "10.1038/s41467-022-32392-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github",
+  "nonlh",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 34,
+  "source": "europepmc:PMC9381578"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3235131,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8f740aeb1332dab0cd189105f6cfbf2d43716bac958892783eb6a0eb607e2b22",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41467-022-32392-z.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41467-022-32392-z.pdf"
+ },
+ "pmcid": "PMC9381578",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/evotron-evolver-sampling",
+ "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback",
+ "year": "2022"
+}
diff --git a/sources/experimental/exfab-qiaseq-flex/record.json b/sources/experimental/exfab-qiaseq-flex/record.json
new file mode 100644
index 0000000..794d197
--- /dev/null
+++ b/sources/experimental/exfab-qiaseq-flex/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.18"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/exfab-qiaseq-flex/exfab__Opentrons_Flex_ExFAB",
+   "commit": "30bf26a9014b1fdb0a135ddfb1135d21aab4c1f9",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "exfab/Opentrons_Flex_ExFAB",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 26,
+   "status": "cloned",
+   "url": "https://github.com/exfab/Opentrons_Flex_ExFAB"
+  }
+ ],
+ "dois": [
+  "10.17504/protocols.io.n2bvjer3pgk5"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.17504/protocols.io.n2bvjer3pgk5:\n  europepmc: no Europe PMC full text",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "flex",
+ "simulator": "verified",
+ "slug": "experimental/exfab-qiaseq-flex",
+ "title": "Automated QIAseq FX DNA Library Preparation on the Opentrons Flex",
+ "year": ""
+}
diff --git a/sources/experimental/exposomics-384-flex/record.json b/sources/experimental/exposomics-384-flex/record.json
new file mode 100644
index 0000000..67418f9
--- /dev/null
+++ b/sources/experimental/exposomics-384-flex/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.20"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/exposomics-384-flex/apat594__384wellplate-Exposomics-Opentrons-Protocols",
+   "commit": "b0584daa76e9e14e836350f24cd492bb272fbfd7",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "yes",
+   "repo": "apat594/384wellplate-Exposomics-Opentrons-Protocols",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 212,
+   "status": "cloned",
+   "url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/exposomics-384-flex",
+ "title": "Opentrons Flex 384-well protein-precipitation sample preparation for nontargeted exposomics",
+ "year": ""
+}
diff --git a/sources/experimental/findus/record.json b/sources/experimental/findus/record.json
new file mode 100644
index 0000000..f993035
--- /dev/null
+++ b/sources/experimental/findus/record.json
@@ -0,0 +1,66 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/findus/FBarthels__FINDUS",
+   "commit": "ec5df076bab124d1a7adec654500ea6f5a8d34ac",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "FBarthels/FINDUS",
+   "robot_mentions": [],
+   "size_kb": 518718,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/FBarthels/FINDUS"
+  }
+ ],
+ "doi_primary": "10.1177/2472630319877374",
+ "dois": [
+  "10.1177/2472630319877374"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1177/2472630319877374:\n  europepmc: no Europe PMC full text for this ",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://slas-technology.org/article/S2472630322010251/pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://journals.sagepub.com/doi/pdf/10.1177/2472630319877374"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/findus",
+ "title": "FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences",
+ "year": "2020"
+}
diff --git a/sources/experimental/fish-fluidics/record.json b/sources/experimental/fish-fluidics/record.json
new file mode 100644
index 0000000..39c4b70
--- /dev/null
+++ b/sources/experimental/fish-fluidics/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/fish-fluidics/dzhaojie__Fluidics-system-for-FISH",
+   "commit": "7e7971b46a98a0035f7fd6710f885483a9e4701a",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "dzhaojie/Fluidics-system-for-FISH",
+   "robot_mentions": [],
+   "size_kb": 7704,
+   "status": "cloned",
+   "url": "https://github.com/dzhaojie/Fluidics-system-for-FISH"
+  }
+ ],
+ "doi_primary": "10.1016/j.ohx.2022.e00343",
+ "dois": [
+  "10.1016/j.ohx.2022.e00343"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 33,
+  "sections": 33,
+  "source": "europepmc:PMC9358477"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 6218810,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "b8cf553c0b8397270cfa53a9ba10f9086064d205176ca885595e1a287e30b74d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9358477?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9358477.1/PMC9358477.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9358477.1/PMC9358477.1.pdf"
+ },
+ "pmcid": "PMC9358477",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/fish-fluidics",
+ "title": "An open source 16-channel fluidics system for automating sequential FISH-based imaging",
+ "year": "2022"
+}
diff --git a/sources/experimental/flat-agar-celegans-ot2/record.json b/sources/experimental/flat-agar-celegans-ot2/record.json
new file mode 100644
index 0000000..0a746f7
--- /dev/null
+++ b/sources/experimental/flat-agar-celegans-ot2/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.20",
+    "2.28"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/flat-agar-celegans-ot2/Arcadia-Science__menisquish-flat-agar",
+   "commit": "73368d5f2e65af7c40560b0387522a2e503c0547",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 3,
+   "py_files": 4,
+   "redistributable": "yes",
+   "repo": "Arcadia-Science/menisquish-flat-agar",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 2749,
+   "status": "cloned",
+   "url": "https://github.com/Arcadia-Science/menisquish-flat-agar"
+  }
+ ],
+ "dois": [
+  "10.57844/arcadia-h01v-2nxt"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.57844/arcadia-h01v-2nxt:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/flat-agar-celegans-ot2",
+ "title": "Flat agar and optimized media enable high-throughput C. elegans imaging in 96-well plates",
+ "year": ""
+}
diff --git a/sources/experimental/flex-genomics-di-omics/record.json b/sources/experimental/flex-genomics-di-omics/record.json
new file mode 100644
index 0000000..c829b1f
--- /dev/null
+++ b/sources/experimental/flex-genomics-di-omics/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.21"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/flex-genomics-di-omics/di-omics__ot-flex-automation",
+   "commit": "c041408eb61ca3c5253c44d083a4e9c3fa8c7133",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 13,
+   "py_files": 30,
+   "redistributable": "no",
+   "repo": "di-omics/ot-flex-automation",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 142,
+   "status": "cloned",
+   "url": "https://github.com/di-omics/ot-flex-automation"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/flex-genomics-di-omics",
+ "title": "Opentrons Flex whole-genome / methylation / TIP-seq workflows (di-omics)",
+ "year": ""
+}
diff --git a/sources/experimental/flyspresso-embryo-ihc/record.json b/sources/experimental/flyspresso-embryo-ihc/record.json
new file mode 100644
index 0000000..bfbab61
--- /dev/null
+++ b/sources/experimental/flyspresso-embryo-ihc/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/flyspresso-embryo-ihc/janelia-pypi__hybridizer_python",
+   "commit": "5f21f4d0dd2ef446e6b9aebb1d5b94526ac4131e",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "janelia-pypi/hybridizer_python",
+   "robot_mentions": [],
+   "size_kb": 56,
+   "status": "cloned",
+   "url": "https://github.com/janelia-pypi/hybridizer_python"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-021-89676-5",
+ "dois": [
+  "10.1038/s41598-021-89676-5"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 31,
+  "source": "europepmc:PMC8119710"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 9374172,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8ade28a84a1bb9380c363be5aadd133c9f6b169dfc3abacad194e9e8f157ce98",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41598-021-89676-5.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41598-021-89676-5.pdf"
+ },
+ "pmcid": "PMC8119710",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/flyspresso-embryo-ihc",
+ "title": "An open-source semi-automated robotics pipeline for embryo immunohistochemistry",
+ "year": "2021"
+}
diff --git a/sources/experimental/formulations-prep-shampoo/record.json b/sources/experimental/formulations-prep-shampoo/record.json
new file mode 100644
index 0000000..46d5d3c
--- /dev/null
+++ b/sources/experimental/formulations-prep-shampoo/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/formulations-prep-shampoo/sustainable-processes__formulations-prep",
+   "commit": "a715cec009bd651d9c3e836d6a506070cb9c5835",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "sustainable-processes/formulations-prep",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 82220,
+   "status": "cloned",
+   "url": "https://github.com/sustainable-processes/formulations-prep"
+  }
+ ],
+ "doi_primary": "10.1038/s41597-024-03573-w",
+ "dois": [
+  "10.1038/s41597-024-03573-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 23,
+  "source": "europepmc:PMC11222379"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3072068,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "1e595246b57deba11126c242f9dbe009e592147c90022c2fe5c98833f24de844",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11222379?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11222379.1/PMC11222379.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11222379.1/PMC11222379.1.pdf"
+ },
+ "pmcid": "PMC11222379",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/formulations-prep-shampoo",
+ "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset",
+ "year": "2024"
+}
diff --git a/sources/experimental/gfp-codon-burden-ot2/record.json b/sources/experimental/gfp-codon-burden-ot2/record.json
new file mode 100644
index 0000000..3493ffa
--- /dev/null
+++ b/sources/experimental/gfp-codon-burden-ot2/record.json
@@ -0,0 +1,75 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.18"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/gfp-codon-burden-ot2/alexismhill3__gfp_deoptimization_burden",
+   "commit": "80cddc02491db83dd2c682500b9b32a6d97f156c",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 63,
+   "py_files": 200,
+   "redistributable": "yes",
+   "repo": "alexismhill3/gfp_deoptimization_burden",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 63594,
+   "status": "cloned",
+   "url": "https://github.com/alexismhill3/gfp_deoptimization_burden"
+  }
+ ],
+ "doi_primary": "10.1186/s13036-025-00521-z",
+ "dois": [
+  "10.1186/s13036-025-00521-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 14,
+  "source": "europepmc:PMC12100883"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 2240328,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "2809c99b5403fb038af36ce17774131b02a5e3a09589a34b598dd4decc1e685c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12100883?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12100883.1/PMC12100883.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12100883.1/PMC12100883.1.pdf"
+ },
+ "pmcid": "PMC12100883",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/gfp-codon-burden-ot2",
+ "title": "Codon usage modulates the relationship between the burden and yield of protein overexpression",
+ "year": "2025"
+}
diff --git a/sources/experimental/gpcr-livecell-ot2/record.json b/sources/experimental/gpcr-livecell-ot2/record.json
new file mode 100644
index 0000000..daaf6ca
--- /dev/null
+++ b/sources/experimental/gpcr-livecell-ot2/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/acssensors.2c01341",
+ "dois": [
+  "10.1021/acssensors.2c01341"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/acssensors.2c01341:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9994309?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9994309.1/PMC9994309.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9994309.2/PMC9994309.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9994309.3/PMC9994309.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC9994309&blobtype=pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://pubs.acs.org/doi/pdf/10.1021/acssensors.2c01341"
+   }
+  ]
+ },
+ "pmcid": "PMC9994309",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/gpcr-livecell-ot2",
+ "title": "GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System",
+ "year": "2023"
+}
diff --git a/sources/experimental/greenaway-halogenation/record.json b/sources/experimental/greenaway-halogenation/record.json
new file mode 100644
index 0000000..1bb6658
--- /dev/null
+++ b/sources/experimental/greenaway-halogenation/record.json
@@ -0,0 +1,55 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.9"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/greenaway-halogenation/GreenawayLab__automated_halogenation_of_pharmaceuticals",
+   "commit": "b78bd71e409c26f356ec6071fd1b2c75a4ba2535",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 9,
+   "py_files": 11,
+   "redistributable": "yes",
+   "repo": "GreenawayLab/automated_halogenation_of_pharmaceuticals",
+   "robot_mentions": [],
+   "size_kb": 28972,
+   "status": "cloned",
+   "url": "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals"
+  }
+ ],
+ "dois": [
+  "10.26434/chemrxiv.15000393"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.26434/chemrxiv.15000393:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/greenaway-halogenation",
+ "title": "An automated platform for tailored late-stage halogenation of pharmaceuticals",
+ "year": ""
+}
diff --git a/sources/experimental/greenaway-mocs/record.json b/sources/experimental/greenaway-mocs/record.json
new file mode 100644
index 0000000..2de209c
--- /dev/null
+++ b/sources/experimental/greenaway-mocs/record.json
@@ -0,0 +1,74 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.9"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/greenaway-mocs/GreenawayLab__development-automated-workflow-mocs",
+   "commit": "8df90c063af7eca3f58ad7ce1e984d9004079da1",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 5,
+   "py_files": 12,
+   "redistributable": "no",
+   "repo": "GreenawayLab/development-automated-workflow-mocs",
+   "robot_mentions": [],
+   "size_kb": 2472,
+   "status": "cloned",
+   "url": "https://github.com/GreenawayLab/development-automated-workflow-mocs"
+  }
+ ],
+ "doi_primary": "10.1002/anie.202424270",
+ "dois": [
+  "10.1002/anie.202424270"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 13,
+  "source": "europepmc:PMC12144869"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3062660,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "941d9e2e1d40172411db55f6c17ec26accf82adc953fd59a4a5da47f76afb0e3",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12144869?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12144869.1/PMC12144869.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12144869.1/PMC12144869.1.pdf"
+ },
+ "pmcid": "PMC12144869",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/greenaway-mocs",
+ "title": "Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages",
+ "year": "2025"
+}
diff --git a/sources/experimental/greenaway-pocs/record.json b/sources/experimental/greenaway-pocs/record.json
new file mode 100644
index 0000000..06359a5
--- /dev/null
+++ b/sources/experimental/greenaway-pocs/record.json
@@ -0,0 +1,79 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.9"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/greenaway-pocs/GreenawayLab__Streamlining-Automated-Discovery-POCs",
+   "commit": "7a5b468ba06ac157500f1d8b73b141174d268425",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 6,
+   "py_files": 29,
+   "redistributable": "no",
+   "repo": "GreenawayLab/Streamlining-Automated-Discovery-POCs",
+   "robot_mentions": [],
+   "size_kb": 10392,
+   "status": "cloned",
+   "url": "https://github.com/GreenawayLab/Streamlining-Automated-Discovery-POCs"
+  }
+ ],
+ "doi_primary": "10.1039/d3sc06133g",
+ "dois": [
+  "10.1039/d3sc06133g"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 9,
+  "sections": 18,
+  "source": "europepmc:PMC11062116"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3369080,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "3ab72e72759dbc9d036509b08c7ddde0a22930cf83226d13913f38f2cfd02dfa",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://pubs.rsc.org/en/content/articlepdf/2024/sc/d3sc06133g"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11062116?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11062116.1/PMC11062116.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11062116.1/PMC11062116.1.pdf"
+ },
+ "pmcid": "PMC11062116",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/greenaway-pocs",
+ "title": "Streamlining the automated discovery of porous organic cages",
+ "year": "2024"
+}
diff --git a/sources/experimental/har1eyk-starlet-protein-extraction/record.json b/sources/experimental/har1eyk-starlet-protein-extraction/record.json
new file mode 100644
index 0000000..87ab6d6
--- /dev/null
+++ b/sources/experimental/har1eyk-starlet-protein-extraction/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/har1eyk-starlet-protein-extraction/har1eyk__hamilton-starlet-scripts",
+   "commit": "34c1677c54d65874c0b05ee18937c708ce5c6c3e",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 5,
+   "redistributable": "no",
+   "repo": "har1eyk/hamilton-starlet-scripts",
+   "robot_mentions": [],
+   "size_kb": 305,
+   "status": "cloned",
+   "url": "https://github.com/har1eyk/hamilton-starlet-scripts"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "hamilton",
+ "simulator": "not run",
+ "slug": "experimental/har1eyk-starlet-protein-extraction",
+ "title": "hamilton-starlet-scripts (PyLabRobot STARlet protein extraction / Orange G volume tests)",
+ "year": ""
+}
diff --git a/sources/experimental/helao-async/record.json b/sources/experimental/helao-async/record.json
new file mode 100644
index 0000000..09c631c
--- /dev/null
+++ b/sources/experimental/helao-async/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/helao-async/High-Throughput-Experimentation__helao-async",
+   "commit": "cc07dbd7deaf22236b0ec4caad6f05761981b180",
+   "default_branch": "unstable",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 1045,
+   "redistributable": "no",
+   "repo": "High-Throughput-Experimentation/helao-async",
+   "robot_mentions": [],
+   "size_kb": 35684,
+   "status": "cloned",
+   "url": "https://github.com/High-Throughput-Experimentation/helao-async"
+  }
+ ],
+ "dois": [
+  "10.1039/d3dd00193h"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d3dd00193h:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/helao-async",
+ "title": "HELAO-async: autonomous electrochemistry/high-throughput experimentation orchestration (Caltech/TRI)",
+ "year": ""
+}
diff --git a/sources/experimental/ht-hcr-sea-urchin/record.json b/sources/experimental/ht-hcr-sea-urchin/record.json
new file mode 100644
index 0000000..4ca61c9
--- /dev/null
+++ b/sources/experimental/ht-hcr-sea-urchin/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ht-hcr-sea-urchin/ylee-sio__HL_HTHCR",
+   "commit": "83eaf3c59a9e4ebac92fa3e0fabb50d9ec098ac0",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 3,
+   "redistributable": "no",
+   "repo": "ylee-sio/HL_HTHCR",
+   "robot_mentions": [],
+   "size_kb": 73,
+   "status": "cloned",
+   "url": "https://github.com/ylee-sio/HL_HTHCR"
+  }
+ ],
+ "doi_primary": "10.1242/dev.204814",
+ "dois": [
+  "10.1242/dev.204814"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 20,
+  "source": "europepmc:PMC12516323"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 10818646,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "9c3885f0a643e0f09648a592eacdf6a1a5a59091e530577193073d4e74aa6e44",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12516323?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12516323.1/PMC12516323.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12516323.1/PMC12516323.1.pdf"
+ },
+ "pmcid": "PMC12516323",
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/ht-hcr-sea-urchin",
+ "title": "Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos",
+ "year": "2025"
+}
diff --git a/sources/experimental/hydra-hydrogel-plates/record.json b/sources/experimental/hydra-hydrogel-plates/record.json
new file mode 100644
index 0000000..45dbf6c
--- /dev/null
+++ b/sources/experimental/hydra-hydrogel-plates/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/hydra-hydrogel-plates/Synthetic-Physiology-Lab__hydra-hts-hydrogel-analysis",
+   "commit": "7e4e4076db4d91b315777a8f785ffb3f9f3a2725",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "Synthetic-Physiology-Lab/hydra-hts-hydrogel-analysis",
+   "robot_mentions": [],
+   "size_kb": 11,
+   "status": "cloned",
+   "url": "https://github.com/Synthetic-Physiology-Lab/hydra-hts-hydrogel-analysis"
+  }
+ ],
+ "doi_primary": "10.1038/s44172-025-00575-3",
+ "dois": [
+  "10.1038/s44172-025-00575-3"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 41,
+  "source": "europepmc:PMC12749810"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 12012463,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "776e8ebb9705945eb210a58e6a5ecdb4d3e89473e4b6025151945b295f03b6a7",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12749810?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12749810.1/PMC12749810.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12749810.1/PMC12749810.1.pdf"
+ },
+ "pmcid": "PMC12749810",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/hydra-hydrogel-plates",
+ "title": "Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing",
+ "year": "2025"
+}
diff --git a/sources/experimental/hydrogel-crosslink-ot2/record.json b/sources/experimental/hydrogel-crosslink-ot2/record.json
new file mode 100644
index 0000000..287502e
--- /dev/null
+++ b/sources/experimental/hydrogel-crosslink-ot2/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/hydrogel-crosslink-ot2/JamesSummers240__Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-",
+   "commit": "e1a74a0e517f6f56b7c03a6e7e3570cb285d7633",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-",
+   "robot_mentions": [],
+   "size_kb": 3,
+   "status": "cloned",
+   "url": "https://github.com/JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/hydrogel-crosslink-ot2",
+ "title": "Semi-autonomous synthesis and modelling of chemically cross-linked hydrogels (OT-2)",
+ "year": ""
+}
diff --git a/sources/experimental/hyrad-adna-capture/record.json b/sources/experimental/hyrad-adna-capture/record.json
new file mode 100644
index 0000000..7d93b8f
--- /dev/null
+++ b/sources/experimental/hyrad-adna-capture/record.json
@@ -0,0 +1,79 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.7"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/hyrad-adna-capture/TomaszSuchan__opentrons-hyRAD",
+   "commit": "54e2a7f67a8777bcffa001914a2a6030e18b3cb8",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "TomaszSuchan/opentrons-hyRAD",
+   "robot_mentions": [],
+   "size_kb": 3,
+   "status": "cloned",
+   "url": "https://github.com/TomaszSuchan/opentrons-hyRAD"
+  }
+ ],
+ "doi_primary": "10.1111/1755-0998.13518",
+ "dois": [
+  "10.1111/1755-0998.13518"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 16,
+  "source": "europepmc:PMC9291508"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 1678679,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "48d1222d9873b56c96090f67028ad2b473e6284090c85e93b680fd765a39e752",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1755-0998.13518"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9291508?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9291508.1/PMC9291508.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9291508.1/PMC9291508.1.pdf"
+ },
+ "pmcid": "PMC9291508",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "verified",
+ "slug": "experimental/hyrad-adna-capture",
+ "title": "Performance and automation of ancient DNA capture with RNA hyRAD probes",
+ "year": "2022"
+}
diff --git a/sources/experimental/icfree-cfps/record.json b/sources/experimental/icfree-cfps/record.json
new file mode 100644
index 0000000..1b6d19c
--- /dev/null
+++ b/sources/experimental/icfree-cfps/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/icfree-cfps/brsynth__icfree-ml",
+   "commit": "d436e7f8dd052bf17fbab26a41e6251f1aa3175b",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 21,
+   "redistributable": "yes",
+   "repo": "brsynth/icfree-ml",
+   "robot_mentions": [],
+   "size_kb": 5747,
+   "status": "cloned",
+   "url": "https://github.com/brsynth/icfree-ml"
+  }
+ ],
+ "doi_primary": "10.1016/j.isci.2025.113599",
+ "dois": [
+  "10.1016/j.isci.2025.113599"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 33,
+  "source": "europepmc:PMC12529354"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5096186,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "9c45756014dbc1faddd16abe2addebae98de620d513d15c536c4e243835a94d0",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12529354?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12529354.1/PMC12529354.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12529354.1/PMC12529354.1.pdf"
+ },
+ "pmcid": "PMC12529354",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/icfree-cfps",
+ "title": "An AI-driven workflow for the accelerated optimization of cell-free protein synthesis",
+ "year": "2025"
+}
diff --git a/sources/experimental/illumina-dnaprep-flowbot/record.json b/sources/experimental/illumina-dnaprep-flowbot/record.json
new file mode 100644
index 0000000..67c2740
--- /dev/null
+++ b/sources/experimental/illumina-dnaprep-flowbot/record.json
@@ -0,0 +1,47 @@
+{
+ "code": [],
+ "doi_primary": "10.1038/s41598-024-58963-2",
+ "dois": [
+  "10.1038/s41598-024-58963-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 2,
+  "sections": 14,
+  "source": "europepmc:PMC11001922"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1266579,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8d01cffea8083d8be3e3c4839bab1e52191ccacd7557063301c5b313984a872d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41598-024-58963-2.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41598-024-58963-2.pdf"
+ },
+ "pmcid": "PMC11001922",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/illumina-dnaprep-flowbot",
+ "title": "Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot",
+ "year": "2024"
+}
diff --git a/sources/experimental/imperial-colony-picker/record.json b/sources/experimental/imperial-colony-picker/record.json
new file mode 100644
index 0000000..e8cd3a7
--- /dev/null
+++ b/sources/experimental/imperial-colony-picker/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/imperial-colony-picker/Imperial-Opentrons-Users__automated-colony-picker",
+   "commit": "ca3bb24493afff96dd41dabfe6c0ce1fa41c5e10",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 33,
+   "redistributable": "no",
+   "repo": "Imperial-Opentrons-Users/automated-colony-picker",
+   "robot_mentions": [],
+   "size_kb": 5256,
+   "status": "cloned",
+   "url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/imperial-colony-picker",
+ "title": "Automated colony picker add-on for the OT-2 (Imperial SSB MRes; cited by Slowpoke)",
+ "year": ""
+}
diff --git a/sources/experimental/imswitch/record.json b/sources/experimental/imswitch/record.json
new file mode 100644
index 0000000..a00b0b8
--- /dev/null
+++ b/sources/experimental/imswitch/record.json
@@ -0,0 +1,63 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/imswitch/ImSwitch__ImSwitch",
+   "commit": "37bf1df6de0ee4746b05bef9684c782e4995b2e8",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 484,
+   "redistributable": "no",
+   "repo": "ImSwitch/ImSwitch",
+   "robot_mentions": [],
+   "size_kb": 212410,
+   "status": "cloned",
+   "url": "https://github.com/ImSwitch/ImSwitch"
+  }
+ ],
+ "dois": [
+  "10.21105/joss.03394"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.21105/joss.03394:\n  europepmc: no Europe PMC full text for this DOI\nD",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 226297,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "04d2d9be76aad49b4b445b7a0b27273c5bc478dfb4262314e2f7f0c36b355237",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://joss.theoj.org/papers/10.21105/joss.03394.pdf"
+   }
+  ],
+  "url": "https://joss.theoj.org/papers/10.21105/joss.03394.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/imswitch",
+ "title": "ImSwitch: generalizing microscope control in Python",
+ "year": ""
+}
diff --git a/sources/experimental/ipsc-robot-pyhamilton/record.json b/sources/experimental/ipsc-robot-pyhamilton/record.json
new file mode 100644
index 0000000..a452dd4
--- /dev/null
+++ b/sources/experimental/ipsc-robot-pyhamilton/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ipsc-robot-pyhamilton/stefangolas__iPSC-Robot",
+   "commit": "46389d64d0998061e82f45c613e25d7a3425cde9",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 6,
+   "redistributable": "no",
+   "repo": "stefangolas/iPSC-Robot",
+   "robot_mentions": [],
+   "size_kb": 170,
+   "status": "cloned",
+   "url": "https://github.com/stefangolas/iPSC-Robot"
+  }
+ ],
+ "doi_primary": "10.1101/2020.12.18.423371",
+ "dois": [
+  "10.1101/2020.12.18.423371"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 0,
+  "sections": 0,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 1514439,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "15588ceb8d888421f058727d239f6575c324449a1944b563b1198f6899285977",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/biorxiv/early/2020/12/19/2020.12.18.423371.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/biorxiv/early/2020/12/19/2020.12.18.423371.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "hamilton",
+ "simulator": "not run",
+ "slug": "experimental/ipsc-robot-pyhamilton",
+ "title": "Automated hiPSC culture and sample preparation for 3D live cell microscopy",
+ "year": "2020"
+}
diff --git a/sources/experimental/jubiotech-ot2-autoclone/record.json b/sources/experimental/jubiotech-ot2-autoclone/record.json
new file mode 100644
index 0000000..c2bec5c
--- /dev/null
+++ b/sources/experimental/jubiotech-ot2-autoclone/record.json
@@ -0,0 +1,83 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.1",
+    "2.2",
+    "2.8"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/jubiotech-ot2-autoclone/JuBiotech__OT-2-autoclone",
+   "commit": "e499c1ba572dd9023c248bec07113518bd2b4a4e",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "AGPL-3.0",
+   "opentrons_py_files": 7,
+   "py_files": 8,
+   "redistributable": "no",
+   "repo": "JuBiotech/OT-2-autoclone",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 448,
+   "status": "cloned",
+   "url": "https://github.com/JuBiotech/OT-2-autoclone"
+  }
+ ],
+ "doi_primary": "10.1007/s00253-022-12017-7",
+ "dois": [
+  "10.1007/s00253-022-12017-7"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 23,
+  "source": "europepmc:PMC9259529"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 4097486,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "49e7b8af0af7814d325d8db784852ac85fcbbf2ce37733d45f5e5a24816aee5d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://link.springer.com/content/pdf/10.1007/s00253-022-12017-7.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9259529?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9259529.1/PMC9259529.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9259529.1/PMC9259529.1.pdf"
+ },
+ "pmcid": "PMC9259529",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/jubiotech-ot2-autoclone",
+ "title": "Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation",
+ "year": "2022"
+}
diff --git a/sources/experimental/kedar-balance-integration/record.json b/sources/experimental/kedar-balance-integration/record.json
new file mode 100644
index 0000000..738e6ef
--- /dev/null
+++ b/sources/experimental/kedar-balance-integration/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/kedar-balance-integration/Kedar-Materials-by-Design-Lab__opentrons-balance",
+   "commit": "8e50e1ec51f5072267bd92f843b896aa85f13adf",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "Kedar-Materials-by-Design-Lab/opentrons-balance",
+   "robot_mentions": [],
+   "size_kb": 1137,
+   "status": "cloned",
+   "url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/kedar-balance-integration",
+ "title": "Opentrons OT-2 mass-balance integration (application note supplement)",
+ "year": ""
+}
diff --git a/sources/experimental/kitfree-rna-extraction/record.json b/sources/experimental/kitfree-rna-extraction/record.json
new file mode 100644
index 0000000..761a7e9
--- /dev/null
+++ b/sources/experimental/kitfree-rna-extraction/record.json
@@ -0,0 +1,47 @@
+{
+ "code": [],
+ "doi_primary": "10.1038/s41598-021-02742-w",
+ "dois": [
+  "10.1038/s41598-021-02742-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 9,
+  "source": "europepmc:PMC8636496"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1823028,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "f7756b235ad3551d1ddb28064ab75afcc6e630e72a9d5437e29191bc8088d617",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41598-021-02742-w.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41598-021-02742-w.pdf"
+ },
+ "pmcid": "PMC8636496",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/kitfree-rna-extraction",
+ "title": "A high-throughput pipeline for scalable kit-free RNA extraction",
+ "year": "2021"
+}
diff --git a/sources/experimental/krisp-sars2-pooling/record.json b/sources/experimental/krisp-sars2-pooling/record.json
new file mode 100644
index 0000000..ba2b611
--- /dev/null
+++ b/sources/experimental/krisp-sars2-pooling/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/krisp-sars2-pooling/krisp-kwazulu-natal__efficient-SARS-CoV-2-pooled-testing-strategy-code",
+   "commit": "c780540d1fda98dad5bd5cf6fdb983de0908eb91",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 4,
+   "py_files": 6,
+   "redistributable": "yes",
+   "repo": "krisp-kwazulu-natal/efficient-SARS-CoV-2-pooled-testing-strategy-code",
+   "robot_mentions": [],
+   "size_kb": 874,
+   "status": "cloned",
+   "url": "https://github.com/krisp-kwazulu-natal/efficient-SARS-CoV-2-pooled-testing-strategy-code"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-021-96934-z",
+ "dois": [
+  "10.1038/s41598-021-96934-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 17,
+  "source": "europepmc:PMC8423848"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2368917,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "61e89f17a12e5e4af3c76eb4d01ac62b84e688a0de77756f8c0ccbdcc8d218c1",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8423848?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8423848.1/PMC8423848.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8423848.1/PMC8423848.1.pdf"
+ },
+ "pmcid": "PMC8423848",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/krisp-sars2-pooling",
+ "title": "Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing",
+ "year": "2021"
+}
diff --git a/sources/experimental/labdroid-cell-culture/record.json b/sources/experimental/labdroid-cell-culture/record.json
new file mode 100644
index 0000000..676797a
--- /dev/null
+++ b/sources/experimental/labdroid-cell-culture/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/labdroid-cell-culture/labauto__LabDroid_optimizer",
+   "commit": "661ef792d4b7568a2e673178d9f1e6ed3c84ab1b",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 110,
+   "redistributable": "no",
+   "repo": "labauto/LabDroid_optimizer",
+   "robot_mentions": [],
+   "size_kb": 130,
+   "status": "cloned",
+   "url": "https://github.com/labauto/LabDroid_optimizer"
+  }
+ ],
+ "doi_primary": "10.7554/eLife.77007",
+ "dois": [
+  "10.7554/eLife.77007"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 28,
+  "sections": 40,
+  "source": "europepmc:PMC9239686"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 9489408,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8409ac6749896950b9f411dd629e787c630980f1d6d73ec64e9b944b32fbc30f",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9239686?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9239686.1/PMC9239686.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9239686.1/PMC9239686.1.pdf"
+ },
+ "pmcid": "PMC9239686",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/labdroid-cell-culture",
+ "title": "Robotic search for optimal cell culture in regenerative medicine (LabDroid Maholo, iPSC-RPE)",
+ "year": "2022"
+}
diff --git a/sources/experimental/labdroid-phenol-chloroform/record.json b/sources/experimental/labdroid-phenol-chloroform/record.json
new file mode 100644
index 0000000..695413d
--- /dev/null
+++ b/sources/experimental/labdroid-phenol-chloroform/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/labdroid-phenol-chloroform/zenodo-5733820",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "zenodo:5733820",
+   "robot_mentions": [],
+   "size_kb": 29,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.5733820"
+  }
+ ],
+ "doi_primary": "10.12688/f1000research.109251.1",
+ "dois": [
+  "10.12688/f1000research.109251.1"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 14,
+  "source": "europepmc:PMC8931447"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2121661,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "91a83611542594409b057cb7de60ae58e2f9374210d2723125379e81714b429d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://f1000research.com/articles/11-240/v1/pdf"
+   }
+  ],
+  "url": "https://f1000research.com/articles/11-240/v1/pdf"
+ },
+ "pmcid": "PMC8931447",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/labdroid-phenol-chloroform",
+ "title": "Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing",
+ "year": "2022"
+}
diff --git a/sources/experimental/labop/record.json b/sources/experimental/labop/record.json
new file mode 100644
index 0000000..27629a6
--- /dev/null
+++ b/sources/experimental/labop/record.json
@@ -0,0 +1,46 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11",
+    "2.12"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/labop/Bioprotocols__labop",
+   "commit": "2e2bd88150c71a440771fd369f40295dfd622324",
+   "default_branch": "develop",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 10,
+   "py_files": 175,
+   "redistributable": "yes",
+   "repo": "Bioprotocols/labop",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 21011,
+   "status": "cloned",
+   "url": "https://github.com/Bioprotocols/labop"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "nonlh"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/labop",
+ "title": "LabOP (Laboratory Open Protocol language, formerly PAML) - iGEM interlab growth-curve/calibration protocols",
+ "year": ""
+}
diff --git a/sources/experimental/labscriptai-protein-eng/record.json b/sources/experimental/labscriptai-protein-eng/record.json
new file mode 100644
index 0000000..fc57352
--- /dev/null
+++ b/sources/experimental/labscriptai-protein-eng/record.json
@@ -0,0 +1,73 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.15",
+    "2.20",
+    "2.21",
+    "2.22"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/labscriptai-protein-eng/KRATSZ__LabScript-AI",
+   "commit": "04115e4c2177d46cbf1c58397b642fb16e0c52b4",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 27,
+   "py_files": 78,
+   "redistributable": "no",
+   "repo": "KRATSZ/LabScript-AI",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 71367,
+   "status": "cloned",
+   "url": "https://github.com/KRATSZ/LabScript-AI"
+  }
+ ],
+ "doi_primary": "10.1101/2025.09.30.679666",
+ "dois": [
+  "10.1101/2025.09.30.679666"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 12,
+  "sections": 43,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 6717782,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "3a96bb5e120a79027ac15183cdc1a31dcc6f40c9e5b7b25d833276708dc088b6",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/10.1101/2025.09.30.679666v3.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/10.1101/2025.09.30.679666v3.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/labscriptai-protein-eng",
+ "title": "Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows",
+ "year": "2025"
+}
diff --git a/sources/experimental/lego-lhr-stem/record.json b/sources/experimental/lego-lhr-stem/record.json
new file mode 100644
index 0000000..1570d64
--- /dev/null
+++ b/sources/experimental/lego-lhr-stem/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [],
+ "doi_primary": "10.1371/journal.pbio.2001413",
+ "dois": [
+  "10.1371/journal.pbio.2001413"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 14,
+  "source": "europepmc:PMC5360201"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1898850,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "0da6ee426fd5c556a8486aa9717f23309287b9ae47994a1d7a238d464d8e1655",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC5360201?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5360201.1/PMC5360201.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5360201.1/PMC5360201.1.pdf"
+ },
+ "pmcid": "PMC5360201",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/lego-lhr-stem",
+ "title": "Liquid-handling Lego robots and experiments for STEM education and research",
+ "year": "2017"
+}
diff --git a/sources/experimental/llm-rdf-synthesis/record.json b/sources/experimental/llm-rdf-synthesis/record.json
new file mode 100644
index 0000000..2e48da4
--- /dev/null
+++ b/sources/experimental/llm-rdf-synthesis/record.json
@@ -0,0 +1,76 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.14"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/llm-rdf-synthesis/Ruan-Yixiang__LLM-RDF",
+   "commit": "c87b92a3ea9efb6bb46bf9ee6205d5474af7293a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 23,
+   "redistributable": "no",
+   "repo": "Ruan-Yixiang/LLM-RDF",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 203138,
+   "status": "cloned",
+   "url": "https://github.com/Ruan-Yixiang/LLM-RDF"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-024-54457-x",
+ "dois": [
+  "10.1038/s41467-024-54457-x"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 21,
+  "source": "europepmc:PMC11585555"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 1969329,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "978a89d42009585cfbe5736dd70ae2159ad1741443f1d38c9a7e4f282d6a5d28",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11585555?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11585555.1/PMC11585555.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11585555.1/PMC11585555.1.pdf"
+ },
+ "pmcid": "PMC11585555",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/llm-rdf-synthesis",
+ "title": "An automatic end-to-end chemical synthesis development platform powered by large language models",
+ "year": "2024"
+}
diff --git a/sources/experimental/locost-covid-nanopore-ot2/record.json b/sources/experimental/locost-covid-nanopore-ot2/record.json
new file mode 100644
index 0000000..99dbc29
--- /dev/null
+++ b/sources/experimental/locost-covid-nanopore-ot2/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.10"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/locost-covid-nanopore-ot2/JDMirza__Opentrons_LoCost_Covid19",
+   "commit": "bc11e19be5fccab9d9abf328886a1177ba43b528",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 6,
+   "py_files": 6,
+   "redistributable": "no",
+   "repo": "JDMirza/Opentrons_LoCost_Covid19",
+   "robot_mentions": [],
+   "size_kb": 14330,
+   "status": "cloned",
+   "url": "https://github.com/JDMirza/Opentrons_LoCost_Covid19"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/locost-covid-nanopore-ot2",
+ "title": "Opentrons_LoCost_Covid19 (ARTIC LoCost nanopore library prep on OT-2)",
+ "year": ""
+}
diff --git a/sources/experimental/lucks-cellfree-biosensor/record.json b/sources/experimental/lucks-cellfree-biosensor/record.json
new file mode 100644
index 0000000..46a2784
--- /dev/null
+++ b/sources/experimental/lucks-cellfree-biosensor/record.json
@@ -0,0 +1,67 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/lucks-cellfree-biosensor/LucksLab__Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024",
+   "commit": "939b0ac1fdc7fd8f023898eb527679f4d889f7ea",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024",
+   "robot_mentions": [],
+   "size_kb": 9828,
+   "status": "cloned",
+   "url": "https://github.com/LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024"
+  }
+ ],
+ "doi_primary": "10.1101/2024.10.13.618078",
+ "dois": [
+  "10.1101/2024.10.13.618078"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 2,
+  "sections": 14,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1501135,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "695d9b1cad7b8e1067aeec8354a6ef4d37d4b983fee81438358d2302cfa54758",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/lucks-cellfree-biosensor",
+ "title": "Semi-automated production of cell-free biosensors",
+ "year": "2024"
+}
diff --git a/sources/experimental/lysostaphin-turbidity/record.json b/sources/experimental/lysostaphin-turbidity/record.json
new file mode 100644
index 0000000..9ff267b
--- /dev/null
+++ b/sources/experimental/lysostaphin-turbidity/record.json
@@ -0,0 +1,76 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.8"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/lysostaphin-turbidity/JuBiotech__Supplement-to-Prigolovkin-et-al.-2025",
+   "commit": "e2d1d810b85525ec9ba481ae537a80a598376992",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "AGPL-3.0",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "JuBiotech/Supplement-to-Prigolovkin-et-al.-2025",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 1097,
+   "status": "cloned",
+   "url": "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025"
+  }
+ ],
+ "doi_primary": "10.1186/s12934-025-02911-w",
+ "dois": [
+  "10.1186/s12934-025-02911-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 13,
+  "source": "europepmc:PMC12836826"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2623092,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "2127ce5b2c818d66974af5c3919af2453f3790df717bb18790da7fdab9194259",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12836826?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12836826.1/PMC12836826.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12836826.1/PMC12836826.1.pdf"
+ },
+ "pmcid": "PMC12836826",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/lysostaphin-turbidity",
+ "title": "Turbid but accurate: automating lysostaphin quantification including uncertainty quantification",
+ "year": "2026"
+}
diff --git a/sources/experimental/madsci-ad-sdl/record.json b/sources/experimental/madsci-ad-sdl/record.json
new file mode 100644
index 0000000..84ebf79
--- /dev/null
+++ b/sources/experimental/madsci-ad-sdl/record.json
@@ -0,0 +1,63 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/madsci-ad-sdl/AD-SDL__MADSci",
+   "commit": "b584e0f3e1c6d195ac42c1dd307f28830585c30f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "unclear",
+   "opentrons_py_files": 0,
+   "py_files": 431,
+   "redistributable": "no",
+   "repo": "AD-SDL/MADSci",
+   "robot_mentions": [],
+   "size_kb": 74769,
+   "status": "cloned",
+   "url": "https://github.com/AD-SDL/MADSci"
+  }
+ ],
+ "dois": [
+  "10.21105/joss.09416"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.21105/joss.09416:\n  europepmc: no Europe PMC full text for this DOI\nD",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 363393,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "553b1d4990f27b0cca977b26699621fda2ec5491176150f3c85d2b48de6aff4c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://joss.theoj.org/papers/10.21105/joss.09416.pdf"
+   }
+  ],
+  "url": "https://joss.theoj.org/papers/10.21105/joss.09416.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "scheduling",
+ "simulator": "not run",
+ "slug": "experimental/madsci-ad-sdl",
+ "title": "MADSci: A modular Python-based framework to enable autonomous science",
+ "year": ""
+}
diff --git a/sources/experimental/mantis-shrimpy/record.json b/sources/experimental/mantis-shrimpy/record.json
new file mode 100644
index 0000000..34ed54e
--- /dev/null
+++ b/sources/experimental/mantis-shrimpy/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/mantis-shrimpy/czbiohub-sf__shrimPy",
+   "commit": "e87d54c922681edbaf04185a32bd9b856a428560",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 142,
+   "redistributable": "yes",
+   "repo": "czbiohub-sf/shrimPy",
+   "robot_mentions": [],
+   "size_kb": 5253,
+   "status": "cloned",
+   "url": "https://github.com/czbiohub-sf/shrimPy"
+  }
+ ],
+ "doi_primary": "10.1093/pnasnexus/pgae323",
+ "dois": [
+  "10.1093/pnasnexus/pgae323"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 29,
+  "source": "europepmc:PMC11393572"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 30053013,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "b84026e4b38348b7de9288481d7fb9a3493fbf49429db570a57fc2684f854517",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11393572?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11393572.1/PMC11393572.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11393572.1/PMC11393572.1.pdf"
+ },
+ "pmcid": "PMC11393572",
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/mantis-shrimpy",
+ "title": "Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells",
+ "year": "2024"
+}
diff --git a/sources/experimental/maple-fly-robot/record.json b/sources/experimental/maple-fly-robot/record.json
new file mode 100644
index 0000000..8055da1
--- /dev/null
+++ b/sources/experimental/maple-fly-robot/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/maple-fly-robot/FlySorterLLC__MAPLEControlSoftware",
+   "commit": "591eddcab80b10104d0cb67857e144edbeee6f96",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "GPL-2.0",
+   "opentrons_py_files": 0,
+   "py_files": 28,
+   "redistributable": "no",
+   "repo": "FlySorterLLC/MAPLEControlSoftware",
+   "robot_mentions": [],
+   "size_kb": 72619,
+   "status": "cloned",
+   "url": "https://github.com/FlySorterLLC/MAPLEControlSoftware"
+  }
+ ],
+ "doi_primary": "10.7554/eLife.37166",
+ "dois": [
+  "10.7554/eLife.37166"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 27,
+  "sections": 51,
+  "source": "europepmc:PMC6193762"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5307307,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "36fe791383ddd8cf75172d7c332045dc4d00fc478b11da7be15f9aa56993dc01",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC6193762?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6193762.1/PMC6193762.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6193762.1/PMC6193762.1.pdf"
+ },
+ "pmcid": "PMC6193762",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/maple-fly-robot",
+ "title": "MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping",
+ "year": "2018"
+}
diff --git a/sources/experimental/marchantia-agro-transformation/record.json b/sources/experimental/marchantia-agro-transformation/record.json
new file mode 100644
index 0000000..de299b6
--- /dev/null
+++ b/sources/experimental/marchantia-agro-transformation/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [],
+ "doi_primary": "10.1111/tpj.70118",
+ "dois": [
+  "10.1111/tpj.70118"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 23,
+  "source": "europepmc:PMC11993085"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 29503591,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "ec5b3827533dbdacf9972b3ccc6c229348fb67008ca491d210a4fceec8145027",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11993085?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11993085.1/PMC11993085.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11993085.1/PMC11993085.1.pdf"
+ },
+ "pmcid": "PMC11993085",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/marchantia-agro-transformation",
+ "title": "Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation",
+ "year": "2025"
+}
diff --git a/sources/experimental/massspecpreppy/record.json b/sources/experimental/massspecpreppy/record.json
new file mode 100644
index 0000000..cd72eaf
--- /dev/null
+++ b/sources/experimental/massspecpreppy/record.json
@@ -0,0 +1,67 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.12",
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/massspecpreppy/stemicha__MassSpecPreppy",
+   "commit": "1d3e1c558c6f033c279b58b54e3cb02c7f5dafeb",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 10,
+   "py_files": 10,
+   "redistributable": "no",
+   "repo": "stemicha/MassSpecPreppy",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 23272,
+   "status": "cloned",
+   "url": "https://github.com/stemicha/MassSpecPreppy"
+  }
+ ],
+ "doi_primary": "10.1002/pmic.202300294",
+ "dois": [
+  "10.1002/pmic.202300294"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1002/pmic.202300294:\n  europepmc: no Europe PMC full text for this DO",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.202300294"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/massspecpreppy",
+ "title": "MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics",
+ "year": "2024"
+}
diff --git a/sources/experimental/memplex-printing/record.json b/sources/experimental/memplex-printing/record.json
new file mode 100644
index 0000000..e19412b
--- /dev/null
+++ b/sources/experimental/memplex-printing/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/memplex-printing/ccmeyer__printing-platform",
+   "commit": "35a071270529ffc125ab873d954c27f2925add49",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 15,
+   "redistributable": "yes",
+   "repo": "ccmeyer/printing-platform",
+   "robot_mentions": [],
+   "size_kb": 17099,
+   "status": "cloned",
+   "url": "https://github.com/ccmeyer/printing-platform"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-025-59471-1",
+ "dois": [
+  "10.1038/s41467-025-59471-1"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 37,
+  "source": "europepmc:PMC12065789"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 14965773,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "dec8cecbe399f66e694fcdd1032e90ce96300b039701864834ba7c62bfc692d1",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12065789?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12065789.1/PMC12065789.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12065789.1/PMC12065789.1.pdf"
+ },
+ "pmcid": "PMC12065789",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/memplex-printing",
+ "title": "Designer artificial environments for membrane protein synthesis",
+ "year": "2025"
+}
diff --git a/sources/experimental/metclo-ot2/record.json b/sources/experimental/metclo-ot2/record.json
new file mode 100644
index 0000000..b2f8946
--- /dev/null
+++ b/sources/experimental/metclo-ot2/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.3"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/metclo-ot2/Edinburgh-Genome-Foundry__OT2Metclo",
+   "commit": "e4ac05c535bf8129f29883b9f5b399445165d231",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "Edinburgh-Genome-Foundry/OT2Metclo",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 1205,
+   "status": "cloned",
+   "url": "https://github.com/Edinburgh-Genome-Foundry/OT2Metclo"
+  }
+ ],
+ "doi_primary": "10.1007/978-1-0716-0908-8_9",
+ "dois": [
+  "10.1007/978-1-0716-0908-8_9"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1007/978-1-0716-0908-8_9:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/metclo-ot2",
+ "title": "MetCloOT2: Automated MetClo assembly on Opentrons OT-2 (MSc project, based on Lin & O Callaghan 2018/2020)",
+ "year": "2020"
+}
diff --git a/sources/experimental/miniaturized-16s-mosquito/record.json b/sources/experimental/miniaturized-16s-mosquito/record.json
new file mode 100644
index 0000000..30591bb
--- /dev/null
+++ b/sources/experimental/miniaturized-16s-mosquito/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "host": "www.protocols.io",
+   "status": "not code: protocol text",
+   "url": "https://www.protocols.io/view/high-throughput-miniaturized-16s-rrna-amplicon-lib-u2ieyce"
+  }
+ ],
+ "doi_primary": "10.1128/mSystems.00166-18",
+ "dois": [
+  "10.1128/mSystems.00166-18"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 13,
+  "source": "europepmc:PMC6222042"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1122280,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "5fd36089adb9485ef1ea63f175982884154109ea3dd122375a19ee1f0c8d9b02",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC6222042?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6222042.1/PMC6222042.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6222042.1/PMC6222042.1.pdf"
+ },
+ "pmcid": "PMC6222042",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/miniaturized-16s-mosquito",
+ "title": "High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity",
+ "year": "2018"
+}
diff --git a/sources/experimental/mngs-384-miniaturized/record.json b/sources/experimental/mngs-384-miniaturized/record.json
new file mode 100644
index 0000000..286b48a
--- /dev/null
+++ b/sources/experimental/mngs-384-miniaturized/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [],
+ "doi_primary": "10.1371/journal.pone.0206194",
+ "dois": [
+  "10.1371/journal.pone.0206194"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 10,
+  "source": "europepmc:PMC6328170"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1932304,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "06d55cd751c5448138eda5f8ae33973360ef3c1f3f275ba1dfd70d7d01803d74",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC6328170?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6328170.1/PMC6328170.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC6328170.1/PMC6328170.1.pdf"
+ },
+ "pmcid": "PMC6328170",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/mngs-384-miniaturized",
+ "title": "Miniaturization and optimization of 384-well compatible RNA sequencing library preparation",
+ "year": "2019"
+}
diff --git a/sources/experimental/mobile-robot-burger-2020/record.json b/sources/experimental/mobile-robot-burger-2020/record.json
new file mode 100644
index 0000000..0b0b8e3
--- /dev/null
+++ b/sources/experimental/mobile-robot-burger-2020/record.json
@@ -0,0 +1,51 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "none public (ROS code not released)"
+  }
+ ],
+ "doi_primary": "10.1038/s41586-020-2442-2",
+ "dois": [
+  "10.1038/s41586-020-2442-2"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41586-020-2442-2:\n  europepmc: no Europe PMC full text for this",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 1985168,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "4aeb478c4fac0c1a97d91487cd79f848e0b2f14d7b85184b14c24cf96b4ff50e",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://strathprints.strath.ac.uk/74759/1/Burger_etal_Nature_2020_A_mobile_robotic.pdf"
+   }
+  ],
+  "url": "https://strathprints.strath.ac.uk/74759/1/Burger_etal_Nature_2020_A_mobile_robotic.pdf"
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/mobile-robot-burger-2020",
+ "title": "A mobile robotic chemist (Burger et al.)",
+ "year": "2020"
+}
diff --git a/sources/experimental/mobile-robots-dai-2024/record.json b/sources/experimental/mobile-robots-dai-2024/record.json
new file mode 100644
index 0000000..f011b3f
--- /dev/null
+++ b/sources/experimental/mobile-robots-dai-2024/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/mobile-robots-dai-2024/zenodo-11174257",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 8,
+   "redistributable": "no",
+   "repo": "zenodo:11174257",
+   "robot_mentions": [],
+   "size_kb": 20,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.11174257"
+  }
+ ],
+ "doi_primary": "10.1038/s41586-024-08173-7",
+ "dois": [
+  "10.1038/s41586-024-08173-7"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 9,
+  "sections": 32,
+  "source": "europepmc:PMC11602721"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 9385240,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "02fff0f58b1d3d0b7644b969557e8c58ccf58e86caf8c575930390b83820bfcc",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11602721?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11602721.1/PMC11602721.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11602721.1/PMC11602721.1.pdf"
+ },
+ "pmcid": "PMC11602721",
+ "readiness": "partial",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/mobile-robots-dai-2024",
+ "title": "Autonomous mobile robots for exploratory synthetic chemistry",
+ "year": "2024"
+}
diff --git a/sources/experimental/msd-biochem-assays-ot2/record.json b/sources/experimental/msd-biochem-assays-ot2/record.json
new file mode 100644
index 0000000..2337add
--- /dev/null
+++ b/sources/experimental/msd-biochem-assays-ot2/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.12"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/msd-biochem-assays-ot2/MSDLLCpapers__Opentrons-OT2-BioChemical-Assays",
+   "commit": "049682a0fa28be281d8c069dc08e80e2b243a246",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "yes",
+   "repo": "MSDLLCpapers/Opentrons-OT2-BioChemical-Assays",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 21,
+   "status": "cloned",
+   "url": "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2024.100205",
+ "dois": [
+  "10.1016/j.slast.2024.100205"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slast.2024.100205:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "verified",
+ "slug": "experimental/msd-biochem-assays-ot2",
+ "title": "Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler",
+ "year": "2024"
+}
diff --git a/sources/experimental/mxene-aerogel-al/record.json b/sources/experimental/mxene-aerogel-al/record.json
new file mode 100644
index 0000000..55e3631
--- /dev/null
+++ b/sources/experimental/mxene-aerogel-al/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/mxene-aerogel-al/oshin71__Programmable-MXene-Aerogel",
+   "commit": "7a863476a0911dabd3401428601b3d048b68ee2e",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 8,
+   "redistributable": "yes",
+   "repo": "oshin71/Programmable-MXene-Aerogel",
+   "robot_mentions": [],
+   "size_kb": 496,
+   "status": "cloned",
+   "url": "https://github.com/oshin71/Programmable-MXene-Aerogel"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-024-49011-8",
+ "dois": [
+  "10.1038/s41467-024-49011-8"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 27,
+  "source": "europepmc:PMC11144242"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3908686,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "d729ab71eb2d6e7dcead2d2f7b0fdbab657dbb6fb5f332613fd0b4dce71ac5ca",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11144242?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11144242.1/PMC11144242.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11144242.1/PMC11144242.1.pdf"
+ },
+ "pmcid": "PMC11144242",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/mxene-aerogel-al",
+ "title": "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties",
+ "year": "2024"
+}
diff --git a/sources/experimental/myra-cfe-platform/record.json b/sources/experimental/myra-cfe-platform/record.json
new file mode 100644
index 0000000..338908d
--- /dev/null
+++ b/sources/experimental/myra-cfe-platform/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/myra-cfe-platform/Mo42-mb__Myra_automation",
+   "commit": "48fd760d983610169a3794ec5e1da05709129ca0",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 3,
+   "redistributable": "no",
+   "repo": "Mo42-mb/Myra_automation",
+   "robot_mentions": [],
+   "size_kb": 33,
+   "status": "cloned",
+   "url": "https://github.com/Mo42-mb/Myra_automation"
+  }
+ ],
+ "doi_primary": "10.1093/synbio/ysag010",
+ "dois": [
+  "10.1093/synbio/ysag010"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 21,
+  "source": "europepmc:PMC13561876"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1435611,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "66329e4f03e856996fbde1c00881a870e84a3c8adf90fdcef2c31eb31b0c2fe5",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13561876?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13561876.1/PMC13561876.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13561876.1/PMC13561876.1.pdf"
+ },
+ "pmcid": "PMC13561876",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/myra-cfe-platform",
+ "title": "A liquid handling platform for standardized quantification of cell-free enzymatic activity",
+ "year": "2026"
+}
diff --git a/sources/experimental/myrplate-flex-casting/record.json b/sources/experimental/myrplate-flex-casting/record.json
new file mode 100644
index 0000000..b3029ce
--- /dev/null
+++ b/sources/experimental/myrplate-flex-casting/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.18"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/myrplate-flex-casting/Hosseinat11502__MyrplateTissueCasting-8channel1mltip-Version-15",
+   "commit": "224bad083b0b0092d1795f6ba6d3fed401d667a7",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 3,
+   "py_files": 3,
+   "redistributable": "yes",
+   "repo": "Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 54815,
+   "status": "cloned",
+   "url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/myrplate-flex-casting",
+ "title": "myrPlate engineered connective tissue casting on Opentrons Flex",
+ "year": ""
+}
diff --git a/sources/experimental/navigate-2024/record.json b/sources/experimental/navigate-2024/record.json
new file mode 100644
index 0000000..38b60ef
--- /dev/null
+++ b/sources/experimental/navigate-2024/record.json
@@ -0,0 +1,90 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/navigate-2024/TheDeanLab__navigate",
+   "commit": "da14920d7b40d048a5d2225a7846d11f78e05212",
+   "default_branch": "develop",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 498,
+   "redistributable": "yes",
+   "repo": "TheDeanLab/navigate",
+   "robot_mentions": [],
+   "size_kb": 444685,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/TheDeanLab/navigate"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-024-02413-4",
+ "dois": [
+  "10.1038/s41592-024-02413-4"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41592-024-02413-4:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11540721?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11540721.1/PMC11540721.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11540721.2/PMC11540721.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11540721.3/PMC11540721.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC11540721&blobtype=pdf"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://www.nature.com/articles/s41592-024-02413-4.pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC11540721",
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/navigate-2024",
+ "title": "Navigate: an open-source platform for smart light-sheet microscopy",
+ "year": "2024"
+}
diff --git a/sources/experimental/newcastle-neg-opentrons/record.json b/sources/experimental/newcastle-neg-opentrons/record.json
new file mode 100644
index 0000000..03559af
--- /dev/null
+++ b/sources/experimental/newcastle-neg-opentrons/record.json
@@ -0,0 +1,46 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.3",
+    "2.8"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/newcastle-neg-opentrons/NewcastleUni-NetworkEcologyGroup__Opentrons",
+   "commit": "f8d2d2950b1120f036242beca20b254a0dc89856",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 56,
+   "py_files": 57,
+   "redistributable": "no",
+   "repo": "NewcastleUni-NetworkEcologyGroup/Opentrons",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 2745,
+   "status": "cloned",
+   "url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/newcastle-neg-opentrons",
+ "title": "Newcastle Network Ecology Group OT-2 protocol and labware collection",
+ "year": ""
+}
diff --git a/sources/experimental/nfkb-luciferase-ot2/record.json b/sources/experimental/nfkb-luciferase-ot2/record.json
new file mode 100644
index 0000000..d9760e3
--- /dev/null
+++ b/sources/experimental/nfkb-luciferase-ot2/record.json
@@ -0,0 +1,35 @@
+{
+ "code": [],
+ "doi_primary": "10.1016/j.slast.2024.100155",
+ "dois": [
+  "10.1016/j.slast.2024.100155"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slast.2024.100155:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/nfkb-luciferase-ot2",
+ "title": "Luciferase reporter assay for NF-kB activation automated by an open-source liquid handling platform",
+ "year": "2024"
+}
diff --git a/sources/experimental/nioz-ot2-database/record.json b/sources/experimental/nioz-ot2-database/record.json
new file mode 100644
index 0000000..9fdb972
--- /dev/null
+++ b/sources/experimental/nioz-ot2-database/record.json
@@ -0,0 +1,51 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.11",
+    "2.12",
+    "2.13",
+    "2.18",
+    "2.20",
+    "2.27",
+    "2.9"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/nioz-ot2-database/MolLabNIOZ__OT2",
+   "commit": "80f3cb4eb9524a09abb8353945c932c3e111efb4",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 213,
+   "py_files": 222,
+   "redistributable": "no",
+   "repo": "MolLabNIOZ/OT2",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 120811,
+   "status": "cloned",
+   "url": "https://github.com/MolLabNIOZ/OT2"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/nioz-ot2-database",
+ "title": "MolLabNIOZ/OT2 protocol database (NIOZ molecular ecology)",
+ "year": ""
+}
diff --git a/sources/experimental/olh-turbidostat-plr/record.json b/sources/experimental/olh-turbidostat-plr/record.json
new file mode 100644
index 0000000..4dabc9f
--- /dev/null
+++ b/sources/experimental/olh-turbidostat-plr/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/olh-turbidostat-plr/chory-lab__plr-turbidostat",
+   "commit": "410e7f49005d6ad249ba880ad1195ad9462458da",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 39,
+   "redistributable": "no",
+   "repo": "chory-lab/plr-turbidostat",
+   "robot_mentions": [],
+   "size_kb": 205,
+   "status": "cloned",
+   "url": "https://github.com/chory-lab/plr-turbidostat"
+  }
+ ],
+ "doi_primary": "10.64898/2026.03.02.709168",
+ "dois": [
+  "10.64898/2026.03.02.709168"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 15,
+  "sections": 18,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 15248126,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "f11970571c8f3622818554eb2df35184d6e35dbb2ccae674fa2ba608734b721b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "pylabrobot",
+ "simulator": "not run",
+ "slug": "experimental/olh-turbidostat-plr",
+ "title": "A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments",
+ "year": "2026"
+}
diff --git a/sources/experimental/openblend-media/record.json b/sources/experimental/openblend-media/record.json
new file mode 100644
index 0000000..27a1fca
--- /dev/null
+++ b/sources/experimental/openblend-media/record.json
@@ -0,0 +1,74 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.2"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/openblend-media/abiedermann__openblend_public",
+   "commit": "a6dfa2deea30f9c234e1b0c35989dd5876bdf166",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 5,
+   "py_files": 6,
+   "redistributable": "yes",
+   "repo": "abiedermann/openblend_public",
+   "robot_mentions": [],
+   "size_kb": 29,
+   "status": "cloned",
+   "url": "https://github.com/abiedermann/openblend_public"
+  }
+ ],
+ "doi_primary": "10.1002/bit.27947",
+ "dois": [
+  "10.1002/bit.27947"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 12,
+  "source": "europepmc:PMC9298315"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3206595,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "6a158ff0b93633236c4cafca3721fef10239bc26c735dfa44cda1608ca2b0916",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9298315?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9298315.1/PMC9298315.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9298315.1/PMC9298315.1.pdf"
+ },
+ "pmcid": "PMC9298315",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/openblend-media",
+ "title": "Modular development enables rapid design of media for alternative hosts",
+ "year": "2022"
+}
diff --git a/sources/experimental/openflexure-autofocus/record.json b/sources/experimental/openflexure-autofocus/record.json
new file mode 100644
index 0000000..495a77b
--- /dev/null
+++ b/sources/experimental/openflexure-autofocus/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/openflexure-autofocus/openflexure__openflexure-microscope-server",
+   "commit": "4b2f7eb0ba3068f1beb781e3454b63e5535eacbd",
+   "host": "gitlab.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 95,
+   "redistributable": "no",
+   "repo": "openflexure/openflexure-microscope-server",
+   "robot_mentions": [],
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://gitlab.com/openflexure/openflexure-microscope-server"
+  }
+ ],
+ "doi_primary": "10.1111/jmi.13064",
+ "dois": [
+  "10.1111/jmi.13064"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1111/jmi.13064:\n  europepmc: no Europe PMC full text for this DOI\nDow",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.13064"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/openflexure-autofocus",
+ "title": "Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope",
+ "year": "2022"
+}
diff --git a/sources/experimental/openframe-openaf/record.json b/sources/experimental/openframe-openaf/record.json
new file mode 100644
index 0000000..cfeb792
--- /dev/null
+++ b/sources/experimental/openframe-openaf/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/openframe-openaf/ImperialCollegeLondon__openAF",
+   "commit": "cdf1a6102835e58463d7fa4439fc7dfa25f81eb7",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-2-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 2,
+   "redistributable": "yes",
+   "repo": "ImperialCollegeLondon/openAF",
+   "robot_mentions": [],
+   "size_kb": 605,
+   "status": "cloned",
+   "url": "https://github.com/ImperialCollegeLondon/openAF"
+  }
+ ],
+ "doi_primary": "10.1111/jmi.13219",
+ "dois": [
+  "10.1111/jmi.13219"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 12,
+  "source": "europepmc:PMC10953376"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2722749,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "5a957df7b9ea84a8df9a4754be4a44b75725c4d556e189811831213465ee36c6",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10953376?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10953376.1/PMC10953376.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10953376.1/PMC10953376.1.pdf"
+ },
+ "pmcid": "PMC10953376",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/openframe-openaf",
+ "title": "openFrame: modular open microscopy platform with single-shot optical autofocus",
+ "year": "2023"
+}
diff --git a/sources/experimental/opentrons-covid19-dev/record.json b/sources/experimental/opentrons-covid19-dev/record.json
new file mode 100644
index 0000000..22f098a
--- /dev/null
+++ b/sources/experimental/opentrons-covid19-dev/record.json
@@ -0,0 +1,43 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0",
+    "2.2"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/opentrons-covid19-dev/Opentrons__covid19",
+   "commit": "67a6a76bffdc2d000a9fe89161152c39f027e490",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 53,
+   "py_files": 53,
+   "redistributable": "yes",
+   "repo": "Opentrons/covid19",
+   "robot_mentions": [],
+   "size_kb": 33222,
+   "status": "cloned",
+   "url": "https://github.com/Opentrons/covid19"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/opentrons-covid19-dev",
+ "title": "Opentrons/covid19 (OT-2 COVID-19 RT-qPCR station development repo, Opentrons + Open Medicine Institute)",
+ "year": ""
+}
diff --git a/sources/experimental/opentrons-physicalai-hf/record.json b/sources/experimental/opentrons-physicalai-hf/record.json
new file mode 100644
index 0000000..f6c0dee
--- /dev/null
+++ b/sources/experimental/opentrons-physicalai-hf/record.json
@@ -0,0 +1,28 @@
+{
+ "code": [
+  {
+   "host": "huggingface.co",
+   "status": "not code: dataset",
+   "url": "https://huggingface.co/datasets/Opentrons/PhysicalAI"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/opentrons-physicalai-hf",
+ "title": "Opentrons/PhysicalAI (Hugging Face dataset of Flex teleoperation episodes)",
+ "year": ""
+}
diff --git a/sources/experimental/openworkstation/record.json b/sources/experimental/openworkstation/record.json
new file mode 100644
index 0000000..a4647b3
--- /dev/null
+++ b/sources/experimental/openworkstation/record.json
@@ -0,0 +1,74 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/openworkstation/SebastianEggert__OpenWorkstation",
+   "commit": "703d6fea22b22df26b132af3de64b6c87f0c79f3",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "CC-BY-SA-4.0",
+   "opentrons_py_files": 26,
+   "py_files": 55,
+   "redistributable": "no",
+   "repo": "SebastianEggert/OpenWorkstation",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 163426,
+   "status": "cloned",
+   "url": "https://github.com/SebastianEggert/OpenWorkstation"
+  }
+ ],
+ "doi_primary": "10.1016/j.ohx.2020.e00152",
+ "dois": [
+  "10.1016/j.ohx.2020.e00152"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 11,
+  "sections": 52,
+  "source": "europepmc:PMC9041211"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 4928490,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "afc98616bb912885e5255186f52005f310001b12863f72e1479ff08b1f51475c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9041211?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9041211.1/PMC9041211.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9041211.1/PMC9041211.1.pdf"
+ },
+ "pmcid": "PMC9041211",
+ "readiness": "ready",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/openworkstation",
+ "title": "OpenWorkstation: A modular open-source technology for automated in vitro workflows",
+ "year": "2020"
+}
diff --git a/sources/experimental/organa/record.json b/sources/experimental/organa/record.json
new file mode 100644
index 0000000..947180c
--- /dev/null
+++ b/sources/experimental/organa/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/organa/ac-rad__organa",
+   "commit": "c36e80caf90af38dd18e71aa585489813a745612",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 13,
+   "redistributable": "no",
+   "repo": "ac-rad/organa",
+   "robot_mentions": [],
+   "size_kb": 6579,
+   "status": "cloned",
+   "url": "https://github.com/ac-rad/organa"
+  }
+ ],
+ "dois": [
+  "10.1016/j.matt.2024.10.015"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.matt.2024.10.015:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/organa",
+ "title": "ORGANA: a robotic assistant for automated chemistry experimentation and characterization",
+ "year": ""
+}
diff --git a/sources/experimental/ot2-cherrypick/record.json b/sources/experimental/ot2-cherrypick/record.json
new file mode 100644
index 0000000..687ee8e
--- /dev/null
+++ b/sources/experimental/ot2-cherrypick/record.json
@@ -0,0 +1,57 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.15",
+    "2.24"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ot2-cherrypick/HiteSit__OT2_CherryPick",
+   "commit": "5c3bda5b67c1ae17aa4987a44f107b4e2131fb7f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 7,
+   "py_files": 127,
+   "redistributable": "no",
+   "repo": "HiteSit/OT2_CherryPick",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 5040,
+   "status": "cloned",
+   "url": "https://github.com/HiteSit/OT2_CherryPick"
+  }
+ ],
+ "dois": [
+  "10.26434/chemrxiv.15000637"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.26434/chemrxiv.15000637:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ot2-cherrypick",
+ "title": "OT2-CherryPick: A Zero-Install Web Platform for Orchestrating Complex Liquid Handling on the Opentrons OT-2",
+ "year": ""
+}
diff --git a/sources/experimental/ot2-moclo-jove/record.json b/sources/experimental/ot2-moclo-jove/record.json
new file mode 100644
index 0000000..e93ebb2
--- /dev/null
+++ b/sources/experimental/ot2-moclo-jove/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ot2-moclo-jove/emernic__OT2_MoClo_JoVE",
+   "commit": "d3a28d409ea48e0f66b1f5cf96b4ebcf838b9513",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 3,
+   "py_files": 11,
+   "redistributable": "yes",
+   "repo": "emernic/OT2_MoClo_JoVE",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 33701,
+   "status": "cloned",
+   "url": "https://github.com/emernic/OT2_MoClo_JoVE"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ot2-moclo-jove",
+ "title": "Modular Cloning with the OT2 (OT2_MoClo_JoVE)",
+ "year": ""
+}
diff --git a/sources/experimental/ot2-proteomics-thesis/record.json b/sources/experimental/ot2-proteomics-thesis/record.json
new file mode 100644
index 0000000..19b9b0d
--- /dev/null
+++ b/sources/experimental/ot2-proteomics-thesis/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.24"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ot2-proteomics-thesis/martineingolfsrud__Opentrons-OT-2-performance-assessment",
+   "commit": "b711145a925b3c8d58e5ac0e0739b2d720a53f71",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 12,
+   "py_files": 12,
+   "redistributable": "no",
+   "repo": "martineingolfsrud/Opentrons-OT-2-performance-assessment",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 992,
+   "status": "cloned",
+   "url": "https://github.com/martineingolfsrud/Opentrons-OT-2-performance-assessment"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ot2-proteomics-thesis",
+ "title": "Automated Versus Manual Proteomics Sample Preparation: A Comparative Evaluation of Liquid Handling Workflows (MSc thesis)",
+ "year": ""
+}
diff --git a/sources/experimental/ot2-yeast-spot-assay/record.json b/sources/experimental/ot2-yeast-spot-assay/record.json
new file mode 100644
index 0000000..b328e51
--- /dev/null
+++ b/sources/experimental/ot2-yeast-spot-assay/record.json
@@ -0,0 +1,56 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.0"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ot2-yeast-spot-assay/bioinfo-tsukuba__ot2_spot_assay",
+   "commit": "a93c8c2fdcf130924626008470ef1953bee4f170",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 3,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "bioinfo-tsukuba/ot2_spot_assay",
+   "robot_mentions": [],
+   "size_kb": 899,
+   "status": "cloned",
+   "url": "https://github.com/bioinfo-tsukuba/ot2_spot_assay"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2022.12.001",
+ "dois": [
+  "10.1016/j.slast.2022.12.001"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slast.2022.12.001:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ot2-yeast-spot-assay",
+ "title": "Automation of yeast spot assays using an affordable liquid handling robot",
+ "year": "2023"
+}
diff --git a/sources/experimental/ot2eye/record.json b/sources/experimental/ot2eye/record.json
new file mode 100644
index 0000000..94b0c7a
--- /dev/null
+++ b/sources/experimental/ot2eye/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ot2eye/bioinfo-tsukuba__ot2eye",
+   "commit": "c672fcdf72059cbf2388bb5bba3562667e5cea6a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "yes",
+   "repo": "bioinfo-tsukuba/ot2eye",
+   "robot_mentions": [],
+   "size_kb": 484740,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/bioinfo-tsukuba/ot2eye"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2026.100410",
+ "dois": [
+  "10.1016/j.slast.2026.100410"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slast.2026.100410:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/ot2eye",
+ "title": "OT2Eye: Detection of labware conditions to monitor and extend affordable liquid-handling robots",
+ "year": "2026"
+}
diff --git a/sources/experimental/pac832-galr1-ot2/record.json b/sources/experimental/pac832-galr1-ot2/record.json
new file mode 100644
index 0000000..af13ac3
--- /dev/null
+++ b/sources/experimental/pac832-galr1-ot2/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.19",
+    "2.20"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pac832-galr1-ot2/douglasyao__pac-832-supplementary-data",
+   "commit": "59a80d8505302f9780d143e596086b7f7d620947",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 31,
+   "py_files": 31,
+   "redistributable": "no",
+   "repo": "douglasyao/pac-832-supplementary-data",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 145,
+   "status": "cloned",
+   "url": "https://github.com/douglasyao/pac-832-supplementary-data"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/pac832-galr1-ot2",
+ "title": "PAC-832: A selective small-molecule antagonist of galanin receptor 1 (GalR1) - supplementary data and OT-2 protocols",
+ "year": ""
+}
diff --git a/sources/experimental/panda-bear/record.json b/sources/experimental/panda-bear/record.json
new file mode 100644
index 0000000..92929e4
--- /dev/null
+++ b/sources/experimental/panda-bear/record.json
@@ -0,0 +1,60 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/panda-bear/BU-KABlab__PANDA-BEAR",
+   "commit": "11e70281fbb8617aeb798575a66c91d42f91cc82",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-2.0",
+   "opentrons_py_files": 1,
+   "py_files": 266,
+   "redistributable": "no",
+   "repo": "BU-KABlab/PANDA-BEAR",
+   "robot_mentions": [],
+   "size_kb": 2215320,
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://github.com/BU-KABlab/PANDA-BEAR"
+  }
+ ],
+ "doi_primary": "10.1039/d4mh00797b",
+ "dois": [
+  "10.1039/d4mh00797b"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d4mh00797b:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://pubs.rsc.org/en/content/articlepdf/2024/MH/D4MH00797B"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/panda-bear",
+ "title": "PANDA: a self-driving lab for studying electrodeposited polymer films",
+ "year": "2024"
+}
diff --git a/sources/experimental/parseq-pyhamilton/record.json b/sources/experimental/parseq-pyhamilton/record.json
new file mode 100644
index 0000000..e4a5066
--- /dev/null
+++ b/sources/experimental/parseq-pyhamilton/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/parseq-pyhamilton/finyl__parseq-pyhamilton",
+   "commit": "202a0eb95666ab9596b7ce8995009a25c9b20f38",
+   "default_branch": "dev",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 18,
+   "redistributable": "no",
+   "repo": "finyl/parseq-pyhamilton",
+   "robot_mentions": [],
+   "size_kb": 3510,
+   "status": "cloned",
+   "url": "https://github.com/finyl/parseq-pyhamilton"
+  }
+ ],
+ "doi_primary": "10.1101/2023.12.12.571337",
+ "dois": [
+  "10.1101/2023.12.12.571337"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 12,
+  "sections": 33,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 8832026,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "4856aa96b19e438653f2418b36491928a89755dce2c588eec8821f07d9581ceb",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/biorxiv/early/2023/12/12/2023.12.12.571337.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/biorxiv/early/2023/12/12/2023.12.12.571337.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "hamilton",
+ "simulator": "not run",
+ "slug": "experimental/parseq-pyhamilton",
+ "title": "parSEQ:  Probe and Rescue Sequencing for Advanced Variant Retrieval from DNA Pool",
+ "year": "2023"
+}
diff --git a/sources/experimental/pasta-spatial/record.json b/sources/experimental/pasta-spatial/record.json
new file mode 100644
index 0000000..baefd7f
--- /dev/null
+++ b/sources/experimental/pasta-spatial/record.json
@@ -0,0 +1,95 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.7"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pasta-spatial/SizunJiangLab__PASTA",
+   "commit": "c19210f08dea21fb259e2a1063162f0c4e50edba",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "SizunJiangLab/PASTA",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 2949,
+   "status": "cloned",
+   "url": "https://github.com/SizunJiangLab/PASTA"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-026-03200-z",
+ "dois": [
+  "10.1038/s41592-026-03200-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41592-026-03200-z:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13539481?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13539481.1/PMC13539481.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13539481.2/PMC13539481.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13539481.3/PMC13539481.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC13539481&blobtype=pdf"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://www.nature.com/articles/s41592-026-03200-z.pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC13539481",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/pasta-spatial",
+ "title": "PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology",
+ "year": "2026"
+}
diff --git a/sources/experimental/peg-solubility-assay/record.json b/sources/experimental/peg-solubility-assay/record.json
new file mode 100644
index 0000000..c06fd4c
--- /dev/null
+++ b/sources/experimental/peg-solubility-assay/record.json
@@ -0,0 +1,64 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.5"
+   ],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/peg-solubility-assay/ch__sormanni",
+   "commit": "dd8018d2dac08baa56aaf4f3b025936d6fcf75f6",
+   "host": "gitlab.developers.cam.ac.uk",
+   "licence": "none",
+   "opentrons_py_files": 3,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "ch/sormanni/peg-solubility-assay",
+   "robot_mentions": [],
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://gitlab.developers.cam.ac.uk/ch/sormanni/peg-solubility-assay"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-021-01126-4",
+ "dois": [
+  "10.1038/s41598-021-01126-4"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 30,
+  "source": "europepmc:PMC8578320"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2472812,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "0fcf78faecf7a9ead907ce384a45a2d47b8e909e181ed6a03d453b35a5972e99",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41598-021-01126-4.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41598-021-01126-4.pdf"
+ },
+ "pmcid": "PMC8578320",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/peg-solubility-assay",
+ "title": "An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement",
+ "year": "2021"
+}
diff --git a/sources/experimental/phage-cocktails-robotics/record.json b/sources/experimental/phage-cocktails-robotics/record.json
new file mode 100644
index 0000000..2a2ce89
--- /dev/null
+++ b/sources/experimental/phage-cocktails-robotics/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/phage-cocktails-robotics/zenodo-17594564",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-nc-nd-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "zenodo:17594564",
+   "robot_mentions": [],
+   "size_kb": 103037,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.17594564"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-026-68684-x",
+ "dois": [
+  "10.1038/s41467-026-68684-x"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 20,
+  "source": "europepmc:PMC12960834"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 9533173,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "21cdc9f2592439a59cf87f95bc78a10b77bcadbd9d92133534400e5e203f28e9",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12960834?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12960834.1/PMC12960834.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12960834.1/PMC12960834.1.pdf"
+ },
+ "pmcid": "PMC12960834",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/phage-cocktails-robotics",
+ "title": "High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails",
+ "year": "2026"
+}
diff --git a/sources/experimental/photobioreactor-fluorescence/record.json b/sources/experimental/photobioreactor-fluorescence/record.json
new file mode 100644
index 0000000..1456139
--- /dev/null
+++ b/sources/experimental/photobioreactor-fluorescence/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/photobioreactor-fluorescence/borjaggarcia__fluorescence-monitoring",
+   "commit": "a9381f46d59eab8629a9178c3c80ba33a18d6dfc",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 15,
+   "redistributable": "yes",
+   "repo": "borjaggarcia/fluorescence-monitoring",
+   "robot_mentions": [],
+   "size_kb": 65,
+   "status": "cloned",
+   "url": "https://github.com/borjaggarcia/fluorescence-monitoring"
+  }
+ ],
+ "doi_primary": "10.3390/bios15030128",
+ "dois": [
+  "10.3390/bios15030128"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 12,
+  "sections": 16,
+  "source": "europepmc:PMC11940672"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 5833679,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "6e8a2395b2ade0af50365aa7c00ffe0d7f21470a3da42a17401b26e568644803",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11940672?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11940672.1/PMC11940672.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11940672.1/PMC11940672.1.pdf"
+ },
+ "pmcid": "PMC11940672",
+ "readiness": "partial",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/photobioreactor-fluorescence",
+ "title": "Integration of Fluorescence Spectroscopy into a Photobioreactor for the Monitoring of Cyanobacteria",
+ "year": "2025"
+}
diff --git a/sources/experimental/pioreactor/record.json b/sources/experimental/pioreactor/record.json
new file mode 100644
index 0000000..9ad374c
--- /dev/null
+++ b/sources/experimental/pioreactor/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pioreactor/pioreactor__pioreactor",
+   "commit": "0ae14c035c8a7ae1e52f273872a46ed3fd036b1c",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 248,
+   "redistributable": "yes",
+   "repo": "pioreactor/pioreactor",
+   "robot_mentions": [],
+   "size_kb": 179854,
+   "status": "cloned",
+   "url": "https://github.com/pioreactor/pioreactor"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/pioreactor",
+ "title": "Pioreactor open-source bioreactor software (used in published studies)",
+ "year": ""
+}
diff --git a/sources/experimental/pipette-show/record.json b/sources/experimental/pipette-show/record.json
new file mode 100644
index 0000000..86581af
--- /dev/null
+++ b/sources/experimental/pipette-show/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pipette-show/Global-Biofoundries-Alliance__pipette-show",
+   "commit": "db8e2543a00dcaf6723102b4c72bd3463abc56eb",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "Global-Biofoundries-Alliance/pipette-show",
+   "robot_mentions": [],
+   "size_kb": 47466,
+   "status": "cloned",
+   "url": "https://github.com/Global-Biofoundries-Alliance/pipette-show"
+  }
+ ],
+ "doi_primary": "10.1021/acssynbio.1c00494",
+ "dois": [
+  "10.1021/acssynbio.1c00494"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 2,
+  "sections": 10,
+  "source": "europepmc:PMC8859850"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1681329,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "4a724061156e2d33502f05f24af7fce2778fac7f88efc08c53f851498e1261df",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8859850?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8859850.1/PMC8859850.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8859850.1/PMC8859850.1.pdf"
+ },
+ "pmcid": "PMC8859850",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/pipette-show",
+ "title": "Pipette Show: An Open Source Web Application to Support Pipetting into Microplates",
+ "year": "2022"
+}
diff --git a/sources/experimental/plant-phenotyping-ot2/record.json b/sources/experimental/plant-phenotyping-ot2/record.json
new file mode 100644
index 0000000..ae9be8a
--- /dev/null
+++ b/sources/experimental/plant-phenotyping-ot2/record.json
@@ -0,0 +1,63 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/plant-phenotyping-ot2/Synthetic-Automated-Systems__automated_phenotyping_system",
+   "commit": "1c01bbed3dcb5b677fcf8a4e3c3171c605365392",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 2,
+   "py_files": 5,
+   "redistributable": "yes",
+   "repo": "Synthetic-Automated-Systems/automated_phenotyping_system",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 266243,
+   "status": "cloned",
+   "url": "https://github.com/Synthetic-Automated-Systems/automated_phenotyping_system"
+  }
+ ],
+ "dois": [
+  "10.1002/aisy.202500624"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1002/aisy.202500624:\n  europepmc: no Europe PMC full text for this DO",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/aisy.202500624"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/plant-phenotyping-ot2",
+ "title": "Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience",
+ "year": ""
+}
diff --git a/sources/experimental/plastic-substitutes-al/record.json b/sources/experimental/plastic-substitutes-al/record.json
new file mode 100644
index 0000000..15d3431
--- /dev/null
+++ b/sources/experimental/plastic-substitutes-al/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/plastic-substitutes-al/chentl__MatAL",
+   "commit": "fc2b9f98032f22bdd4f938c14717d014f7b235f2",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "BSD-3-Clause-Clear",
+   "opentrons_py_files": 0,
+   "py_files": 10,
+   "redistributable": "no",
+   "repo": "chentl/MatAL",
+   "robot_mentions": [],
+   "size_kb": 312,
+   "status": "cloned",
+   "url": "https://github.com/chentl/MatAL"
+  }
+ ],
+ "doi_primary": "10.1038/s41565-024-01635-z",
+ "dois": [
+  "10.1038/s41565-024-01635-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 43,
+  "source": "europepmc:PMC11186784"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2530152,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "35048b7f9f91b18b6888fdb1ef8eac15bb284c7066b6ce99a8c42b609ffbe7f6",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41565-024-01635-z.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41565-024-01635-z.pdf"
+ },
+ "pmcid": "PMC11186784",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/plastic-substitutes-al",
+ "title": "Machine intelligence-accelerated discovery of all-natural plastic substitutes",
+ "year": "2024"
+}
diff --git a/sources/experimental/polar-sarscov2-ot2/record.json b/sources/experimental/polar-sarscov2-ot2/record.json
new file mode 100644
index 0000000..20e6905
--- /dev/null
+++ b/sources/experimental/polar-sarscov2-ot2/record.json
@@ -0,0 +1,56 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.5"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/polar-sarscov2-ot2/Zanecrc1__POLAR-SARS-CoV-2-Automation-for-OT-2",
+   "commit": "df0341841597a00a4ddf1006e940504e138cfb28",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "yes",
+   "repo": "Zanecrc1/POLAR-SARS-CoV-2-Automation-for-OT-2",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 1394,
+   "status": "cloned",
+   "url": "https://github.com/Zanecrc1/POLAR-SARS-CoV-2-Automation-for-OT-2"
+  }
+ ],
+ "dois": [
+  "10.17504/protocols.io.bearjad6"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.17504/protocols.io.bearjad6:\n  europepmc: no Europe PMC full text for",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/polar-sarscov2-ot2",
+ "title": "POLAR: Pathogen-Oriented Low-cost Assembly & Re-sequencing SARS-CoV-2 (OT-2 automation)",
+ "year": ""
+}
diff --git a/sources/experimental/polybot-pedot/record.json b/sources/experimental/polybot-pedot/record.json
new file mode 100644
index 0000000..f8f908c
--- /dev/null
+++ b/sources/experimental/polybot-pedot/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/polybot-pedot/polybot-nexus__PEDOT_PSS_supporting_data",
+   "commit": "4bbe0271925222e99d9c01ab7f4d63a013d51ad3",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "polybot-nexus/PEDOT_PSS_supporting_data",
+   "robot_mentions": [],
+   "size_kb": 1555,
+   "status": "cloned",
+   "url": "https://github.com/polybot-nexus/PEDOT_PSS_supporting_data"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-024-55655-3",
+ "dois": [
+  "10.1038/s41467-024-55655-3"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 17,
+  "source": "europepmc:PMC11833048"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3150116,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "d0db0ddeb0f9f180139c8c8a32d4fcb97d73c53a1be7f2656cc0a1568ce61617",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11833048?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11833048.1/PMC11833048.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11833048.1/PMC11833048.1.pdf"
+ },
+ "pmcid": "PMC11833048",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/polybot-pedot",
+ "title": "Autonomous platform for solution processing of electronic polymers (Polybot)",
+ "year": "2025"
+}
diff --git a/sources/experimental/polymer-protein-hybrids/record.json b/sources/experimental/polymer-protein-hybrids/record.json
new file mode 100644
index 0000000..91e57ac
--- /dev/null
+++ b/sources/experimental/polymer-protein-hybrids/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/polymer-protein-hybrids/webbtheosim__PPH_public",
+   "commit": "ade5d0cd2a716944c0a40c6eceb613ac83a4661f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "webbtheosim/PPH_public",
+   "robot_mentions": [],
+   "size_kb": 27,
+   "status": "cloned",
+   "url": "https://github.com/webbtheosim/PPH_public"
+  }
+ ],
+ "doi_primary": "10.1002/adma.202201809",
+ "dois": [
+  "10.1002/adma.202201809"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 33,
+  "source": "europepmc:PMC9339531"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 1964890,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "e99ae9da50022d0c52f7822fdd52ac181e849af85f1ab9af77869f37ba21c2b8",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9339531?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9339531.1/PMC9339531.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9339531.1/PMC9339531.1.pdf"
+ },
+ "pmcid": "PMC9339531",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/polymer-protein-hybrids",
+ "title": "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids",
+ "year": "2022"
+}
diff --git a/sources/experimental/polymerization-planner/record.json b/sources/experimental/polymerization-planner/record.json
new file mode 100644
index 0000000..c44444f
--- /dev/null
+++ b/sources/experimental/polymerization-planner/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/polymerization-planner/GormleyLab__polymerization_planner",
+   "commit": "1a4974b2e17fdbf49234749050606bd010465847",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 8,
+   "redistributable": "yes",
+   "repo": "GormleyLab/polymerization_planner",
+   "robot_mentions": [],
+   "size_kb": 4501,
+   "status": "cloned",
+   "url": "https://github.com/GormleyLab/polymerization_planner"
+  }
+ ],
+ "doi_primary": "10.1021/acspolymersau.5c00067",
+ "dois": [
+  "10.1021/acspolymersau.5c00067"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 26,
+  "source": "europepmc:PMC12903423"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 4262601,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "5b4a4f6dfff54a99eef972236b9e3b0197f409984fd3d406b069aea7e3be31c0",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12903423?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12903423.1/PMC12903423.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12903423.1/PMC12903423.1.pdf"
+ },
+ "pmcid": "PMC12903423",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/polymerization-planner",
+ "title": "Automation-Assisted Photoinduced Atom Transfer Radical Polymerization",
+ "year": "2026"
+}
diff --git a/sources/experimental/pozzo-ot2-doe/record.json b/sources/experimental/pozzo-ot2-doe/record.json
new file mode 100644
index 0000000..6f2112a
--- /dev/null
+++ b/sources/experimental/pozzo-ot2-doe/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pozzo-ot2-doe/pozzo-research-group__OT2Protocols",
+   "commit": "2386dae2b7f18a8a42fb8b4a0b8d2c6b2f3ff440",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 8,
+   "py_files": 37,
+   "redistributable": "yes",
+   "repo": "pozzo-research-group/OT2Protocols",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 28952,
+   "status": "cloned",
+   "url": "https://github.com/pozzo-research-group/OT2Protocols"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/pozzo-ot2-doe",
+ "title": "Pozzo group OT-2 design-of-experiments protocols",
+ "year": ""
+}
diff --git a/sources/experimental/pr-pr/record.json b/sources/experimental/pr-pr/record.json
new file mode 100644
index 0000000..52cb336
--- /dev/null
+++ b/sources/experimental/pr-pr/record.json
@@ -0,0 +1,35 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/sb4001728",
+ "dois": [
+  "10.1021/sb4001728"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/sb4001728:\n  europepmc: no Europe PMC full text for this DOI\nDow",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "tecan",
+ "simulator": "not run",
+ "slug": "experimental/pr-pr",
+ "title": "PR-PR: cross-platform laboratory automation system",
+ "year": "2014"
+}
diff --git a/sources/experimental/prism-protocol-gen/record.json b/sources/experimental/prism-protocol-gen/record.json
new file mode 100644
index 0000000..21c2c07
--- /dev/null
+++ b/sources/experimental/prism-protocol-gen/record.json
@@ -0,0 +1,63 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.12"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/prism-protocol-gen/ramanathanlab__PRISM",
+   "commit": "0f3fe4dfbbd8e022fc650794e027af5a7b6c4851",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 4,
+   "py_files": 56,
+   "redistributable": "yes",
+   "repo": "ramanathanlab/PRISM",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 138557,
+   "status": "cloned",
+   "url": "https://github.com/ramanathanlab/PRISM"
+  }
+ ],
+ "dois": [
+  "10.1039/d6dd00004e"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d6dd00004e:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://pubs.rsc.org/en/content/articlepdf/2026/DD/D6DD00004E"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/prism-protocol-gen",
+ "title": "PRISM: Protocol Refinement through Intelligent Simulation Modeling",
+ "year": ""
+}
diff --git a/sources/experimental/protein-corona-ot2/record.json b/sources/experimental/protein-corona-ot2/record.json
new file mode 100644
index 0000000..9d1d0ce
--- /dev/null
+++ b/sources/experimental/protein-corona-ot2/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [],
+ "doi_primary": "10.1007/s00216-020-02726-1",
+ "dois": [
+  "10.1007/s00216-020-02726-1"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1007/s00216-020-02726-1:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7483600?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7483600.1/PMC7483600.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7483600.2/PMC7483600.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7483600.3/PMC7483600.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7483600&blobtype=pdf"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://link.springer.com/content/pdf/10.1007/s00216-020-02726-1.pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC7483600",
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/protein-corona-ot2",
+ "title": "Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data",
+ "year": "2020"
+}
diff --git a/sources/experimental/proteoautonet/record.json b/sources/experimental/proteoautonet/record.json
new file mode 100644
index 0000000..ab5a99f
--- /dev/null
+++ b/sources/experimental/proteoautonet/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/proteoautonet/guomics-lab__ProteoAutoNet",
+   "commit": "8aff52f7ae59f9cf695e5f69aa836a9b001973ab",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 11,
+   "redistributable": "no",
+   "repo": "guomics-lab/ProteoAutoNet",
+   "robot_mentions": [],
+   "size_kb": 37474,
+   "status": "cloned",
+   "url": "https://github.com/guomics-lab/ProteoAutoNet"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-026-68484-3",
+ "dois": [
+  "10.1038/s41467-026-68484-3"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 33,
+  "source": "europepmc:PMC12916966"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 4079016,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "66cec0892b2edfa62a2abe1d76c2a96c06f7bbc01d2fb6924a7681b851472db1",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12916966?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12916966.1/PMC12916966.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12916966.1/PMC12916966.1.pdf"
+ },
+ "pmcid": "PMC12916966",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/proteoautonet",
+ "title": "ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning",
+ "year": "2026"
+}
diff --git a/sources/experimental/pudu-synbio-ot2/record.json b/sources/experimental/pudu-synbio-ot2/record.json
new file mode 100644
index 0000000..0d044a0
--- /dev/null
+++ b/sources/experimental/pudu-synbio-ot2/record.json
@@ -0,0 +1,50 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13",
+    "2.14",
+    "2.20",
+    "2.21",
+    "2.22",
+    "2.23"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pudu-synbio-ot2/RudgeLab__PUDU",
+   "commit": "1214d2f9efd557aa84bc96502379554174355eae",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 28,
+   "py_files": 38,
+   "redistributable": "yes",
+   "repo": "RudgeLab/PUDU",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 5658,
+   "status": "cloned",
+   "url": "https://github.com/RudgeLab/PUDU"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/pudu-synbio-ot2",
+ "title": "PUDU (Protocol Unified Design Unit) - OT-2 synthetic biology workflows",
+ "year": ""
+}
diff --git a/sources/experimental/pvlab-solubility-dropcast-ot2/record.json b/sources/experimental/pvlab-solubility-dropcast-ot2/record.json
new file mode 100644
index 0000000..8cc5346
--- /dev/null
+++ b/sources/experimental/pvlab-solubility-dropcast-ot2/record.json
@@ -0,0 +1,45 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.16"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pvlab-solubility-dropcast-ot2/PV-Lab__Robotic_Liquid_Handling",
+   "commit": "a7e1db2bca46c2bf0321481701db3cbc964f109a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 23,
+   "py_files": 29,
+   "redistributable": "yes",
+   "repo": "PV-Lab/Robotic_Liquid_Handling",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 277,
+   "status": "cloned",
+   "url": "https://github.com/PV-Lab/Robotic_Liquid_Handling"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/pvlab-solubility-dropcast-ot2",
+ "title": "PV-Lab Robotic_Liquid_Handling (MIT AMLS OT-2 solubility testing / drop casting)",
+ "year": ""
+}
diff --git a/sources/experimental/pycromanager-2021/record.json b/sources/experimental/pycromanager-2021/record.json
new file mode 100644
index 0000000..b1117a5
--- /dev/null
+++ b/sources/experimental/pycromanager-2021/record.json
@@ -0,0 +1,94 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pycromanager-2021/micro-manager__pycro-manager",
+   "commit": "c9c8acd1969fb5e55619d8284b6c1fd96fc236b4",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 84,
+   "redistributable": "yes",
+   "repo": "micro-manager/pycro-manager",
+   "robot_mentions": [],
+   "size_kb": 42994,
+   "status": "cloned",
+   "url": "https://github.com/micro-manager/pycro-manager"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-021-01087-6",
+ "dois": [
+  "10.1038/s41592-021-01087-6"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s41592-021-01087-6:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 1253167,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "5a39707db30ddf6d716cfa4fb32d4363e2ccd5800da8647f4d93494994c41b5d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8532176?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8532176.1/PMC8532176.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8532176.2/PMC8532176.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8532176.3/PMC8532176.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8532176&blobtype=pdf"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "http://www.nature.com/articles/s41592-021-01087-6.pdf"
+   }
+  ],
+  "url": "http://www.nature.com/articles/s41592-021-01087-6.pdf"
+ },
+ "pmcid": "PMC8532176",
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/pycromanager-2021",
+ "title": "Pycro-Manager: open-source software for customized and reproducible microscope control",
+ "year": "2021"
+}
diff --git a/sources/experimental/pymmcore-plus-mda/record.json b/sources/experimental/pymmcore-plus-mda/record.json
new file mode 100644
index 0000000..edc864d
--- /dev/null
+++ b/sources/experimental/pymmcore-plus-mda/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pymmcore-plus-mda/pymmcore-plus__pymmcore-plus",
+   "commit": "f8884a64419fbbfb02a42917ed8e889e0d611bce",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 141,
+   "redistributable": "yes",
+   "repo": "pymmcore-plus/pymmcore-plus",
+   "robot_mentions": [],
+   "size_kb": 3152,
+   "status": "cloned",
+   "url": "https://github.com/pymmcore-plus/pymmcore-plus"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/pymmcore-plus-mda",
+ "title": "pymmcore-plus + useq-schema (multi-dimensional acquisition engine)",
+ "year": ""
+}
diff --git a/sources/experimental/pysted/record.json b/sources/experimental/pysted/record.json
new file mode 100644
index 0000000..a921405
--- /dev/null
+++ b/sources/experimental/pysted/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/pysted/FLClab__pySTED",
+   "commit": "7239e34eb4e52302de2186a57577c3b030aa0ed8",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "CC-BY-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 16,
+   "redistributable": "no",
+   "repo": "FLClab/pySTED",
+   "robot_mentions": [],
+   "size_kb": 17411,
+   "status": "cloned",
+   "url": "https://github.com/FLClab/pySTED"
+  }
+ ],
+ "doi_primary": "10.1038/s42256-024-00903-w",
+ "dois": [
+  "10.1038/s42256-024-00903-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 10,
+  "sections": 51,
+  "source": "europepmc:PMC11491398"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 11336966,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "e434a720e7b55edac5540fc8ad95a207e1195b3c4f50720c2ba8d8f2976873ac",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11491398?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11491398.1/PMC11491398.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11491398.1/PMC11491398.1.pdf"
+ },
+ "pmcid": "PMC11491398",
+ "readiness": "partial",
+ "robot_platform": "imaging",
+ "simulator": "not run",
+ "slug": "experimental/pysted",
+ "title": "Development of AI-assisted microscopy frameworks through realistic simulation with pySTED",
+ "year": "2024"
+}
diff --git a/sources/experimental/radiolabeling-psma-ot2/record.json b/sources/experimental/radiolabeling-psma-ot2/record.json
new file mode 100644
index 0000000..9a498e1
--- /dev/null
+++ b/sources/experimental/radiolabeling-psma-ot2/record.json
@@ -0,0 +1,35 @@
+{
+ "code": [],
+ "doi_primary": "10.1002/jlcr.4085",
+ "dois": [
+  "10.1002/jlcr.4085"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1002/jlcr.4085:\n  europepmc: no Europe PMC full text for this DOI\nDow",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/radiolabeling-psma-ot2",
+ "title": "Automated radiolabeling and handling of 177 Lu- and 225 Ac-PSMA-617 using a robotic pipettor",
+ "year": "2024"
+}
diff --git a/sources/experimental/raft-polymerization-platform/record.json b/sources/experimental/raft-polymerization-platform/record.json
new file mode 100644
index 0000000..9ba5559
--- /dev/null
+++ b/sources/experimental/raft-polymerization-platform/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/raft-polymerization-platform/zenodo-7379060",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "other-open",
+   "opentrons_py_files": 0,
+   "py_files": 4,
+   "redistributable": "no",
+   "repo": "zenodo:7379060",
+   "robot_mentions": [],
+   "size_kb": 1042,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.7379060"
+  }
+ ],
+ "doi_primary": "10.1039/d2dd00100d",
+ "dois": [
+  "10.1039/d2dd00100d"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 17,
+  "source": "europepmc:PMC7616994"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2176917,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "283ae28a0bb349c172608e973536f23c4898c603dfe53aeeccf5935c9ca0713c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7616994?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7616994.1/PMC7616994.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7616994.1/PMC7616994.1.pdf"
+ },
+ "pmcid": "PMC7616994",
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/raft-polymerization-platform",
+ "title": "A fully automated platform for photoinitiated RAFT polymerization",
+ "year": "2023"
+}
diff --git a/sources/experimental/reacsight/record.json b/sources/experimental/reacsight/record.json
new file mode 100644
index 0000000..ad37147
--- /dev/null
+++ b/sources/experimental/reacsight/record.json
@@ -0,0 +1,68 @@
+{
+ "code": [
+  {
+   "files": 1,
+   "files_downloaded": 0,
+   "files_skipped_size": [
+    "raw-data.zip"
+   ],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "repo": "zenodo:4776009",
+   "size_kb": 0,
+   "status": "zenodo: no files within the size limit",
+   "url": "https://doi.org/10.5281/zenodo.4776009"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-022-31033-9",
+ "dois": [
+  "10.1038/s41467-022-31033-9"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 22,
+  "source": "europepmc:PMC9188569"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3595427,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "25f865e18254b410efdf05cf203a065f0b08ae8977a5c2c39d7b96511dbe55b2",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9188569?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9188569.1/PMC9188569.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9188569.1/PMC9188569.1.pdf"
+ },
+ "pmcid": "PMC9188569",
+ "readiness": "partial",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/reacsight",
+ "title": "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight",
+ "year": "2022"
+}
diff --git a/sources/experimental/retro-10x-ot2/record.json b/sources/experimental/retro-10x-ot2/record.json
new file mode 100644
index 0000000..e02dfd6
--- /dev/null
+++ b/sources/experimental/retro-10x-ot2/record.json
@@ -0,0 +1,43 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.12"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/retro-10x-ot2/retrobiosciences__opentrons-10x",
+   "commit": "5fcab28493ee8d85522a7cc939fe7e37d17d0520",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "retrobiosciences/opentrons-10x",
+   "robot_mentions": [],
+   "size_kb": 5544,
+   "status": "cloned",
+   "url": "https://github.com/retrobiosciences/opentrons-10x"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/retro-10x-ot2",
+ "title": "OT-2 10x scRNA-seq library prep (Retro Biosciences)",
+ "year": ""
+}
diff --git a/sources/experimental/robochem/record.json b/sources/experimental/robochem/record.json
new file mode 100644
index 0000000..34d2ebc
--- /dev/null
+++ b/sources/experimental/robochem/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/robochem/Noel-Research-Group__Robochem_v1.0",
+   "commit": "2983246c2df0d4d08ff39651282b938e50ae8490",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 61,
+   "redistributable": "yes",
+   "repo": "Noel-Research-Group/Robochem_v1.0",
+   "robot_mentions": [],
+   "size_kb": 14804,
+   "status": "cloned",
+   "url": "https://github.com/Noel-Research-Group/Robochem_v1.0"
+  }
+ ],
+ "doi_primary": "10.1126/science.adj1817",
+ "dois": [
+  "10.1126/science.adj1817"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1126/science.adj1817:\n  europepmc: no Europe PMC full text for this D",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/robochem",
+ "title": "Automated self-optimization, intensification, and scale-up of photocatalysis in flow (RoboChem)",
+ "year": "2024"
+}
diff --git a/sources/experimental/roboctab/record.json b/sources/experimental/roboctab/record.json
new file mode 100644
index 0000000..f88c3d5
--- /dev/null
+++ b/sources/experimental/roboctab/record.json
@@ -0,0 +1,79 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.15",
+    "2.22"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/roboctab/tomstamour__RoboCTAB",
+   "commit": "eaf187fb6bfad3e5e4555ebe58d4e793b5309c0d",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "tomstamour/RoboCTAB",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 203,
+   "status": "cloned",
+   "url": "https://github.com/tomstamour/RoboCTAB"
+  }
+ ],
+ "doi_primary": "10.3390/plants14152263",
+ "dois": [
+  "10.3390/plants14152263"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 2,
+  "sections": 21,
+  "source": "europepmc:PMC12348566"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 976812,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "7c511a332acfcf02bfb56eca4eab22fa7f34ee2d2d692fa9b0e79daa718390a3",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12348566?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12348566.1/PMC12348566.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12348566.1/PMC12348566.1.pdf"
+ },
+ "pmcid": "PMC12348566",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/roboctab",
+ "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping",
+ "year": "2025"
+}
diff --git a/sources/experimental/roborna-nirvana/record.json b/sources/experimental/roborna-nirvana/record.json
new file mode 100644
index 0000000..949ed6f
--- /dev/null
+++ b/sources/experimental/roborna-nirvana/record.json
@@ -0,0 +1,65 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/roborna-nirvana/strubelab__roboRNA",
+   "commit": "42a432153362299dea8d8e8a5c840a2dd4bc3337",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "strubelab/roboRNA",
+   "robot_mentions": [],
+   "size_kb": 100940,
+   "status": "cloned",
+   "url": "https://github.com/strubelab/roboRNA"
+  }
+ ],
+ "doi_primary": "10.1038/s41598-023-47190-w",
+ "dois": [
+  "10.1038/s41598-023-47190-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 18,
+  "source": "europepmc:PMC10663496"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1776221,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "03fcf27a698f773fc54880cd14610d37bbd2a449da9c37758c368d1e33e98882",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s41598-023-47190-w.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s41598-023-47190-w.pdf"
+ },
+ "pmcid": "PMC10663496",
+ "readiness": "partial",
+ "robot_platform": "tecan",
+ "simulator": "not run",
+ "slug": "experimental/roborna-nirvana",
+ "title": "An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing",
+ "year": "2023"
+}
diff --git a/sources/experimental/robotic-titration-cv-ot2/record.json b/sources/experimental/robotic-titration-cv-ot2/record.json
new file mode 100644
index 0000000..6db57ce
--- /dev/null
+++ b/sources/experimental/robotic-titration-cv-ot2/record.json
@@ -0,0 +1,56 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/robotic-titration-cv-ot2/yuanlee0325__HTE-robotic-titration-using-computer-vision",
+   "commit": "fc6b80ab1e71d448208f901bbe0e18d3d5fc21f4",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 3,
+   "py_files": 30,
+   "redistributable": "yes",
+   "repo": "yuanlee0325/HTE-robotic-titration-using-computer-vision",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 1479,
+   "status": "cloned",
+   "url": "https://github.com/yuanlee0325/HTE-robotic-titration-using-computer-vision"
+  }
+ ],
+ "dois": [
+  "10.1039/d4dd00334a"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d4dd00334a:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/robotic-titration-cv-ot2",
+ "title": "High-throughput robotic colourimetric titrations using computer vision",
+ "year": ""
+}
diff --git a/sources/experimental/roche-pipetting-performance-ot2/record.json b/sources/experimental/roche-pipetting-performance-ot2/record.json
new file mode 100644
index 0000000..0ed2f8a
--- /dev/null
+++ b/sources/experimental/roche-pipetting-performance-ot2/record.json
@@ -0,0 +1,58 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.14"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/roche-pipetting-performance-ot2/arthur-theuer__pipetting-performance",
+   "commit": "990a9207ae9fd097e1f63c0c058811a1ed9650e8",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 2,
+   "py_files": 9,
+   "redistributable": "no",
+   "repo": "arthur-theuer/pipetting-performance",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 2401,
+   "status": "cloned",
+   "url": "https://github.com/arthur-theuer/pipetting-performance"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2024.100180",
+ "dois": [
+  "10.1016/j.slast.2024.100180"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.slast.2024.100180:\n  europepmc: no Europe PMC full text for th",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "licence": "cc by-nc-nd",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/roche-pipetting-performance-ot2",
+ "title": "Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment",
+ "year": "2024"
+}
diff --git a/sources/experimental/rtwizard-antigen-ot2/record.json b/sources/experimental/rtwizard-antigen-ot2/record.json
new file mode 100644
index 0000000..03e9d67
--- /dev/null
+++ b/sources/experimental/rtwizard-antigen-ot2/record.json
@@ -0,0 +1,44 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.13"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/rtwizard-antigen-ot2/BenHinnant__rtWIZARD",
+   "commit": "06961b5e2ea003b97fdb736dac90b44832792f3f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 7,
+   "py_files": 10,
+   "redistributable": "no",
+   "repo": "BenHinnant/rtWIZARD",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 123,
+   "status": "cloned",
+   "url": "https://github.com/BenHinnant/rtWIZARD"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/rtwizard-antigen-ot2",
+ "title": "rtWIZARD: OT-2 running 42 rapid antigen tests in parallel",
+ "year": ""
+}
diff --git a/sources/experimental/sample-protein-sdl/record.json b/sources/experimental/sample-protein-sdl/record.json
new file mode 100644
index 0000000..2cd721f
--- /dev/null
+++ b/sources/experimental/sample-protein-sdl/record.json
@@ -0,0 +1,64 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sample-protein-sdl/zenodo-10048592",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 20,
+   "redistributable": "no",
+   "repo": "zenodo:10048592",
+   "robot_mentions": [],
+   "size_kb": 128417,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.10048592"
+  }
+ ],
+ "doi_primary": "10.1038/s44286-023-00002-4",
+ "dois": [
+  "10.1038/s44286-023-00002-4"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1038/s44286-023-00002-4:\n  europepmc: Server error '500 ' for url 'ht",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3974899,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "b92d71dcea6ac40249842a4ec135a4e616f0fc518b48a6093b35e0ef1a7ebe3d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.nature.com/articles/s44286-023-00002-4.pdf"
+   }
+  ],
+  "url": "https://www.nature.com/articles/s44286-023-00002-4.pdf"
+ },
+ "pmcid": "PMC10926838",
+ "readiness": "partial",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/sample-protein-sdl",
+ "title": "Self-driving laboratories to autonomously navigate the protein fitness landscape (SAMPLE)",
+ "year": "2024"
+}
diff --git a/sources/experimental/sapp-dmx-protein-design/record.json b/sources/experimental/sapp-dmx-protein-design/record.json
new file mode 100644
index 0000000..94bda58
--- /dev/null
+++ b/sources/experimental/sapp-dmx-protein-design/record.json
@@ -0,0 +1,73 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.5"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sapp-dmx-protein-design/bwicky__SAPP_DMX",
+   "commit": "70b695f55a765289b212143e120a0af65bdefba5",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 1,
+   "py_files": 7,
+   "redistributable": "yes",
+   "repo": "bwicky/SAPP_DMX",
+   "robot_mentions": [],
+   "size_kb": 7468,
+   "status": "cloned",
+   "url": "https://github.com/bwicky/SAPP_DMX"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-026-76740-9",
+ "dois": [
+  "10.1038/s41467-026-76740-9"
+ ],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 37,
+  "source": "europepmc:PMC13586242"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2128497,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "7631a95745ac6dba497b3f77491a2d4ed1acac44118de9c0df6416b6c037a7cf",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC13586242?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13586242.1/PMC13586242.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13586242.1/PMC13586242.1.pdf"
+ },
+ "pmcid": "PMC13586242",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "failed",
+ "slug": "experimental/sapp-dmx-protein-design",
+ "title": "Accelerating protein design by scaling experimental characterization",
+ "year": "2026"
+}
diff --git a/sources/experimental/sd2-yeast-replication/record.json b/sources/experimental/sd2-yeast-replication/record.json
new file mode 100644
index 0000000..bf0618d
--- /dev/null
+++ b/sources/experimental/sd2-yeast-replication/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sd2-yeast-replication/rpgoldman__replication-paper-data-analysis",
+   "commit": "62e46526a829b1b0f215f50bc04384ab56d0487f",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 3,
+   "redistributable": "yes",
+   "repo": "rpgoldman/replication-paper-data-analysis",
+   "robot_mentions": [],
+   "size_kb": 12529,
+   "status": "cloned",
+   "url": "https://github.com/rpgoldman/replication-paper-data-analysis"
+  }
+ ],
+ "doi_primary": "10.1093/synbio/ysac018",
+ "dois": [
+  "10.1093/synbio/ysac018"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 11,
+  "sections": 35,
+  "source": "europepmc:PMC9583850"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3330153,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8112d64574dc0ce915fda93a389a4399ea4ea2345cf1128fb37dc1b577a8b974",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC9583850?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9583850.1/PMC9583850.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9583850.1/PMC9583850.1.pdf"
+ },
+ "pmcid": "PMC9583850",
+ "readiness": "partial",
+ "robot_platform": "protocol_language",
+ "simulator": "not run",
+ "slug": "experimental/sd2-yeast-replication",
+ "title": "Highly-automated, high-throughput replication of yeast-based logic circuit design assessments (SD2/Strateos/Aquarium)",
+ "year": "2022"
+}
diff --git a/sources/experimental/sdl-demo-clslab/record.json b/sources/experimental/sdl-demo-clslab/record.json
new file mode 100644
index 0000000..ba72b8e
--- /dev/null
+++ b/sources/experimental/sdl-demo-clslab/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sdl-demo-clslab/sparks-baird__self-driving-lab-demo",
+   "commit": "051e91e34b63e5ce357df3db7e7425186c5c635c",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 160,
+   "redistributable": "yes",
+   "repo": "sparks-baird/self-driving-lab-demo",
+   "robot_mentions": [],
+   "size_kb": 223317,
+   "status": "cloned",
+   "url": "https://github.com/sparks-baird/self-driving-lab-demo"
+  }
+ ],
+ "dois": [
+  "10.1016/j.matt.2022.11.007"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.matt.2022.11.007:\n  europepmc: no Europe PMC full text for thi",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "ready",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/sdl-demo-clslab",
+ "title": "What is a minimal working example for a self-driving laboratory? (SDL-Demo / CLSLab:Light)",
+ "year": ""
+}
diff --git a/sources/experimental/sdl-enzyme-flex/record.json b/sources/experimental/sdl-enzyme-flex/record.json
new file mode 100644
index 0000000..c583a77
--- /dev/null
+++ b/sources/experimental/sdl-enzyme-flex/record.json
@@ -0,0 +1,72 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sdl-enzyme-flex/putzsebastian__sdl-enzymes-optimization",
+   "commit": "d51650c9054ac230284efec034c43a650cd5c4c3",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 10,
+   "redistributable": "yes",
+   "repo": "putzsebastian/sdl-enzymes-optimization",
+   "robot_mentions": [],
+   "size_kb": 109,
+   "status": "cloned",
+   "url": "https://github.com/putzsebastian/sdl-enzymes-optimization"
+  }
+ ],
+ "doi_primary": "10.1002/bit.70038",
+ "dois": [
+  "10.1002/bit.70038"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 18,
+  "source": "europepmc:PMC12503018"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 2065399,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "8cfa3acfbd9d93cc94fb6a570ad986c21c80d330ce0a92a8be09a2579c2f3a6d",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12503018?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12503018.1/PMC12503018.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12503018.1/PMC12503018.1.pdf"
+ },
+ "pmcid": "PMC12503018",
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/sdl-enzyme-flex",
+ "title": "Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab",
+ "year": "2025"
+}
diff --git a/sources/experimental/sdl-guide-gormley/record.json b/sources/experimental/sdl-guide-gormley/record.json
new file mode 100644
index 0000000..daeb66b
--- /dev/null
+++ b/sources/experimental/sdl-guide-gormley/record.json
@@ -0,0 +1,86 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sdl-guide-gormley/GormleyLab__SDLGuide",
+   "commit": "0e05c18ee6c38f3db193a7a7ddd10be1f1d2e60d",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 8,
+   "redistributable": "yes",
+   "repo": "GormleyLab/SDLGuide",
+   "robot_mentions": [],
+   "size_kb": 69054,
+   "status": "cloned",
+   "url": "https://github.com/GormleyLab/SDLGuide"
+  }
+ ],
+ "doi_primary": "10.1039/d5dd00525f",
+ "dois": [
+  "10.1039/d5dd00525f"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 25,
+  "source": "europepmc:PMC13071554"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "licence": "cc by",
+  "redistributable": "unknown",
+  "status": "not_found",
+  "tried": [
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13071554.1/PMC13071554.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13071554.2/PMC13071554.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13071554.3/PMC13071554.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC13071554&blobtype=pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://pubs.rsc.org/en/content/articlepdf/2026/DD/D5DD00525F"
+   }
+  ]
+ },
+ "pmcid": "PMC13071554",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/sdl-guide-gormley",
+ "title": "A user's guide to your first self-driving liquid handling lab",
+ "year": "2026"
+}
diff --git a/sources/experimental/sdl-nano-acsnano/record.json b/sources/experimental/sdl-nano-acsnano/record.json
new file mode 100644
index 0000000..89540f0
--- /dev/null
+++ b/sources/experimental/sdl-nano-acsnano/record.json
@@ -0,0 +1,58 @@
+{
+ "code": [
+  {
+   "status": "no public code",
+   "url": "none found"
+  }
+ ],
+ "doi_primary": "10.1021/acsnano.4c17504",
+ "dois": [
+  "10.1021/acsnano.4c17504"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 41,
+  "source": "europepmc:PMC11912568"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 7091872,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "1a79a6c11a4611a928ab738a868d9a99ce6d5c8106e6382411740e1b6e6d517b",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11912568?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11912568.1/PMC11912568.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11912568.1/PMC11912568.1.pdf"
+ },
+ "pmcid": "PMC11912568",
+ "readiness": "no",
+ "robot_platform": "synthesis",
+ "simulator": "not run",
+ "slug": "experimental/sdl-nano-acsnano",
+ "title": "A Self-Driving Lab for Nano- and Advanced Materials Synthesis",
+ "year": "2025"
+}
diff --git a/sources/experimental/slab-scheduling/record.json b/sources/experimental/slab-scheduling/record.json
new file mode 100644
index 0000000..821b42a
--- /dev/null
+++ b/sources/experimental/slab-scheduling/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/slab-scheduling/labauto__SLab.jl",
+   "commit": "f836b0bee406aa7cbbf18f2ce282ebf8de77ea63",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "labauto/SLab.jl",
+   "robot_mentions": [],
+   "size_kb": 14,
+   "status": "cloned",
+   "url": "https://github.com/labauto/SLab.jl"
+  }
+ ],
+ "doi_primary": "10.1177/24726303211021790",
+ "dois": [
+  "10.1177/24726303211021790"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 21,
+  "source": "europepmc:PMC8641030"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc",
+ "pdf": {
+  "bytes": 990320,
+  "licence": "cc by-nc",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "fb5b0ab08a3c14788701f2bba66042ce7e152adaee7c5b008e78ade215274f3c",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://slas-technology.org/article/S2472630322011359/pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8641030?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8641030.1/PMC8641030.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8641030.1/PMC8641030.1.pdf"
+ },
+ "pmcid": "PMC8641030",
+ "readiness": "ready",
+ "robot_platform": "scheduling",
+ "simulator": "not run",
+ "slug": "experimental/slab-scheduling",
+ "title": "Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints",
+ "year": "2021"
+}
diff --git a/sources/experimental/snails-slow-pipetting/record.json b/sources/experimental/snails-slow-pipetting/record.json
new file mode 100644
index 0000000..f0eb256
--- /dev/null
+++ b/sources/experimental/snails-slow-pipetting/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/snails-slow-pipetting/dholab__SNAILS",
+   "commit": "39839691d09f5b0e3dd274c7426d4d4314d3d7f3",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 5,
+   "redistributable": "no",
+   "repo": "dholab/SNAILS",
+   "robot_mentions": [],
+   "size_kb": 4914,
+   "status": "cloned",
+   "url": "https://github.com/dholab/SNAILS"
+  }
+ ],
+ "doi_primary": "10.1186/s12864-021-07500-w",
+ "dois": [
+  "10.1186/s12864-021-07500-w"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 30,
+  "source": "europepmc:PMC7953553"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 1275152,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "f1da5c699d24bfeb8bef3123e32c71524751d43db85cc3d2447674c9ce4720ba",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-021-07500-w"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7953553?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7953553.1/PMC7953553.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7953553.1/PMC7953553.1.pdf"
+ },
+ "pmcid": "PMC7953553",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/snails-slow-pipetting",
+ "title": "Consistent ultra-long DNA sequencing with automated slow pipetting",
+ "year": "2021"
+}
diff --git a/sources/experimental/solubility-hein/record.json b/sources/experimental/solubility-hein/record.json
new file mode 100644
index 0000000..b3b1374
--- /dev/null
+++ b/sources/experimental/solubility-hein/record.json
@@ -0,0 +1,68 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/solubility-hein/heingroup__automated_solubility_h1",
+   "commit": "54af0348984cfdd574e0780879e08dd8b04d3878",
+   "host": "gitlab.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 0,
+   "py_files": 53,
+   "redistributable": "no",
+   "repo": "heingroup/automated_solubility_h1",
+   "robot_mentions": [],
+   "status": "cloned (partial: code, configs and docs only)",
+   "url": "https://gitlab.com/heingroup/automated_solubility_h1"
+  }
+ ],
+ "doi_primary": "10.1016/j.isci.2021.102176",
+ "dois": [
+  "10.1016/j.isci.2021.102176"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 8,
+  "sections": 30,
+  "source": "europepmc:PMC7921605"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 2759620,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "fa224d86c209819a172e243662fb6c45bfd7b23445c6aae42a0d3bcb7b9a1498",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7921605?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7921605.1/PMC7921605.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7921605.1/PMC7921605.1.pdf"
+ },
+ "pmcid": "PMC7921605",
+ "readiness": "partial",
+ "robot_platform": "characterisation",
+ "simulator": "not run",
+ "slug": "experimental/solubility-hein",
+ "title": "Automated solubility screening platform using computer vision",
+ "year": "2021"
+}
diff --git a/sources/experimental/sources.json b/sources/experimental/sources.json
new file mode 100644
index 0000000..a64ad5b
--- /dev/null
+++ b/sources/experimental/sources.json
@@ -0,0 +1,4334 @@
+[
+ {
+  "slug": "alabos-alab",
+  "dois": [
+   "10.1039/d4dd00129j"
+  ],
+  "title": "AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories (A-Lab)",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/dd/d4dd00129j",
+  "known_code": [
+   "https://github.com/CederGroupHub/alab_management"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "scheduling",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ant-cloning",
+  "dois": [
+   "10.1021/acssynbio.0c00240"
+  ],
+  "title": "Automated cloning by natural transformation (ANT) OT-2 workflow",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.0c00240",
+  "known_code": [
+   "https://github.com/ljm176/ANTCloning"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "autoprotocol-dnada",
+  "dois": [
+   "10.1021/acssynbio.3c00292"
+  ],
+  "title": "Automated Platform for the Plasmid Construction Process (DNAda -> Autoprotocol)",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.3c00292",
+  "known_code": [
+   "https://github.com/JBEI/dnada"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "protocol_language",
+  "code_licence": "Apache-2.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "beckham-enzyme-pipeline",
+  "dois": [
+   "10.1038/s41598-024-64938-0"
+  ],
+  "title": "Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline",
+  "paper_url": "https://www.nature.com/articles/s41598-024-64938-0",
+  "known_code": [
+   "https://github.com/beckham-lab/opentrons"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none (no LICENSE file)",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "blots-ot2",
+  "dois": [
+   "10.1002/cpz1.70454"
+  ],
+  "title": "Bacterial Lysis Observation Over Time Assay (BLOTS) for High-Throughput Isolation and Screening",
+  "paper_url": "https://doi.org/10.1002/cpz1.70454",
+  "known_code": [
+   "https://github.com/eyaplab/BLOTS-OT2"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "cayman-his-elisa",
+  "dois": [
+   "10.17504/protocols.io.n92ld4x3nl5b"
+  ],
+  "title": "An Opentrons OT-2 workflow for the Cayman His-tag detection ELISA kit",
+  "paper_url": "https://dx.doi.org/10.17504/protocols.io.n92ld4x3nl5b",
+  "known_code": [
+   "https://github.com/Arcadia-Science/cayman-his-elisa-opentrons-workflow"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemputer-acra",
+  "dois": [
+   "10.1038/s42004-026-01993-w"
+  ],
+  "title": "Verification and execution of the scientific literature via chemputation augmented by large language models",
+  "paper_url": "https://www.nature.com/articles/s42004-026-01993-w",
+  "known_code": [
+   "https://github.com/croningp/acra"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "protocol_language",
+  "code_licence": "(LICENSE present, unrecognised text)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemputer-blueprints",
+  "dois": [
+   "10.1038/s41467-024-54238-6"
+  ],
+  "title": "Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer",
+  "paper_url": "https://www.nature.com/articles/s41467-024-54238-6",
+  "known_code": [
+   "https://gitlab.com/croningroup/chemputer/xdl"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "protocol_language",
+  "code_licence": "see GitLab (unverified)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemputer-peptide",
+  "dois": [
+   "10.1038/s41467-025-62344-2"
+  ],
+  "title": "Universal peptide synthesis via solid-phase methods fused with chemputation",
+  "paper_url": "https://www.nature.com/articles/s41467-025-62344-2",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.15948769"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "synthesis",
+  "code_licence": "Zenodo (check)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "clairify-xdl",
+  "dois": [
+   "10.1007/s10514-023-10136-2"
+  ],
+  "title": "Large language models for chemistry robotics (CLAIRify: NL -> XDL)",
+  "paper_url": "https://link.springer.com/article/10.1007/s10514-023-10136-2",
+  "known_code": [
+   "https://github.com/ac-rad/xdl-generation"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "protocol_language",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "culturomics-isolation",
+  "dois": [
+   "10.1002/imo2.70037"
+  ],
+  "title": "Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex communities",
+  "paper_url": "https://doi.org/10.1002/imo2.70037",
+  "known_code": [
+   "https://github.com/microenvgen/Culturomics"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "damplab-moclo-transformation",
+  "dois": [
+   "10.1093/synbio/ysac004"
+  ],
+  "title": "A linear programming-based strategy to save pipette tips in automated DNA assembly (with DAMP Lab MoClo/transformation workflow)",
+  "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac004/6542944",
+  "known_code": [
+   "https://github.com/DAMPLAB/OT2-MoClo-Transformation-Ecoli"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "no_protocol_found",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "eda-event-driven",
+  "dois": [
+   "10.1038/s41592-022-01589-x"
+  ],
+  "title": "Event-driven acquisition for content-enriched microscopy",
+  "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613693/",
+  "known_code": [
+   "https://github.com/wl-stepp/eda_plugin"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ester-library-synthesis",
+  "dois": [
+   "10.1039/d2cc05670d"
+  ],
+  "title": "Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction",
+  "paper_url": "https://doi.org/10.1039/d2cc05670d",
+  "known_code": [
+   "https://github.com/rz-flask/concise-ester-library-synthesis"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "etsted",
+  "dois": [
+   "10.1038/s41592-022-01588-y"
+  ],
+  "title": "Event-triggered STED imaging",
+  "paper_url": "https://www.nature.com/articles/s41592-022-01588-y",
+  "known_code": [
+   "https://github.com/jonatanalvelid/etSTED-widget"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "evolver-2018",
+  "dois": [
+   "10.1038/nbt.4151"
+  ],
+  "title": "Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER",
+  "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035058/",
+  "known_code": [
+   "https://github.com/FYNCH-BIO/dpu"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "bioreactor",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "exfab-qiaseq-flex",
+  "dois": [
+   "10.17504/protocols.io.n2bvjer3pgk5"
+  ],
+  "title": "Automated QIAseq FX DNA Library Preparation on the Opentrons Flex",
+  "paper_url": "https://dx.doi.org/10.17504/protocols.io.n2bvjer3pgk5",
+  "known_code": [
+   "https://github.com/exfab/Opentrons_Flex_ExFAB"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "flex",
+  "code_licence": "GPL-3.0",
+  "simulator": "verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "flat-agar-celegans-ot2",
+  "dois": [
+   "10.57844/arcadia-h01v-2nxt"
+  ],
+  "title": "Flat agar and optimized media enable high-throughput C. elegans imaging in 96-well plates",
+  "paper_url": "https://doi.org/10.57844/arcadia-h01v-2nxt",
+  "known_code": [
+   "https://github.com/Arcadia-Science/menisquish-flat-agar"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "formulations-prep-shampoo",
+  "dois": [
+   "10.1038/s41597-024-03573-w"
+  ],
+  "title": "Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset",
+  "paper_url": "https://www.nature.com/articles/s41597-024-03573-w",
+  "known_code": [
+   "https://github.com/sustainable-processes/formulations-prep"
+  ],
+  "found_by": [
+   "amass",
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "gfp-codon-burden-ot2",
+  "dois": [
+   "10.1186/s13036-025-00521-z"
+  ],
+  "title": "Codon usage modulates the relationship between the burden and yield of protein overexpression",
+  "paper_url": "https://doi.org/10.1186/s13036-025-00521-z",
+  "known_code": [
+   "https://github.com/alexismhill3/gfp_deoptimization_burden"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "greenaway-halogenation",
+  "dois": [
+   "10.26434/chemrxiv.15000393"
+  ],
+  "title": "An automated platform for tailored late-stage halogenation of pharmaceuticals",
+  "paper_url": "https://chemrxiv.org/engage/chemrxiv/article-details/15000393",
+  "known_code": [
+   "https://github.com/GreenawayLab/automated_halogenation_of_pharmaceuticals"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "greenaway-mocs",
+  "dois": [
+   "10.1002/anie.202424270"
+  ],
+  "title": "Development of an Automated Workflow for Screening the Assembly and Host-Guest Behavior of Metal-Organic Cages",
+  "paper_url": "https://doi.org/10.1002/anie.202424270",
+  "known_code": [
+   "https://github.com/GreenawayLab/development-automated-workflow-mocs"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "greenaway-pocs",
+  "dois": [
+   "10.1039/d3sc06133g"
+  ],
+  "title": "Streamlining the automated discovery of porous organic cages",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc06133g",
+  "known_code": [
+   "https://github.com/GreenawayLab/Streamlining-Automated-Discovery-POCs"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "hyrad-adna-capture",
+  "dois": [
+   "10.1111/1755-0998.13518"
+  ],
+  "title": "Performance and automation of ancient DNA capture with RNA hyRAD probes",
+  "paper_url": "https://doi.org/10.1111/1755-0998.13518",
+  "known_code": [
+   "https://github.com/TomaszSuchan/opentrons-hyRAD"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "jubiotech-ot2-autoclone",
+  "dois": [
+   "10.1007/s00253-022-12017-7"
+  ],
+  "title": "Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation",
+  "paper_url": "https://doi.org/10.1007/s00253-022-12017-7",
+  "known_code": [
+   "https://github.com/JuBiotech/OT-2-autoclone"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "AGPL-3.0",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "labop",
+  "dois": [],
+  "title": "LabOP (Laboratory Open Protocol language, formerly PAML) - iGEM interlab growth-curve/calibration protocols",
+  "paper_url": "https://bioprotocols.github.io/labop/",
+  "known_code": [
+   "https://github.com/Bioprotocols/labop"
+  ],
+  "found_by": [
+   "github",
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "protocol_language",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "lucks-cellfree-biosensor",
+  "dois": [
+   "10.1101/2024.10.13.618078"
+  ],
+  "title": "Semi-automated production of cell-free biosensors",
+  "paper_url": "https://www.biorxiv.org/content/10.1101/2024.10.13.618078v1",
+  "known_code": [
+   "https://github.com/LucksLab/Brown_Phillips_Semi-Automated_Biosensor_Manufacturing_2024"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "lysostaphin-turbidity",
+  "dois": [
+   "10.1186/s12934-025-02911-w"
+  ],
+  "title": "Turbid but accurate: automating lysostaphin quantification including uncertainty quantification",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12836826/",
+  "known_code": [
+   "https://github.com/JuBiotech/Supplement-to-Prigolovkin-et-al.-2025"
+  ],
+  "found_by": [
+   "amass",
+   "github"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "AGPL-3.0",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "mantis-shrimpy",
+  "dois": [
+   "10.1093/pnasnexus/pgae323"
+  ],
+  "title": "Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells",
+  "paper_url": "https://academic.oup.com/pnasnexus/article/3/9/pgae323/7742297",
+  "known_code": [
+   "https://github.com/czbiohub-sf/shrimPy"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "massspecpreppy",
+  "dois": [
+   "10.1002/pmic.202300294"
+  ],
+  "title": "MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics",
+  "paper_url": "https://doi.org/10.1002/pmic.202300294",
+  "known_code": [
+   "https://github.com/stemicha/MassSpecPreppy"
+  ],
+  "found_by": [
+   "amass",
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "GPL-3.0",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "msd-biochem-assays-ot2",
+  "dois": [
+   "10.1016/j.slast.2024.100205"
+  ],
+  "title": "Automation of biochemical assays using an open-sourced, inexpensive robotic liquid handler",
+  "paper_url": "https://doi.org/10.1016/j.slast.2024.100205",
+  "known_code": [
+   "https://github.com/MSDLLCpapers/Opentrons-OT2-BioChemical-Assays"
+  ],
+  "found_by": [
+   "amass",
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "Apache-2.0",
+  "simulator": "verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "navigate-2024",
+  "dois": [
+   "10.1038/s41592-024-02413-4"
+  ],
+  "title": "Navigate: an open-source platform for smart light-sheet microscopy",
+  "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540721/",
+  "known_code": [
+   "https://github.com/TheDeanLab/navigate"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "BSD-style (LICENSE.md)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "openflexure-autofocus",
+  "dois": [
+   "10.1111/jmi.13064"
+  ],
+  "title": "Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope",
+  "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13064",
+  "known_code": [
+   "https://gitlab.com/openflexure/openflexure-microscope-server"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "openworkstation",
+  "dois": [
+   "10.1016/j.ohx.2020.e00152"
+  ],
+  "title": "OpenWorkstation: A modular open-source technology for automated in vitro workflows",
+  "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067220300468",
+  "known_code": [
+   "https://github.com/SebastianEggert/OpenWorkstation"
+  ],
+  "found_by": [
+   "amass",
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "plate_transport",
+  "code_licence": "CC BY-SA (repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "panda-bear",
+  "dois": [
+   "10.1039/d4mh00797b"
+  ],
+  "title": "PANDA: a self-driving lab for studying electrodeposited polymer films",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2024/mh/d4mh00797b",
+  "known_code": [
+   "https://github.com/BU-KABlab/PANDA-BEAR"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "characterisation",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "plant-phenotyping-ot2",
+  "dois": [
+   "10.1002/aisy.202500624"
+  ],
+  "title": "Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience",
+  "paper_url": "https://doi.org/10.1002/aisy.202500624",
+  "known_code": [
+   "https://github.com/Synthetic-Automated-Systems/automated_phenotyping_system"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pycromanager-2021",
+  "dois": [
+   "10.1038/s41592-021-01087-6"
+  ],
+  "title": "Pycro-Manager: open-source software for customized and reproducible microscope control",
+  "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532176/",
+  "known_code": [
+   "https://github.com/micro-manager/pycro-manager"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pymmcore-plus-mda",
+  "dois": [],
+  "title": "pymmcore-plus + useq-schema (multi-dimensional acquisition engine)",
+  "paper_url": "https://pymmcore-plus.github.io/pymmcore-plus/",
+  "known_code": [
+   "https://github.com/pymmcore-plus/pymmcore-plus"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "imaging",
+  "code_licence": "BSD-3-Clause",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "roboctab",
+  "dois": [
+   "10.3390/plants14152263"
+  ],
+  "title": "High-Throughput DNA Extraction Using Robotic Automation (RoboCTAB) for Large-Scale Genotyping",
+  "paper_url": "https://www.mdpi.com/2223-7747/14/15/2263",
+  "known_code": [
+   "https://github.com/tomstamour/RoboCTAB"
+  ],
+  "found_by": [
+   "amass",
+   "github",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "roche-pipetting-performance-ot2",
+  "dois": [
+   "10.1016/j.slast.2024.100180"
+  ],
+  "title": "Deep integration of low-cost liquid handling robots in an industrial pharmaceutical development environment",
+  "paper_url": "https://doi.org/10.1016/j.slast.2024.100180",
+  "known_code": [
+   "https://github.com/arthur-theuer/pipetting-performance"
+  ],
+  "found_by": [
+   "amass",
+   "github"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "GPL-3.0",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sapp-dmx-protein-design",
+  "dois": [
+   "10.1038/s41467-026-76740-9"
+  ],
+  "title": "Accelerating protein design by scaling experimental characterization",
+  "paper_url": "https://doi.org/10.1038/s41467-026-76740-9",
+  "known_code": [
+   "https://github.com/bwicky/SAPP_DMX"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "failed",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sdl-demo-clslab",
+  "dois": [
+   "10.1016/j.matt.2022.11.007"
+  ],
+  "title": "What is a minimal working example for a self-driving laboratory? (SDL-Demo / CLSLab:Light)",
+  "paper_url": "https://www.cell.com/matter/fulltext/S2590-2385(22)00651-1",
+  "known_code": [
+   "https://github.com/sparks-baird/self-driving-lab-demo"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "characterisation",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "slab-scheduling",
+  "dois": [
+   "10.1177/24726303211021790"
+  ],
+  "title": "Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints",
+  "paper_url": "https://journals.sagepub.com/doi/10.1177/24726303211021790",
+  "known_code": [
+   "https://github.com/labauto/SLab.jl"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "ready",
+  "robot_platform": "scheduling",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "tidytron",
+  "dois": [
+   "10.1016/j.slast.2023.08.007"
+  ],
+  "title": "TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 robots",
+  "paper_url": "https://doi.org/10.1016/j.slast.2023.08.007",
+  "known_code": [
+   "https://github.com/PlantSynBioLab/TidyTron"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "ready",
+  "robot_platform": "ot2",
+  "code_licence": "Apache-2.0",
+  "simulator": "partly_verified",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "a-lab-2023",
+  "dois": [
+   "10.1038/s41586-023-06734-w"
+  ],
+  "title": "An autonomous laboratory for the accelerated synthesis of novel materials (A-Lab)",
+  "paper_url": "https://www.nature.com/articles/s41586-023-06734-w",
+  "known_code": [
+   "https://github.com/njszym/ARROWS"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "none (ARROWS); see repos",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ac-training-lab",
+  "dois": [],
+  "title": "Acceleration Consortium Training Lab (remote-access SDL modules incl. Hello-World, sample transfer)",
+  "paper_url": "https://github.com/AccelerationConsortium/ac-training-lab",
+  "known_code": [
+   "https://github.com/AccelerationConsortium/ac-training-lab"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "plate_transport",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ada-thin-films",
+  "dois": [
+   "10.1126/sciadv.aaz8867"
+  ],
+  "title": "Self-driving laboratory for accelerated discovery of thin-film materials (Ada)",
+  "paper_url": "https://www.science.org/doi/10.1126/sciadv.aaz8867",
+  "known_code": [
+   "https://github.com/berlinguette/ada"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "afion-plasmonic",
+  "dois": [
+   "10.1038/s41467-025-56788-9"
+  ],
+  "title": "Self-driving lab for the photochemical synthesis of plasmonic nanoparticles (AFION)",
+  "paper_url": "https://www.nature.com/articles/s41467-025-56788-9",
+  "known_code": [
+   "https://github.com/Taylorwutianyi/AFION-LAB"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "agentex-genetic-codes",
+  "dois": [
+   "10.1038/s41586-026-10949-y"
+  ],
+  "title": "Automated prototyping of genetic codes",
+  "paper_url": "https://doi.org/10.1038/s41586-026-10949-y",
+  "known_code": [
+   "https://github.com/FelixRadford/AGENTEX"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ahtech-electrochem",
+  "dois": [
+   "10.1126/sciadv.adu4391"
+  ],
+  "title": "A high-throughput experimentation platform for data-driven discovery in electrochemistry (AHTech)",
+  "paper_url": "https://www.science.org/doi/10.1126/sciadv.adu4391",
+  "known_code": [
+   "https://github.com/Liu-Lab-JHU/AHTech"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "characterisation",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ai4pd-flex-protein-purification",
+  "dois": [],
+  "title": "Opentrons Flex protein purification and molecular biology scripts (AI4PD Lab)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/AI4PDLab/Opentrons_Flex_Protocols"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "aliquot-niaid",
+  "dois": [],
+  "title": "ALIQUOT: Automated Liquid handling Infection Quantification Using OpenTrons (NIH/NIAID QVEU)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/QVEU/ALIQUOT"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "aml-drug-synergy-pyhamilton",
+  "dois": [
+   "10.1016/j.slasd.2023.04.004"
+  ],
+  "title": "High-throughput approaches to uncover synergistic drug combinations in leukemia",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10449086/",
+  "known_code": [
+   "https://github.com/stefangolas/drug_dilutions"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "hamilton",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "amplicon-seq-bisanz",
+  "dois": [],
+  "title": "AmpliconSeq (16S amplicon library OT-2 scripts, Bisanz lab)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/jbisanz/AmpliconSeq"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "angelovangel-ot2-ngs",
+  "dois": [],
+  "title": "angelovangel/opentrons (KAUST Bioscience core NGS/Sanger OT-2 + Flex protocols)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/angelovangel/opentrons"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "aquarium",
+  "dois": [
+   "10.1093/synbio/ysad005"
+  ],
+  "title": "Aquarium laboratory operating system (UW BIOFAB) - used in SD2 robustness studies",
+  "paper_url": "https://academic.oup.com/synbio/article/8/1/ysad005/7069301",
+  "known_code": [
+   "https://github.com/aquariumbio/aquarium"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "protocol_language",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "artic-normalisation-esr",
+  "dois": [],
+  "title": "ESR-NZ ARTIC normalisation/end-repair/barcoding (OT-2)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/ESR-NZ/opentrons_protocols"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "auto-sp-proteomics",
+  "dois": [
+   "10.1021/acs.analchem.5c00886"
+  ],
+  "title": "AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12355475/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "autoprotocol-python",
+  "dois": [],
+  "title": "Autoprotocol-python (Strateos/Transcriptic protocol IR)",
+  "paper_url": "https://autoprotocol.org",
+  "known_code": [
+   "https://github.com/autoprotocol/autoprotocol-python"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "protocol_language",
+  "code_licence": "BSD-3-Clause (LICENSE.rst)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "bean-kasp-anthracnose",
+  "dois": [
+   "10.1186/s13007-023-01071-5"
+  ],
+  "title": "Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10546687/",
+  "known_code": [
+   "https://github.com/McGillHaricots/peas-andlove"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "bear-mechanics",
+  "dois": [
+   "10.1038/s41467-024-48534-4"
+  ],
+  "title": "Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership (BEAR)",
+  "paper_url": "https://www.nature.com/articles/s41467-024-48534-4",
+  "known_code": [
+   "https://github.com/KelseyEng/BEAR_ADTS"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "characterisation",
+  "code_licence": "(LICENSE present, unrecognised)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "biomationscripter",
+  "dois": [],
+  "title": "BiomationScripter: Python library for scripting bio-automation protocols",
+  "paper_url": "https://biomationscripterlib.readthedocs.io",
+  "known_code": [
+   "https://github.com/intbio-ncl/BiomationScripterLib"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "brightfield-biofilm",
+  "dois": [
+   "10.1128/mbio.00448-26"
+  ],
+  "title": "Label-free microscopy enables high-throughput identification of genes controlling biofilm development",
+  "paper_url": "https://journals.asm.org/doi/10.1128/mbio.00448-26",
+  "known_code": [
+   "https://github.com/BridgesLabCMU/Brightfield-biofilm-assay"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "cfrna-pipeline",
+  "dois": [
+   "10.1038/s41596-023-00855-2"
+  ],
+  "title": "An inexpensive semi-automated sample processing pipeline for cell-free RNA (extraction)",
+  "paper_url": "https://doi.org/10.1038/s41596-023-00855-2",
+  "known_code": [
+   "https://github.com/miramou/cfRNA_pipeline_automation"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemcrow",
+  "dois": [
+   "10.1038/s42256-024-00832-8"
+  ],
+  "title": "Augmenting large language models with chemistry tools (ChemCrow)",
+  "paper_url": "https://www.nature.com/articles/s42256-024-00832-8",
+  "known_code": [
+   "https://github.com/ur-whitelab/chemcrow-public"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemos-2020",
+  "dois": [
+   "10.1371/journal.pone.0229862"
+  ],
+  "title": "ChemOS: An orchestration software to democratize autonomous discovery",
+  "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229862",
+  "known_code": [
+   "https://github.com/aspuru-guzik-group/ChemOS"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "scheduling",
+  "code_licence": "Apache-2.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemos2-atlas",
+  "dois": [
+   "10.1039/D4DD00115J"
+  ],
+  "title": "Atlas: a brain for self-driving laboratories (BO library used in ChemOS 2.0 campaigns)",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d4dd00115j",
+  "known_code": [
+   "https://github.com/aspuru-guzik-group/atlas"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chemputer-modules-acscs",
+  "dois": [
+   "10.1021/acscentsci.3c00304"
+  ],
+  "title": "Robotic Modules for the Programmable Chemputation of Molecules and Materials",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acscentsci.3c00304",
+  "known_code": [
+   "https://gitlab.com/croningroup/chemputer"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "chibio-2020",
+  "dois": [
+   "10.1371/journal.pbio.3000794"
+  ],
+  "title": "In situ characterisation and manipulation of biological systems with Chi.Bio",
+  "paper_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000794",
+  "known_code": [
+   "https://github.com/HarrisonSteel/ChiBio"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "bioreactor",
+  "code_licence": "none (no LICENSE file)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "clio-electrolytes",
+  "dois": [
+   "10.1038/s41467-022-32938-1"
+  ],
+  "title": "Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation (Clio)",
+  "paper_url": "https://www.nature.com/articles/s41467-022-32938-1",
+  "known_code": [
+   "https://github.com/BattModels/Clio-PythonAPI"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "characterisation",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "coscientist",
+  "dois": [
+   "10.1038/s41586-023-06792-0"
+  ],
+  "title": "Autonomous chemical research with large language models (Coscientist)",
+  "paper_url": "https://www.nature.com/articles/s41586-023-06792-0",
+  "known_code": [
+   "https://github.com/gomesgroup/coscientist"
+  ],
+  "found_by": [
+   "amass",
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "protocol_language",
+  "code_licence": "(LICENSE present, unrecognised text)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "covid-mastermix-omix",
+  "dois": [
+   "10.1016/j.slast.2024.100195"
+  ],
+  "title": "Development and validation of automated methods for COVID-19 PCR Master Mix preparation",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11639134/",
+  "known_code": [
+   "https://github.com/Donald-OMIX/Liquid_Handler_Methods"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "culturomics-colony-picking",
+  "dois": [
+   "10.1038/s41587-023-01674-2"
+  ],
+  "title": "High-throughput microbial culturomics using automation and machine learning (CAMII colony picker)",
+  "paper_url": "https://www.nature.com/articles/s41587-023-01674-2",
+  "known_code": [
+   "see paper code availability (not verified)"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "damplab-taqpath-ot2",
+  "dois": [
+   "10.17504/protocols.io.brhvm366"
+  ],
+  "title": "Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex RT-PCR (BU DAMP Lab)",
+  "paper_url": "https://doi.org/10.17504/protocols.io.brhvm366",
+  "known_code": [
+   "https://github.com/DAMPLAB/OT2-SARS-CoV2"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "daxi-lightsheet",
+  "dois": [
+   "10.1038/s41592-022-01417-2"
+  ],
+  "title": "DaXi: high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy",
+  "paper_url": "https://www.nature.com/articles/s41592-022-01417-2",
+  "known_code": [
+   "https://github.com/royerlab/daxi"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "CC BY (repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "detectr-covid-ot2",
+  "dois": [],
+  "title": "Mammoth DETECTR COVID-19 assay on OT-2",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/tsdobbs/mammoth-COVID19-assay-OT2"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "dtu-synbio-automation",
+  "dois": [],
+  "title": "DTU Synbio lab automation protocol collection",
+  "paper_url": "https://github.com/DALSA-Lab/dtu_synbio_lab_automation",
+  "known_code": [
+   "https://github.com/DALSA-Lab/dtu_synbio_lab_automation"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "duckbot-jubilee",
+  "dois": [
+   "10.1371/journal.pone.0296717"
+  ],
+  "title": "The Duckbot: A system for automated imaging and manipulation of duckweed",
+  "paper_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0296717",
+  "known_code": [
+   "https://github.com/machineagency/duckbot"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ecoli-protein-expr-purif-ot2",
+  "dois": [],
+  "title": "OT-2 assisted recombinant protein expression and purification in E. coli (Norton-Baker)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/nortonbakerbc/opentrons"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "evogen-ot-library",
+  "dois": [],
+  "title": "EvoGenOT (UCPH EvoGenomics Opentrons protocol library)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/anttonalberdi/EvoGenOT"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "evolver-ddr-elife",
+  "dois": [
+   "10.7554/eLife.67175"
+  ],
+  "title": "Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community (eVOLVER)",
+  "paper_url": "https://elifesciences.org/articles/67175",
+  "known_code": [
+   "https://github.com/khalillab/DDR-eVOLVER-model"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "bioreactor",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "evotron-evolver-sampling",
+  "dois": [
+   "10.1038/s41467-022-32392-z"
+  ],
+  "title": "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback",
+  "paper_url": "https://www.nature.com/articles/s41467-022-32392-z",
+  "known_code": [
+   "https://github.com/santkumar/evotron"
+  ],
+  "found_by": [
+   "amass",
+   "github",
+   "nonlh",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "exposomics-384-flex",
+  "dois": [],
+  "title": "Opentrons Flex 384-well protein-precipitation sample preparation for nontargeted exposomics",
+  "paper_url": "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols",
+  "known_code": [
+   "https://github.com/apat594/384wellplate-Exposomics-Opentrons-Protocols"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "fish-fluidics",
+  "dois": [
+   "10.1016/j.ohx.2022.e00343"
+  ],
+  "title": "An open source 16-channel fluidics system for automating sequential FISH-based imaging",
+  "paper_url": "https://www.sciencedirect.com/science/article/pii/S246806722200088X",
+  "known_code": [
+   "https://github.com/dzhaojie/Fluidics-system-for-FISH"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "flex-genomics-di-omics",
+  "dois": [],
+  "title": "Opentrons Flex whole-genome / methylation / TIP-seq workflows (di-omics)",
+  "paper_url": "https://github.com/di-omics/ot-flex-automation",
+  "known_code": [
+   "https://github.com/di-omics/ot-flex-automation"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "har1eyk-starlet-protein-extraction",
+  "dois": [],
+  "title": "hamilton-starlet-scripts (PyLabRobot STARlet protein extraction / Orange G volume tests)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/har1eyk/hamilton-starlet-scripts"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "hamilton",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "helao-async",
+  "dois": [
+   "10.1039/d3dd00193h"
+  ],
+  "title": "HELAO-async: autonomous electrochemistry/high-throughput experimentation orchestration (Caltech/TRI)",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d3dd00193h",
+  "known_code": [
+   "https://github.com/High-Throughput-Experimentation/helao-async"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "characterisation",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ht-hcr-sea-urchin",
+  "dois": [
+   "10.1242/dev.204814"
+  ],
+  "title": "Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12516323/",
+  "known_code": [
+   "https://github.com/ylee-sio/HL_HTHCR"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "hydrogel-crosslink-ot2",
+  "dois": [],
+  "title": "Semi-autonomous synthesis and modelling of chemically cross-linked hydrogels (OT-2)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/JamesSummers240/Semi-autonomous-synthesis-and-modelling-of-chemically-cross-linked-hydrogels-"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "icfree-cfps",
+  "dois": [
+   "10.1016/j.isci.2025.113599"
+  ],
+  "title": "An AI-driven workflow for the accelerated optimization of cell-free protein synthesis",
+  "paper_url": "https://doi.org/10.1016/j.isci.2025.113599",
+  "known_code": [
+   "https://github.com/brsynth/icfree-ml"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "imperial-colony-picker",
+  "dois": [],
+  "title": "Automated colony picker add-on for the OT-2 (Imperial SSB MRes; cited by Slowpoke)",
+  "paper_url": "https://github.com/Imperial-Opentrons-Users/automated-colony-picker",
+  "known_code": [
+   "https://github.com/Imperial-Opentrons-Users/automated-colony-picker"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "imswitch",
+  "dois": [
+   "10.21105/joss.03394"
+  ],
+  "title": "ImSwitch: generalizing microscope control in Python",
+  "paper_url": "https://joss.theoj.org/papers/10.21105/joss.03394",
+  "known_code": [
+   "https://github.com/ImSwitch/ImSwitch"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ipsc-robot-pyhamilton",
+  "dois": [
+   "10.1101/2020.12.18.423371"
+  ],
+  "title": "Automated hiPSC culture and sample preparation for 3D live cell microscopy",
+  "paper_url": "https://doi.org/10.1101/2020.12.18.423371",
+  "known_code": [
+   "https://github.com/stefangolas/iPSC-Robot"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "hamilton",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "krisp-sars2-pooling",
+  "dois": [
+   "10.1038/s41598-021-96934-z"
+  ],
+  "title": "Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8423848/",
+  "known_code": [
+   "https://github.com/krisp-kwazulu-natal/efficient-SARS-CoV-2-pooled-testing-strategy-code"
+  ],
+  "found_by": [
+   "amass",
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "labdroid-cell-culture",
+  "dois": [
+   "10.7554/eLife.77007"
+  ],
+  "title": "Robotic search for optimal cell culture in regenerative medicine (LabDroid Maholo, iPSC-RPE)",
+  "paper_url": "https://elifesciences.org/articles/77007",
+  "known_code": [
+   "https://github.com/labauto/LabDroid_optimizer"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "labscriptai-protein-eng",
+  "dois": [
+   "10.1101/2025.09.30.679666"
+  ],
+  "title": "Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows",
+  "paper_url": "https://www.biorxiv.org/content/10.1101/2025.09.30.679666v1.full",
+  "known_code": [
+   "https://github.com/KRATSZ/LabScript-AI"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "llm-rdf-synthesis",
+  "dois": [
+   "10.1038/s41467-024-54457-x"
+  ],
+  "title": "An automatic end-to-end chemical synthesis development platform powered by large language models",
+  "paper_url": "https://www.nature.com/articles/s41467-024-54457-x",
+  "known_code": [
+   "https://github.com/Ruan-Yixiang/LLM-RDF"
+  ],
+  "found_by": [
+   "nonlh",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT (per README badge)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "locost-covid-nanopore-ot2",
+  "dois": [],
+  "title": "Opentrons_LoCost_Covid19 (ARTIC LoCost nanopore library prep on OT-2)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/JDMirza/Opentrons_LoCost_Covid19"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "madsci-ad-sdl",
+  "dois": [
+   "10.21105/joss.09416"
+  ],
+  "title": "MADSci: A modular Python-based framework to enable autonomous science",
+  "paper_url": "https://doi.org/10.21105/joss.09416",
+  "known_code": [
+   "https://github.com/AD-SDL/MADSci"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "scheduling",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "memplex-printing",
+  "dois": [
+   "10.1038/s41467-025-59471-1"
+  ],
+  "title": "Designer artificial environments for membrane protein synthesis",
+  "paper_url": "https://www.nature.com/articles/s41467-025-59471-1",
+  "known_code": [
+   "https://github.com/ccmeyer/printing-platform"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "metclo-ot2",
+  "dois": [
+   "10.1007/978-1-0716-0908-8_9"
+  ],
+  "title": "MetCloOT2: Automated MetClo assembly on Opentrons OT-2 (MSc project, based on Lin & O Callaghan 2018/2020)",
+  "paper_url": "https://doi.org/10.1007/978-1-0716-0908-8_9",
+  "known_code": [
+   "https://github.com/Edinburgh-Genome-Foundry/OT2Metclo"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "mobile-robots-dai-2024",
+  "dois": [
+   "10.1038/s41586-024-08173-7"
+  ],
+  "title": "Autonomous mobile robots for exploratory synthetic chemistry",
+  "paper_url": "https://www.nature.com/articles/s41586-024-08173-7",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.11174257"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "plate_transport",
+  "code_licence": "Zenodo (check per record)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "myra-cfe-platform",
+  "dois": [
+   "10.1093/synbio/ysag010"
+  ],
+  "title": "A liquid handling platform for standardized quantification of cell-free enzymatic activity",
+  "paper_url": "https://academic.oup.com/synbio/article/doi/10.1093/synbio/ysag010",
+  "known_code": [
+   "https://github.com/Mo42-mb/Myra_automation"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "myrplate-flex-casting",
+  "dois": [],
+  "title": "myrPlate engineered connective tissue casting on Opentrons Flex",
+  "paper_url": "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15",
+  "known_code": [
+   "https://github.com/Hosseinat11502/MyrplateTissueCasting-8channel1mltip-Version-15"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "nioz-ot2-database",
+  "dois": [],
+  "title": "MolLabNIOZ/OT2 protocol database (NIOZ molecular ecology)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/MolLabNIOZ/OT2"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "olh-turbidostat-plr",
+  "dois": [
+   "10.64898/2026.03.02.709168"
+  ],
+  "title": "A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments",
+  "paper_url": "https://www.biorxiv.org/content/10.64898/2026.03.02.709168v1.full",
+  "known_code": [
+   "https://github.com/chory-lab/plr-turbidostat"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "pylabrobot",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "openblend-media",
+  "dois": [
+   "10.1002/bit.27947"
+  ],
+  "title": "Modular development enables rapid design of media for alternative hosts",
+  "paper_url": "https://doi.org/10.1002/bit.27947",
+  "known_code": [
+   "https://github.com/abiedermann/openblend_public"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "openframe-openaf",
+  "dois": [
+   "10.1111/jmi.13219"
+  ],
+  "title": "openFrame: modular open microscopy platform with single-shot optical autofocus",
+  "paper_url": "https://onlinelibrary.wiley.com/doi/10.1111/jmi.13219",
+  "known_code": [
+   "https://github.com/ImperialCollegeLondon/openAF"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "BSD",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "opentrons-covid19-dev",
+  "dois": [],
+  "title": "Opentrons/covid19 (OT-2 COVID-19 RT-qPCR station development repo, Opentrons + Open Medicine Institute)",
+  "paper_url": "https://www.protocols.io/groups/opentrons-covid19-testing/publications",
+  "known_code": [
+   "https://github.com/Opentrons/covid19"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "Apache-2.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "organa",
+  "dois": [
+   "10.1016/j.matt.2024.10.015"
+  ],
+  "title": "ORGANA: a robotic assistant for automated chemistry experimentation and characterization",
+  "paper_url": "https://arxiv.org/abs/2401.06949",
+  "known_code": [
+   "https://github.com/ac-rad/organa"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ot2-cherrypick",
+  "dois": [
+   "10.26434/chemrxiv.15000637"
+  ],
+  "title": "OT2-CherryPick: A Zero-Install Web Platform for Orchestrating Complex Liquid Handling on the Opentrons OT-2",
+  "paper_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15000637/v1",
+  "known_code": [
+   "https://github.com/HiteSit/OT2_CherryPick"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ot2-moclo-jove",
+  "dois": [],
+  "title": "Modular Cloning with the OT2 (OT2_MoClo_JoVE)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/emernic/OT2_MoClo_JoVE"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ot2-proteomics-thesis",
+  "dois": [],
+  "title": "Automated Versus Manual Proteomics Sample Preparation: A Comparative Evaluation of Liquid Handling Workflows (MSc thesis)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/martineingolfsrud/Opentrons-OT-2-performance-assessment"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ot2-yeast-spot-assay",
+  "dois": [
+   "10.1016/j.slast.2022.12.001"
+  ],
+  "title": "Automation of yeast spot assays using an affordable liquid handling robot",
+  "paper_url": "https://doi.org/10.1016/j.slast.2022.12.001",
+  "known_code": [
+   "https://github.com/bioinfo-tsukuba/ot2_spot_assay"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pac832-galr1-ot2",
+  "dois": [],
+  "title": "PAC-832: A selective small-molecule antagonist of galanin receptor 1 (GalR1) - supplementary data and OT-2 protocols",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/douglasyao/pac-832-supplementary-data"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "parseq-pyhamilton",
+  "dois": [
+   "10.1101/2023.12.12.571337"
+  ],
+  "title": "parSEQ:  Probe and Rescue Sequencing for Advanced Variant Retrieval from DNA Pool",
+  "paper_url": "https://doi.org/10.1101/2023.12.12.571337",
+  "known_code": [
+   "https://github.com/finyl/parseq-pyhamilton"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "hamilton",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pasta-spatial",
+  "dois": [
+   "10.1038/s41592-026-03200-z"
+  ],
+  "title": "PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13539481/",
+  "known_code": [
+   "https://github.com/SizunJiangLab/PASTA"
+  ],
+  "found_by": [
+   "amass",
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "peg-solubility-assay",
+  "dois": [
+   "10.1038/s41598-021-01126-4"
+  ],
+  "title": "An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8578320/",
+  "known_code": [
+   "https://gitlab.developers.cam.ac.uk/ch/sormanni/peg-solubility-assay"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "phage-cocktails-robotics",
+  "dois": [
+   "10.1038/s41467-026-68684-x"
+  ],
+  "title": "High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails",
+  "paper_url": "https://www.nature.com/articles/s41467-026-68684-x",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.17594564"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "check Zenodo",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "photobioreactor-fluorescence",
+  "dois": [
+   "10.3390/bios15030128"
+  ],
+  "title": "Integration of Fluorescence Spectroscopy into a Photobioreactor for the Monitoring of Cyanobacteria",
+  "paper_url": "https://www.mdpi.com/2079-6374/15/3/128",
+  "known_code": [
+   "https://github.com/borjaggarcia/fluorescence-monitoring"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "bioreactor",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pioreactor",
+  "dois": [],
+  "title": "Pioreactor open-source bioreactor software (used in published studies)",
+  "paper_url": "https://docs.pioreactor.com",
+  "known_code": [
+   "https://github.com/pioreactor/pioreactor"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "bioreactor",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "polar-sarscov2-ot2",
+  "dois": [
+   "10.17504/protocols.io.bearjad6"
+  ],
+  "title": "POLAR: Pathogen-Oriented Low-cost Assembly & Re-sequencing SARS-CoV-2 (OT-2 automation)",
+  "paper_url": "https://doi.org/10.17504/protocols.io.bearjad6",
+  "known_code": [
+   "https://github.com/Zanecrc1/POLAR-SARS-CoV-2-Automation-for-OT-2"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "polybot-pedot",
+  "dois": [
+   "10.1038/s41467-024-55655-3"
+  ],
+  "title": "Autonomous platform for solution processing of electronic polymers (Polybot)",
+  "paper_url": "https://www.nature.com/articles/s41467-024-55655-3",
+  "known_code": [
+   "https://github.com/polybot-nexus/PEDOT_PSS_supporting_data"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "polymerization-planner",
+  "dois": [
+   "10.1021/acspolymersau.5c00067"
+  ],
+  "title": "Automation-Assisted Photoinduced Atom Transfer Radical Polymerization",
+  "paper_url": "https://doi.org/10.1021/acspolymersau.5c00067",
+  "known_code": [
+   "https://github.com/GormleyLab/polymerization_planner"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pozzo-ot2-doe",
+  "dois": [],
+  "title": "Pozzo group OT-2 design-of-experiments protocols",
+  "paper_url": "https://github.com/pozzo-research-group/OT2Protocols",
+  "known_code": [
+   "https://github.com/pozzo-research-group/OT2Protocols"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "prism-protocol-gen",
+  "dois": [
+   "10.1039/d6dd00004e"
+  ],
+  "title": "PRISM: Protocol Refinement through Intelligent Simulation Modeling",
+  "paper_url": "https://doi.org/10.1039/d6dd00004e",
+  "known_code": [
+   "https://github.com/ramanathanlab/PRISM"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pudu-synbio-ot2",
+  "dois": [],
+  "title": "PUDU (Protocol Unified Design Unit) - OT-2 synthetic biology workflows",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/RudgeLab/PUDU"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pvlab-solubility-dropcast-ot2",
+  "dois": [],
+  "title": "PV-Lab Robotic_Liquid_Handling (MIT AMLS OT-2 solubility testing / drop casting)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/PV-Lab/Robotic_Liquid_Handling"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pysted",
+  "dois": [
+   "10.1038/s42256-024-00903-w"
+  ],
+  "title": "Development of AI-assisted microscopy frameworks through realistic simulation with pySTED",
+  "paper_url": "https://www.nature.com/articles/s42256-024-00903-w",
+  "known_code": [
+   "https://github.com/FLClab/pySTED"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "imaging",
+  "code_licence": "CC (Attribution, check NC)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "raft-polymerization-platform",
+  "dois": [
+   "10.1039/d2dd00100d"
+  ],
+  "title": "A fully automated platform for photoinitiated RAFT polymerization",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2023/dd/d2dd00100d",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.7379060"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "check Zenodo",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "reacsight",
+  "dois": [
+   "10.1038/s41467-022-31033-9"
+  ],
+  "title": "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight",
+  "paper_url": "https://www.nature.com/articles/s41467-022-31033-9",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.4776009"
+  ],
+  "found_by": [
+   "amass",
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "bioreactor",
+  "code_licence": "check Zenodo",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "retro-10x-ot2",
+  "dois": [],
+  "title": "OT-2 10x scRNA-seq library prep (Retro Biosciences)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/retrobiosciences/opentrons-10x"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "robochem",
+  "dois": [
+   "10.1126/science.adj1817"
+  ],
+  "title": "Automated self-optimization, intensification, and scale-up of photocatalysis in flow (RoboChem)",
+  "paper_url": "https://www.science.org/doi/10.1126/science.adj1817",
+  "known_code": [
+   "https://github.com/Noel-Research-Group/Robochem_v1.0"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "synthesis",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "roborna-nirvana",
+  "dois": [
+   "10.1038/s41598-023-47190-w"
+  ],
+  "title": "An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10663496/",
+  "known_code": [
+   "https://github.com/strubelab/roboRNA"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "tecan",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "robotic-titration-cv-ot2",
+  "dois": [
+   "10.1039/d4dd00334a"
+  ],
+  "title": "High-throughput robotic colourimetric titrations using computer vision",
+  "paper_url": "https://doi.org/10.1039/d4dd00334a",
+  "known_code": [
+   "https://github.com/yuanlee0325/HTE-robotic-titration-using-computer-vision"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "rtwizard-antigen-ot2",
+  "dois": [],
+  "title": "rtWIZARD: OT-2 running 42 rapid antigen tests in parallel",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/BenHinnant/rtWIZARD"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sample-protein-sdl",
+  "dois": [
+   "10.1038/s44286-023-00002-4"
+  ],
+  "title": "Self-driving laboratories to autonomously navigate the protein fitness landscape (SAMPLE)",
+  "paper_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926838/",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.10048592"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "protocol_language",
+  "code_licence": "check Zenodo",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sd2-yeast-replication",
+  "dois": [
+   "10.1093/synbio/ysac018"
+  ],
+  "title": "Highly-automated, high-throughput replication of yeast-based logic circuit design assessments (SD2/Strateos/Aquarium)",
+  "paper_url": "https://academic.oup.com/synbio/article/7/1/ysac018/6703309",
+  "known_code": [
+   "https://github.com/rpgoldman/replication-paper-data-analysis"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "protocol_language",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sdl-enzyme-flex",
+  "dois": [
+   "10.1002/bit.70038"
+  ],
+  "title": "Optimized Machine Learning for Autonomous Enzymatic Reaction Intensification in a Self-Driving Lab",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12503018/",
+  "known_code": [
+   "https://github.com/putzsebastian/sdl-enzymes-optimization"
+  ],
+  "found_by": [
+   "amass",
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sdl-guide-gormley",
+  "dois": [
+   "10.1039/d5dd00525f"
+  ],
+  "title": "A user's guide to your first self-driving liquid handling lab",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2026/dd/d5dd00525f",
+  "known_code": [
+   "https://github.com/GormleyLab/SDLGuide"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "solubility-hein",
+  "dois": [
+   "10.1016/j.isci.2021.102176"
+  ],
+  "title": "Automated solubility screening platform using computer vision",
+  "paper_url": "https://www.cell.com/iscience/fulltext/S2589-0042(21)00144-0",
+  "known_code": [
+   "https://gitlab.com/heingroup/automated_solubility_h1"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "characterisation",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "spatial-tx-bravo",
+  "dois": [
+   "10.1186/s12864-020-6631-z"
+  ],
+  "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7158132/",
+  "known_code": [
+   "https://github.com/jemten/Bravo_ST"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "star-hardwarex",
+  "dois": [
+   "10.1016/j.ohx.2024.e00524"
+  ],
+  "title": "Sequential Treatment Application Robot (STAR) for high-replication marine experimentation",
+  "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067224000178",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.10048123"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "plate_transport",
+  "code_licence": "check Zenodo",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "tape-organoid-barcoding",
+  "dois": [
+   "10.1038/s41592-020-0737-8"
+  ],
+  "title": "Cell-type-specific signaling networks in heterocellular organoids (TOBis barcoding / robotic organoid extraction)",
+  "paper_url": "https://doi.org/10.1038/s41592-020-0737-8",
+  "known_code": [
+   "https://github.com/TAPE-Lab/OT-2_Code"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "teemi",
+  "dois": [
+   "10.1371/journal.pcbi.1011929"
+  ],
+  "title": "teemi: open-source literate programming for iterative DBTL cycles",
+  "paper_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011929",
+  "known_code": [
+   "https://github.com/hiyama341/teemi"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "tmt-bead-platform-ot2",
+  "dois": [
+   "10.1021/jasms.1c00077"
+  ],
+  "title": "A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8210952/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "trypanosomatid-drug-combo-ot2",
+  "dois": [],
+  "title": "OT-2 protocols for drug combination screening (Trypanosomatics Lab, UNSAM)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/FranAguero07/OT2_protocols"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ufdutton-16s-flex",
+  "dois": [],
+  "title": "UF Dutton Lab Opentrons 16S microbiome workflow (OT-2 + Flex)",
+  "paper_url": null,
+  "known_code": [
+   "https://github.com/UFDuttonLab/lab_automation_opentrons"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "vadr-vacuum-miniprep-flex",
+  "dois": [
+   "10.64898/2026.09.16.746974"
+  ],
+  "title": "An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2",
+  "paper_url": "https://doi.org/10.64898/2026.09.16.746974",
+  "known_code": [
+   "https://github.com/JackATDalton/VADR"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "flex",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "viscous-liquid-bo-ot2",
+  "dois": [
+   "10.1039/d3dd00255a"
+  ],
+  "title": "Optimization of liquid handling parameters for viscous liquid transfers with pipetting robots, a sticky situation",
+  "paper_url": "https://doi.org/10.1039/d3dd00255a",
+  "known_code": [
+   "https://github.com/Quijanove/LiqTransferOptimizer"
+  ],
+  "found_by": [
+   "github"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "worm-food-preference",
+  "dois": [
+   "10.1242/jeb.01955"
+  ],
+  "title": "C. elegans food preference protocol (bacteria and worm spotting on OT-2)",
+  "paper_url": "https://github.com/slhogle/c_elegans_food_preference_protocol",
+  "known_code": [
+   "https://github.com/slhogle/c_elegans_food_preference_protocol"
+  ],
+  "found_by": [
+   "github",
+   "web"
+  ],
+  "readiness": "partial",
+  "robot_platform": "ot2",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "zhao-autonomous-enzyme",
+  "dois": [
+   "10.1038/s41467-025-61209-y"
+  ],
+  "title": "A generalized platform for artificial intelligence-powered autonomous enzyme engineering (iBioFAB)",
+  "paper_url": "https://www.nature.com/articles/s41467-025-61209-y",
+  "known_code": [
+   "https://github.com/Zhao-Group/closed-loop"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "partial",
+  "robot_platform": "scheduling",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "adept-framework",
+  "dois": [
+   "10.1038/s42004-026-01932-9"
+  ],
+  "title": "The ADePT framework for assessing autonomous laboratory robotics",
+  "paper_url": "https://www.nature.com/articles/s42004-026-01932-9",
+  "known_code": [
+   "none found"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ai-chemist-ustc",
+  "dois": [
+   "10.1093/nsr/nwac190"
+  ],
+  "title": "An all-round AI-Chemist with a scientific mind",
+  "paper_url": "https://academic.oup.com/nsr/article/9/10/nwac190/6694179",
+  "known_code": [
+   "none found"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "synthesis",
+  "code_licence": "n/a",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "archemist",
+  "dois": [
+   "10.1109/ICRA46639.2022.9811996"
+  ],
+  "title": "ARChemist: Autonomous Robotic Chemistry System Architecture (Fakhruldeen et al.)",
+  "paper_url": "https://arxiv.org/abs/2204.13571",
+  "known_code": [
+   "https://github.com/cooper-group-uol-robotics/archemist"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "plate_transport",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "aurora-materials",
+  "dois": [
+   "10.1021/acsami.5c02605"
+  ],
+  "title": "AURORA - An Automatic Robotic Platform for Materials Discovery",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acsami.5c02605",
+  "known_code": [
+   "https://github.com/PalmSens/MethodSCRIPT_Examples"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "characterisation",
+  "code_licence": "vendor",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "autopots-proteome",
+  "dois": [
+   "10.1021/acs.analchem.0c04240"
+  ],
+  "title": "Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8140400/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "autorelacs",
+  "dois": [
+   "10.1038/s41598-020-69443-8"
+  ],
+  "title": "AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7381599/",
+  "known_code": [
+   "https://github.com/FrancescoFerrari88/AutoRELACS"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "baybe",
+  "dois": [
+   "10.1039/D5DD00050E"
+  ],
+  "title": "BayBE: Bayesian Back End for design of experiments",
+  "paper_url": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d5dd00050e",
+  "known_code": [
+   "https://github.com/emdgroup/baybe"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "Apache-2.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "bead-digestion-ann",
+  "dois": [
+   "10.1016/j.talanta.2024.125988"
+  ],
+  "title": "Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network",
+  "paper_url": "https://doi.org/10.1016/j.talanta.2024.125988",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "bio-spec-hardwarex",
+  "dois": [
+   "10.1016/j.ohx.2025.e00670"
+  ],
+  "title": "BIO-SPEC: An open-source bench-top parallel bioreactor system",
+  "paper_url": "https://www.sciencedirect.com/science/article/pii/S2468067225000690",
+  "known_code": [
+   "see paper repository (OSF/Zenodo, not verified)"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "bioreactor",
+  "code_licence": "CC BY (hardware, per HardwareX)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "bioclonebot",
+  "dois": [
+   "10.1016/j.ohx.2024.e00516"
+  ],
+  "title": "BioCloneBot: A versatile, low-cost, and open-source automated liquid handler",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10955647/",
+  "known_code": [
+   "https://osf.io/qdp7v"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "see OSF (HardwareX requires open licence)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "catib-screening",
+  "dois": [
+   "10.1186/s12934-024-02319-y"
+  ],
+  "title": "\"High-throughput screening of catalytically active inclusion bodies using laboratory automation and Bayesian optimization\"",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10894497/",
+  "known_code": [
+   "https://github.com/JuBiotech/Supplement-to-Helleckes-Kuesters-et-al.-2023"
+  ],
+  "found_by": [
+   "amass",
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "cellfree-biosensor-ot2",
+  "dois": [
+   "10.1021/acssynbio.4c00703"
+  ],
+  "title": "Semiautomated Production of Cell-Free Biosensors",
+  "paper_url": "https://doi.org/10.1021/acssynbio.4c00703",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "cloudlab-chiral-perovskite",
+  "dois": [
+   "10.1038/s41467-020-15728-5"
+  ],
+  "title": "Autonomous discovery of optically active chiral inorganic perovskite nanocrystals through an intelligent cloud lab",
+  "paper_url": "https://www.nature.com/articles/s41467-020-15728-5",
+  "known_code": [
+   "none found"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "synthesis",
+  "code_licence": "n/a",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "combinatorial-barcode-dna",
+  "dois": [
+   "10.3390/ijms24032549"
+  ],
+  "title": "Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9917336/",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.7415652"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "CC-BY-4.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "covid-fosh-review",
+  "dois": [
+   "10.3389/fmedt.2022.969203"
+  ],
+  "title": "High-throughput and automated screening for COVID-19",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9521367/",
+  "known_code": [
+   "https://www.protocols.io/groups/opentrons-covid19-testing"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "unknown",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "curcumin-formulation-sdl",
+  "dois": [
+   "10.1039/d5dd00171d"
+  ],
+  "title": "Efficient discovery of new medicine formulations using a semi-self-driven robotic formulator",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13576497/",
+  "known_code": [
+   "https://github.com/shorthouse-lab/Ros_SDformulation"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "diy-ot-linear-motion-qpcr",
+  "dois": [
+   "10.1038/s41598-020-70465-5"
+  ],
+  "title": "Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7424513/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "diy-stem-lhr",
+  "dois": [
+   "10.1371/journal.pone.0275688"
+  ],
+  "title": "DIY liquid handling robots for integrated STEM education and life science research",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9645590/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "duckweed-hte",
+  "dois": [
+   "10.1371/journal.pone.0287739"
+  ],
+  "title": "Accelerated high-throughput imaging and phenotyping system for small organisms",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10361482/",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.8060938"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "egf-sequeduct",
+  "dois": [
+   "10.1021/acssynbio.3c00589"
+  ],
+  "title": "Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10877595/",
+  "known_code": [
+   "https://github.com/Edinburgh-Genome-Foundry/Sequeduct"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "endylab-opentrons",
+  "dois": [],
+  "title": "Endy Lab Opentrons protocol collection",
+  "paper_url": "https://github.com/EndyLab/opentrons",
+  "known_code": [
+   "https://github.com/EndyLab/opentrons"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "evobot",
+  "dois": [
+   "10.1177/2472630316689285"
+  ],
+  "title": "New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot",
+  "paper_url": "https://doi.org/10.1177/2472630316689285",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "findus",
+  "dois": [
+   "10.1177/2472630319877374"
+  ],
+  "title": "FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences",
+  "paper_url": "https://doi.org/10.1177/2472630319877374",
+  "known_code": [
+   "https://github.com/FBarthels/FINDUS"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "GPL-3.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "flyspresso-embryo-ihc",
+  "dois": [
+   "10.1038/s41598-021-89676-5"
+  ],
+  "title": "An open-source semi-automated robotics pipeline for embryo immunohistochemistry",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8119710/",
+  "known_code": [
+   "https://github.com/janelia-pypi/hybridizer_python"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "not checked",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "gpcr-livecell-ot2",
+  "dois": [
+   "10.1021/acssensors.2c01341"
+  ],
+  "title": "GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9994309/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "hydra-hydrogel-plates",
+  "dois": [
+   "10.1038/s44172-025-00575-3"
+  ],
+  "title": "Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12749810/",
+  "known_code": [
+   "https://github.com/Synthetic-Physiology-Lab/hydra-hts-hydrogel-analysis"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "illumina-dnaprep-flowbot",
+  "dois": [
+   "10.1038/s41598-024-58963-2"
+  ],
+  "title": "Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11001922/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "kedar-balance-integration",
+  "dois": [],
+  "title": "Opentrons OT-2 mass-balance integration (application note supplement)",
+  "paper_url": "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance",
+  "known_code": [
+   "https://github.com/Kedar-Materials-by-Design-Lab/opentrons-balance"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "kitfree-rna-extraction",
+  "dois": [
+   "10.1038/s41598-021-02742-w"
+  ],
+  "title": "A high-throughput pipeline for scalable kit-free RNA extraction",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8636496/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "labdroid-phenol-chloroform",
+  "dois": [
+   "10.12688/f1000research.109251.1"
+  ],
+  "title": "Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8931447/",
+  "known_code": [
+   "https://doi.org/10.5281/zenodo.5733820"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "CC-BY-4.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "lego-lhr-stem",
+  "dois": [
+   "10.1371/journal.pbio.2001413"
+  ],
+  "title": "Liquid-handling Lego robots and experiments for STEM education and research",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5360201/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "maple-fly-robot",
+  "dois": [
+   "10.7554/eLife.37166"
+  ],
+  "title": "MAPLE (modular automated platform for large-scale experiments), a robot for integrated organism-handling and phenotyping",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6193762/",
+  "known_code": [
+   "https://github.com/FlySorterLLC/MAPLEControlSoftware"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "not checked",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "marchantia-agro-transformation",
+  "dois": [
+   "10.1111/tpj.70118"
+  ],
+  "title": "Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11993085/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "miniaturized-16s-mosquito",
+  "dois": [
+   "10.1128/mSystems.00166-18"
+  ],
+  "title": "High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6222042/",
+  "known_code": [
+   "https://www.protocols.io/view/high-throughput-miniaturized-16s-rrna-amplicon-lib-u2ieyce"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "protocols.io (CC-BY)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "mngs-384-miniaturized",
+  "dois": [
+   "10.1371/journal.pone.0206194"
+  ],
+  "title": "Miniaturization and optimization of 384-well compatible RNA sequencing library preparation",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6328170/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "mobile-robot-burger-2020",
+  "dois": [
+   "10.1038/s41586-020-2442-2"
+  ],
+  "title": "A mobile robotic chemist (Burger et al.)",
+  "paper_url": "https://www.nature.com/articles/s41586-020-2442-2",
+  "known_code": [
+   "none public (ROS code not released)"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "plate_transport",
+  "code_licence": "n/a",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "mxene-aerogel-al",
+  "dois": [
+   "10.1038/s41467-024-49011-8"
+  ],
+  "title": "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11144242/",
+  "known_code": [
+   "https://github.com/oshin71/Programmable-MXene-Aerogel"
+  ],
+  "found_by": [
+   "amass",
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none (data Zenodo BSD-3-Clause-Clear)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "newcastle-neg-opentrons",
+  "dois": [],
+  "title": "Newcastle Network Ecology Group OT-2 protocol and labware collection",
+  "paper_url": "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons",
+  "known_code": [
+   "https://github.com/NewcastleUni-NetworkEcologyGroup/Opentrons"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "nfkb-luciferase-ot2",
+  "dois": [
+   "10.1016/j.slast.2024.100155"
+  ],
+  "title": "Luciferase reporter assay for NF-kB activation automated by an open-source liquid handling platform",
+  "paper_url": "https://doi.org/10.1016/j.slast.2024.100155",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "opentrons-physicalai-hf",
+  "dois": [],
+  "title": "Opentrons/PhysicalAI (Hugging Face dataset of Flex teleoperation episodes)",
+  "paper_url": "https://huggingface.co/datasets/Opentrons/PhysicalAI",
+  "known_code": [
+   "https://huggingface.co/datasets/Opentrons/PhysicalAI"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "flex",
+  "code_licence": "unstated",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "ot2eye",
+  "dois": [
+   "10.1016/j.slast.2026.100410"
+  ],
+  "title": "OT2Eye: Detection of labware conditions to monitor and extend affordable liquid-handling robots",
+  "paper_url": "https://doi.org/10.1016/j.slast.2026.100410",
+  "known_code": [
+   "https://github.com/bioinfo-tsukuba/ot2eye"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pipette-show",
+  "dois": [
+   "10.1021/acssynbio.1c00494"
+  ],
+  "title": "Pipette Show: An Open Source Web Application to Support Pipetting into Microplates",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acssynbio.1c00494",
+  "known_code": [
+   "https://github.com/Global-Biofoundries-Alliance/pipette-show"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "plastic-substitutes-al",
+  "dois": [
+   "10.1038/s41565-024-01635-z"
+  ],
+  "title": "Machine intelligence-accelerated discovery of all-natural plastic substitutes",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11186784/",
+  "known_code": [
+   "https://github.com/chentl/MatAL"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "BSD",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "polymer-protein-hybrids",
+  "dois": [
+   "10.1002/adma.202201809"
+  ],
+  "title": "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids",
+  "paper_url": "https://onlinelibrary.wiley.com/doi/10.1002/adma.202201809",
+  "known_code": [
+   "https://github.com/webbtheosim/PPH_public"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "pr-pr",
+  "dois": [
+   "10.1021/sb4001728"
+  ],
+  "title": "PR-PR: cross-platform laboratory automation system",
+  "paper_url": "https://doi.org/10.1021/sb4001728",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "tecan",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "protein-corona-ot2",
+  "dois": [
+   "10.1007/s00216-020-02726-1"
+  ],
+  "title": "Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7483600/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "proteoautonet",
+  "dois": [
+   "10.1038/s41467-026-68484-3"
+  ],
+  "title": "ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning",
+  "paper_url": "https://doi.org/10.1038/s41467-026-68484-3",
+  "known_code": [
+   "https://github.com/guomics-lab/ProteoAutoNet"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "radiolabeling-psma-ot2",
+  "dois": [
+   "10.1002/jlcr.4085"
+  ],
+  "title": "Automated radiolabeling and handling of 177 Lu- and 225 Ac-PSMA-617 using a robotic pipettor",
+  "paper_url": "https://doi.org/10.1002/jlcr.4085",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sdl-nano-acsnano",
+  "dois": [
+   "10.1021/acsnano.4c17504"
+  ],
+  "title": "A Self-Driving Lab for Nano- and Advanced Materials Synthesis",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/acsnano.4c17504",
+  "known_code": [
+   "none found"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "synthesis",
+  "code_licence": "n/a",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "snails-slow-pipetting",
+  "dois": [
+   "10.1186/s12864-021-07500-w"
+  ],
+  "title": "Consistent ultra-long DNA sequencing with automated slow pipetting",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7953553/",
+  "known_code": [
+   "https://github.com/dholab/SNAILS"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "none",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "sp3-magbead-protocol-repo",
+  "dois": [],
+  "title": "Automated magnetic bead-based digestion protocols for Opentrons OT-2 (proteomics CNB-CBM)",
+  "paper_url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol",
+  "known_code": [
+   "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "summit-flow",
+  "dois": [
+   "10.1002/cmtd.202000051"
+  ],
+  "title": "Summit: benchmarking machine learning methods for reaction optimisation",
+  "paper_url": "https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmtd.202000051",
+  "known_code": [
+   "https://github.com/sustainable-processes/summit"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "MIT",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "swabseq-flex",
+  "dois": [
+   "10.1016/j.diagmicrobio.2026.117519"
+  ],
+  "title": "Automated implementation of the SwabSeq COVID-19 diagnostic assay on the opentrons flex liquid-handling robot",
+  "paper_url": "https://doi.org/10.1016/j.diagmicrobio.2026.117519",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "flex",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "synthetic-cells-robotics",
+  "dois": [
+   "10.1002/adbi.202400671"
+  ],
+  "title": "Scaling Up Synthetic Cell Production Using Robotics and Machine Learning Toward Therapeutic Applications",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12078883/",
+  "known_code": [
+   "https://github.com/IdoGalil/syn-cells-classification"
+  ],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "tecan",
+  "code_licence": "unknown (repo not found)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "takahashi-turbidostat",
+  "dois": [
+   "10.1021/sb500165g"
+  ],
+  "title": "A low cost, customizable turbidostat for use in synthetic circuit characterization",
+  "paper_url": "https://pubs.acs.org/doi/10.1021/sb500165g",
+  "known_code": [
+   "https://github.com/Flexostat/Flexostat-interface"
+  ],
+  "found_by": [
+   "nonlh"
+  ],
+  "readiness": "no",
+  "robot_platform": "bioreactor",
+  "code_licence": "unverified",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "tox-pipetting-robot",
+  "dois": [
+   "10.1371/journal.pone.0179636"
+  ],
+  "title": "A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays",
+  "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5473567/",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "transfection-reagent-agnostic",
+  "dois": [
+   "10.1002/cpz1.968"
+  ],
+  "title": "A Novel, Fully Automated, and Reagent-Agnostic Transient Transfection Protocol",
+  "paper_url": "https://doi.org/10.1002/cpz1.968",
+  "known_code": [],
+  "found_by": [
+   "amass"
+  ],
+  "readiness": "no",
+  "robot_platform": "other",
+  "code_licence": "n/a (no repo)",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ },
+ {
+  "slug": "xchem-opentrons",
+  "dois": [],
+  "title": "XChem Opentrons reaction liquid-handling toolkit",
+  "paper_url": "https://github.com/xchem/opentrons",
+  "known_code": [
+   "https://github.com/xchem/opentrons"
+  ],
+  "found_by": [
+   "web"
+  ],
+  "readiness": "no",
+  "robot_platform": "ot2",
+  "code_licence": "Apache-2.0",
+  "simulator": "not run",
+  "origin": [
+   "expansion search 2026-10-12 (experimental)"
+  ]
+ }
+]
diff --git a/sources/experimental/sp3-magbead-protocol-repo/record.json b/sources/experimental/sp3-magbead-protocol-repo/record.json
new file mode 100644
index 0000000..de2c332
--- /dev/null
+++ b/sources/experimental/sp3-magbead-protocol-repo/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/sp3-magbead-protocol-repo/proteomicscnbcbm__SP3-Magnetic-Beads-Digestion-Protocol",
+   "commit": "75e666ba89eb8546d9351aefc104629b04ed608a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "yes",
+   "repo": "proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol",
+   "robot_mentions": [],
+   "size_kb": 6186,
+   "status": "cloned",
+   "url": "https://github.com/proteomicscnbcbm/SP3-Magnetic-Beads-Digestion-Protocol"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/sp3-magbead-protocol-repo",
+ "title": "Automated magnetic bead-based digestion protocols for Opentrons OT-2 (proteomics CNB-CBM)",
+ "year": ""
+}
diff --git a/sources/experimental/spatial-tx-bravo/record.json b/sources/experimental/spatial-tx-bravo/record.json
new file mode 100644
index 0000000..c0cd20a
--- /dev/null
+++ b/sources/experimental/spatial-tx-bravo/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/spatial-tx-bravo/jemten__Bravo_ST",
+   "commit": "4a8a1a9f8626d00d521ad95334b266d5dca3b0b7",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 0,
+   "redistributable": "no",
+   "repo": "jemten/Bravo_ST",
+   "robot_mentions": [],
+   "size_kb": 34,
+   "status": "cloned",
+   "url": "https://github.com/jemten/Bravo_ST"
+  }
+ ],
+ "doi_primary": "10.1186/s12864-020-6631-z",
+ "dois": [
+  "10.1186/s12864-020-6631-z"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 27,
+  "source": "europepmc:PMC7158132"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3893058,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "1f228f14b79a12016a274bd66f1fba5f102d6eebd2060b02dd73d8adfbf7feea",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": false,
+    "url": "https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-020-6631-z"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7158132?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7158132.1/PMC7158132.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7158132.1/PMC7158132.1.pdf"
+ },
+ "pmcid": "PMC7158132",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/spatial-tx-bravo",
+ "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues",
+ "year": "2020"
+}
diff --git a/sources/experimental/star-hardwarex/record.json b/sources/experimental/star-hardwarex/record.json
new file mode 100644
index 0000000..d0b0010
--- /dev/null
+++ b/sources/experimental/star-hardwarex/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/star-hardwarex/zenodo-10048123",
+   "files": 1,
+   "files_downloaded": 1,
+   "files_skipped_size": [],
+   "host": "doi.org",
+   "licence": "cc-by-4.0",
+   "opentrons_py_files": 0,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "zenodo:10048123",
+   "robot_mentions": [],
+   "size_kb": 9785,
+   "status": "downloaded",
+   "url": "https://doi.org/10.5281/zenodo.10048123"
+  }
+ ],
+ "doi_primary": "10.1016/j.ohx.2024.e00524",
+ "dois": [
+  "10.1016/j.ohx.2024.e00524"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 20,
+  "source": "europepmc:PMC11022082"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 7107418,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "0f1a2cb3fa2b6f28bd3c544ad0f69f7ac76f365daee716251db7a5a07f9f75b6",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC11022082?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11022082.1/PMC11022082.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC11022082.1/PMC11022082.1.pdf"
+ },
+ "pmcid": "PMC11022082",
+ "readiness": "partial",
+ "robot_platform": "plate_transport",
+ "simulator": "not run",
+ "slug": "experimental/star-hardwarex",
+ "title": "Sequential Treatment Application Robot (STAR) for high-replication marine experimentation",
+ "year": "2024"
+}
diff --git a/sources/experimental/summit-flow/record.json b/sources/experimental/summit-flow/record.json
new file mode 100644
index 0000000..fddb6f6
--- /dev/null
+++ b/sources/experimental/summit-flow/record.json
@@ -0,0 +1,59 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/summit-flow/sustainable-processes__summit",
+   "commit": "1de682d05e97adcfb96cd8376e876cef2d6160d3",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 51,
+   "redistributable": "yes",
+   "repo": "sustainable-processes/summit",
+   "robot_mentions": [],
+   "size_kb": 49710,
+   "status": "cloned",
+   "url": "https://github.com/sustainable-processes/summit"
+  }
+ ],
+ "dois": [
+  "10.1002/cmtd.202000051"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1002/cmtd.202000051:\n  europepmc: no Europe PMC full text for this DO",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/cmtd.202000051"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/summit-flow",
+ "title": "Summit: benchmarking machine learning methods for reaction optimisation",
+ "year": ""
+}
diff --git a/sources/experimental/swabseq-flex/record.json b/sources/experimental/swabseq-flex/record.json
new file mode 100644
index 0000000..580689b
--- /dev/null
+++ b/sources/experimental/swabseq-flex/record.json
@@ -0,0 +1,35 @@
+{
+ "code": [],
+ "doi_primary": "10.1016/j.diagmicrobio.2026.117519",
+ "dois": [
+  "10.1016/j.diagmicrobio.2026.117519"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1016/j.diagmicrobio.2026.117519:\n  europepmc: no Europe PMC full text",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/swabseq-flex",
+ "title": "Automated implementation of the SwabSeq COVID-19 diagnostic assay on the opentrons flex liquid-handling robot",
+ "year": "2026"
+}
diff --git a/sources/experimental/synthetic-cells-robotics/record.json b/sources/experimental/synthetic-cells-robotics/record.json
new file mode 100644
index 0000000..165568c
--- /dev/null
+++ b/sources/experimental/synthetic-cells-robotics/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/synthetic-cells-robotics/IdoGalil__syn-cells-classification",
+   "commit": "8c9de52560dc6cb2be23b0f8dd8c853c7576b7d5",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 0,
+   "py_files": 3,
+   "redistributable": "no",
+   "repo": "IdoGalil/syn-cells-classification",
+   "robot_mentions": [],
+   "size_kb": 64194,
+   "status": "cloned",
+   "url": "https://github.com/IdoGalil/syn-cells-classification"
+  }
+ ],
+ "doi_primary": "10.1002/adbi.202400671",
+ "dois": [
+  "10.1002/adbi.202400671"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 9,
+  "sections": 19,
+  "source": "europepmc:PMC12078883"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 3776531,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "dff01b8c236f4f0a0267adf57715217a6b240229fd9524e921d8f5d9b226b1f0",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12078883?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12078883.1/PMC12078883.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12078883.1/PMC12078883.1.pdf"
+ },
+ "pmcid": "PMC12078883",
+ "readiness": "no",
+ "robot_platform": "tecan",
+ "simulator": "not run",
+ "slug": "experimental/synthetic-cells-robotics",
+ "title": "Scaling Up Synthetic Cell Production Using Robotics and Machine Learning Toward Therapeutic Applications",
+ "year": "2025"
+}
diff --git a/sources/experimental/takahashi-turbidostat/record.json b/sources/experimental/takahashi-turbidostat/record.json
new file mode 100644
index 0000000..cc1f410
--- /dev/null
+++ b/sources/experimental/takahashi-turbidostat/record.json
@@ -0,0 +1,77 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/takahashi-turbidostat/Flexostat__Flexostat-interface",
+   "commit": "f5097f4f0571766d13a3009691352923b25b1d4d",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "BSD-3-Clause",
+   "opentrons_py_files": 0,
+   "py_files": 23,
+   "redistributable": "yes",
+   "repo": "Flexostat/Flexostat-interface",
+   "robot_mentions": [],
+   "size_kb": 125,
+   "status": "cloned",
+   "url": "https://github.com/Flexostat/Flexostat-interface"
+  }
+ ],
+ "doi_primary": "10.1021/sb500165g",
+ "dois": [
+  "10.1021/sb500165g"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 13,
+  "source": "europepmc:PMC4304434"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 1665194,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "cc667c14ab478e8f4ffb5dfe7cffb37dfacbd087366e512260fd467f23334bd1",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://pubs.acs.org/doi/pdf/10.1021/sb500165g"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC4304434?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4304434.1/PMC4304434.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4304434.1/PMC4304434.1.pdf"
+ },
+ "pmcid": "PMC4304434",
+ "readiness": "no",
+ "robot_platform": "bioreactor",
+ "simulator": "not run",
+ "slug": "experimental/takahashi-turbidostat",
+ "title": "A low cost, customizable turbidostat for use in synthetic circuit characterization",
+ "year": "2015"
+}
diff --git a/sources/experimental/tape-organoid-barcoding/record.json b/sources/experimental/tape-organoid-barcoding/record.json
new file mode 100644
index 0000000..39f7aa6
--- /dev/null
+++ b/sources/experimental/tape-organoid-barcoding/record.json
@@ -0,0 +1,76 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.10"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/tape-organoid-barcoding/TAPE-Lab__OT-2_Code",
+   "commit": "8e8b387d53d99447331280a84adebae11062a21e",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 7,
+   "py_files": 7,
+   "redistributable": "no",
+   "repo": "TAPE-Lab/OT-2_Code",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 164,
+   "status": "cloned",
+   "url": "https://github.com/TAPE-Lab/OT-2_Code"
+  }
+ ],
+ "doi_primary": "10.1038/s41592-020-0737-8",
+ "dois": [
+  "10.1038/s41592-020-0737-8"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 6,
+  "sections": 32,
+  "source": "europepmc:PMC7060080"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 3802066,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "e354411bdbb5f768ee1f1dd7a91fafc6211d1332c019473ab32519123848515f",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC7060080?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7060080.1/PMC7060080.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC7060080.1/PMC7060080.1.pdf"
+ },
+ "pmcid": "PMC7060080",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/tape-organoid-barcoding",
+ "title": "Cell-type-specific signaling networks in heterocellular organoids (TOBis barcoding / robotic organoid extraction)",
+ "year": "2020"
+}
diff --git a/sources/experimental/teemi/record.json b/sources/experimental/teemi/record.json
new file mode 100644
index 0000000..916fe9a
--- /dev/null
+++ b/sources/experimental/teemi/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/teemi/hiyama341__teemi",
+   "commit": "b330c661ac62b62e33f7f0341b036eddd520591e",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 65,
+   "redistributable": "yes",
+   "repo": "hiyama341/teemi",
+   "robot_mentions": [],
+   "size_kb": 123786,
+   "status": "cloned",
+   "url": "https://github.com/hiyama341/teemi"
+  }
+ ],
+ "doi_primary": "10.1371/journal.pcbi.1011929",
+ "dois": [
+  "10.1371/journal.pcbi.1011929"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 26,
+  "source": "europepmc:PMC10954146"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc0",
+ "pdf": {
+  "bytes": 1610804,
+  "licence": "cc0",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "3146615d2d0d3a6c92977f63688aa91f9981dbea6d08bba1a06fd9845bc7f301",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC10954146?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10954146.1/PMC10954146.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10954146.1/PMC10954146.1.pdf"
+ },
+ "pmcid": "PMC10954146",
+ "readiness": "partial",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/teemi",
+ "title": "teemi: open-source literate programming for iterative DBTL cycles",
+ "year": "2024"
+}
diff --git a/sources/experimental/tidytron/record.json b/sources/experimental/tidytron/record.json
new file mode 100644
index 0000000..b0808b3
--- /dev/null
+++ b/sources/experimental/tidytron/record.json
@@ -0,0 +1,74 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.2"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/tidytron/PlantSynBioLab__TidyTron",
+   "commit": "4d27169b53e8fb974aed01cd7d41d30666e9d9ca",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 37,
+   "py_files": 37,
+   "redistributable": "yes",
+   "repo": "PlantSynBioLab/TidyTron",
+   "robot_mentions": [],
+   "size_kb": 77,
+   "status": "cloned",
+   "url": "https://github.com/PlantSynBioLab/TidyTron"
+  }
+ ],
+ "doi_primary": "10.1016/j.slast.2023.08.007",
+ "dois": [
+  "10.1016/j.slast.2023.08.007"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass",
+  "web"
+ ],
+ "fulltext": {
+  "legends": 5,
+  "sections": 18,
+  "source": "europepmc:PMC12212179"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 1039076,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "5ccd726aa4f461904c93b6f9b151342d11dfdef315e38a0fee9874031dbda2b0",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12212179?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12212179.1/PMC12212179.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12212179.1/PMC12212179.1.pdf"
+ },
+ "pmcid": "PMC12212179",
+ "readiness": "ready",
+ "robot_platform": "ot2",
+ "simulator": "partly_verified",
+ "slug": "experimental/tidytron",
+ "title": "TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 robots",
+ "year": "2024"
+}
diff --git a/sources/experimental/tmt-bead-platform-ot2/record.json b/sources/experimental/tmt-bead-platform-ot2/record.json
new file mode 100644
index 0000000..a163e9b
--- /dev/null
+++ b/sources/experimental/tmt-bead-platform-ot2/record.json
@@ -0,0 +1,66 @@
+{
+ "code": [],
+ "doi_primary": "10.1021/jasms.1c00077",
+ "dois": [
+  "10.1021/jasms.1c00077"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1021/jasms.1c00077:\n  europepmc: Server error '500 ' for url 'https:/",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC8210952?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8210952.1/PMC8210952.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8210952.2/PMC8210952.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC8210952.3/PMC8210952.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8210952&blobtype=pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC8210952",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/tmt-bead-platform-ot2",
+ "title": "A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation",
+ "year": "2021"
+}
diff --git a/sources/experimental/tox-pipetting-robot/record.json b/sources/experimental/tox-pipetting-robot/record.json
new file mode 100644
index 0000000..c863438
--- /dev/null
+++ b/sources/experimental/tox-pipetting-robot/record.json
@@ -0,0 +1,53 @@
+{
+ "code": [],
+ "doi_primary": "10.1371/journal.pone.0179636",
+ "dois": [
+  "10.1371/journal.pone.0179636"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "legends": 7,
+  "sections": 24,
+  "source": "europepmc:PMC5473567"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by",
+ "pdf": {
+  "bytes": 7520186,
+  "licence": "cc by",
+  "pages": null,
+  "redistributable": "yes",
+  "sha256": "5713716a8d29be0f79160e9f8c45dd35751ea141d1d18b5a2050f21339f55bae",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC5473567?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5473567.1/PMC5473567.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5473567.1/PMC5473567.1.pdf"
+ },
+ "pmcid": "PMC5473567",
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/tox-pipetting-robot",
+ "title": "A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays",
+ "year": "2017"
+}
diff --git a/sources/experimental/transfection-reagent-agnostic/record.json b/sources/experimental/transfection-reagent-agnostic/record.json
new file mode 100644
index 0000000..cccb4c3
--- /dev/null
+++ b/sources/experimental/transfection-reagent-agnostic/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [],
+ "doi_primary": "10.1002/cpz1.968",
+ "dois": [
+  "10.1002/cpz1.968"
+ ],
+ "experimental": true,
+ "found_by": [
+  "amass"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1002/cpz1.968:\n  europepmc: no Europe PMC full text for this DOI\nDown",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.968"
+   }
+  ]
+ },
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "other",
+ "simulator": "not run",
+ "slug": "experimental/transfection-reagent-agnostic",
+ "title": "A Novel, Fully Automated, and Reagent-Agnostic Transient Transfection Protocol",
+ "year": "2024"
+}
diff --git a/sources/experimental/trypanosomatid-drug-combo-ot2/record.json b/sources/experimental/trypanosomatid-drug-combo-ot2/record.json
new file mode 100644
index 0000000..1d9c390
--- /dev/null
+++ b/sources/experimental/trypanosomatid-drug-combo-ot2/record.json
@@ -0,0 +1,42 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.11"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/trypanosomatid-drug-combo-ot2/FranAguero07__OT2_protocols",
+   "commit": "d486548b3c150c711e772099e74395efbd931b7a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 3,
+   "py_files": 3,
+   "redistributable": "no",
+   "repo": "FranAguero07/OT2_protocols",
+   "robot_mentions": [],
+   "size_kb": 53624,
+   "status": "cloned",
+   "url": "https://github.com/FranAguero07/OT2_protocols"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/trypanosomatid-drug-combo-ot2",
+ "title": "OT-2 protocols for drug combination screening (Trypanosomatics Lab, UNSAM)",
+ "year": ""
+}
diff --git a/sources/experimental/ufdutton-16s-flex/record.json b/sources/experimental/ufdutton-16s-flex/record.json
new file mode 100644
index 0000000..f8b3698
--- /dev/null
+++ b/sources/experimental/ufdutton-16s-flex/record.json
@@ -0,0 +1,49 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.19",
+    "2.20",
+    "2.22",
+    "2.28",
+    "2.30"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/ufdutton-16s-flex/UFDuttonLab__lab_automation_opentrons",
+   "commit": "285832b280049f76a10168eaee6c9503d3e7542d",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 17,
+   "py_files": 17,
+   "redistributable": "no",
+   "repo": "UFDuttonLab/lab_automation_opentrons",
+   "robot_mentions": [
+    "Flex",
+    "OT-2"
+   ],
+   "size_kb": 255,
+   "status": "cloned",
+   "url": "https://github.com/UFDuttonLab/lab_automation_opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/ufdutton-16s-flex",
+ "title": "UF Dutton Lab Opentrons 16S microbiome workflow (OT-2 + Flex)",
+ "year": ""
+}
diff --git a/sources/experimental/vadr-vacuum-miniprep-flex/record.json b/sources/experimental/vadr-vacuum-miniprep-flex/record.json
new file mode 100644
index 0000000..8b76383
--- /dev/null
+++ b/sources/experimental/vadr-vacuum-miniprep-flex/record.json
@@ -0,0 +1,69 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.23"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/vadr-vacuum-miniprep-flex/JackATDalton__VADR",
+   "commit": "7a814dd871cf87495621dcf49c88d9b2019c34ec",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "none",
+   "opentrons_py_files": 1,
+   "py_files": 1,
+   "redistributable": "no",
+   "repo": "JackATDalton/VADR",
+   "robot_mentions": [
+    "Flex"
+   ],
+   "size_kb": 2721,
+   "status": "cloned",
+   "url": "https://github.com/JackATDalton/VADR"
+  }
+ ],
+ "doi_primary": "10.64898/2026.09.16.746974",
+ "dois": [
+  "10.64898/2026.09.16.746974"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "legends": 3,
+  "sections": 32,
+  "source": "biorxiv"
+ },
+ "journal": "bioRxiv",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "bytes": 19695399,
+  "licence": "",
+  "pages": null,
+  "redistributable": "unknown",
+  "sha256": "16f4f0d2b8eb2119cb8f45dd1c64580b44ddc9887e44bd4aca345f88be154207",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.full.pdf"
+   }
+  ],
+  "url": "https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.full.pdf"
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "flex",
+ "simulator": "not run",
+ "slug": "experimental/vadr-vacuum-miniprep-flex",
+ "title": "An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2",
+ "year": "2026"
+}
diff --git a/sources/experimental/viscous-liquid-bo-ot2/record.json b/sources/experimental/viscous-liquid-bo-ot2/record.json
new file mode 100644
index 0000000..d683857
--- /dev/null
+++ b/sources/experimental/viscous-liquid-bo-ot2/record.json
@@ -0,0 +1,52 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/viscous-liquid-bo-ot2/Quijanove__LiqTransferOptimizer",
+   "commit": "88717ac7aff1ca54efb148d8c5b281ccb6d8909a",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 1,
+   "py_files": 13,
+   "redistributable": "yes",
+   "repo": "Quijanove/LiqTransferOptimizer",
+   "robot_mentions": [],
+   "size_kb": 1961,
+   "status": "cloned",
+   "url": "https://github.com/Quijanove/LiqTransferOptimizer"
+  }
+ ],
+ "dois": [
+  "10.1039/d3dd00255a"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1039/d3dd00255a:\n  europepmc: no Europe PMC full text for this DOI\nDo",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": []
+ },
+ "pmcid": null,
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/viscous-liquid-bo-ot2",
+ "title": "Optimization of liquid handling parameters for viscous liquid transfers with pipetting robots, a sticky situation",
+ "year": ""
+}
diff --git a/sources/experimental/worm-food-preference/record.json b/sources/experimental/worm-food-preference/record.json
new file mode 100644
index 0000000..9402395
--- /dev/null
+++ b/sources/experimental/worm-food-preference/record.json
@@ -0,0 +1,95 @@
+{
+ "code": [
+  {
+   "api_levels": [
+    "2.16"
+   ],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/worm-food-preference/slhogle__c_elegans_food_preference_protocol",
+   "commit": "dec0ae98e41a4582bc573ad9ce91e05c90c38fe1",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "GPL-3.0",
+   "opentrons_py_files": 2,
+   "py_files": 2,
+   "redistributable": "no",
+   "repo": "slhogle/c_elegans_food_preference_protocol",
+   "robot_mentions": [
+    "OT-2"
+   ],
+   "size_kb": 216,
+   "status": "cloned",
+   "url": "https://github.com/slhogle/c_elegans_food_preference_protocol"
+  }
+ ],
+ "doi_primary": "10.1242/jeb.01955",
+ "dois": [
+  "10.1242/jeb.01955"
+ ],
+ "experimental": true,
+ "found_by": [
+  "github",
+  "web"
+ ],
+ "fulltext": {
+  "error": "RuntimeError: Could not get full text for 10.1242/jeb.01955:\n  europepmc: Server error '500 ' for url 'https://www",
+  "source": null
+ },
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pdf": {
+  "licence": "",
+  "redistributable": "unknown",
+  "status": "paywalled_or_not_found",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC1352325?pdf=render"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC1352325.1/PMC1352325.1.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC1352325.2/PMC1352325.2.pdf"
+   },
+   {
+    "http": 404,
+    "manual": false,
+    "ok": false,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC1352325.3/PMC1352325.3.pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1352325&blobtype=pdf"
+   },
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "http://journals.biologists.com/jeb/article-pdf/209/1/89/1255771/89.pdf"
+   }
+  ]
+ },
+ "pmcid": "PMC1352325",
+ "readiness": "partial",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/worm-food-preference",
+ "title": "C. elegans food preference protocol (bacteria and worm spotting on OT-2)",
+ "year": "2006"
+}
diff --git a/sources/experimental/xchem-opentrons/record.json b/sources/experimental/xchem-opentrons/record.json
new file mode 100644
index 0000000..bdd7123
--- /dev/null
+++ b/sources/experimental/xchem-opentrons/record.json
@@ -0,0 +1,40 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/xchem-opentrons/xchem__opentrons",
+   "commit": "3cc288e567414f25813d7ace26cbf643348ce321",
+   "default_branch": "master",
+   "host": "github.com",
+   "licence": "Apache-2.0",
+   "opentrons_py_files": 114,
+   "py_files": 125,
+   "redistributable": "yes",
+   "repo": "xchem/opentrons",
+   "robot_mentions": [],
+   "size_kb": 202,
+   "status": "cloned",
+   "url": "https://github.com/xchem/opentrons"
+  }
+ ],
+ "dois": [],
+ "experimental": true,
+ "found_by": [
+  "web"
+ ],
+ "journal": "",
+ "note": "",
+ "open_access": false,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "",
+ "pmcid": null,
+ "readiness": "no",
+ "robot_platform": "ot2",
+ "simulator": "not run",
+ "slug": "experimental/xchem-opentrons",
+ "title": "XChem Opentrons reaction liquid-handling toolkit",
+ "year": ""
+}
diff --git a/sources/experimental/zhao-autonomous-enzyme/record.json b/sources/experimental/zhao-autonomous-enzyme/record.json
new file mode 100644
index 0000000..5f56e36
--- /dev/null
+++ b/sources/experimental/zhao-autonomous-enzyme/record.json
@@ -0,0 +1,71 @@
+{
+ "code": [
+  {
+   "api_levels": [],
+   "archived": false,
+   "cache_path": "~/.cache/text2wetlab-ingest/code/experimental/zhao-autonomous-enzyme/Zhao-Group__closed-loop",
+   "commit": "9eb76ba84c2f639bfb36ede2651292cd9cd20af2",
+   "default_branch": "main",
+   "host": "github.com",
+   "licence": "MIT",
+   "opentrons_py_files": 0,
+   "py_files": 26,
+   "redistributable": "yes",
+   "repo": "Zhao-Group/closed-loop",
+   "robot_mentions": [],
+   "size_kb": 88,
+   "status": "cloned",
+   "url": "https://github.com/Zhao-Group/closed-loop"
+  }
+ ],
+ "doi_primary": "10.1038/s41467-025-61209-y",
+ "dois": [
+  "10.1038/s41467-025-61209-y"
+ ],
+ "experimental": true,
+ "found_by": [
+  "nonlh"
+ ],
+ "fulltext": {
+  "legends": 4,
+  "sections": 27,
+  "source": "europepmc:PMC12215622"
+ },
+ "journal": "",
+ "note": "",
+ "open_access": true,
+ "origin": [
+  "expansion search 2026-10-12 (experimental)"
+ ],
+ "paper_licence": "cc by-nc-nd",
+ "pdf": {
+  "bytes": 2511419,
+  "licence": "cc by-nc-nd",
+  "pages": null,
+  "redistributable": "no",
+  "sha256": "5dd3a003650325b8ea937647c634c3e21d0eaf490ea5a7d0443fd7ef8aae46d5",
+  "status": "downloaded",
+  "tried": [
+   {
+    "http": 403,
+    "manual": false,
+    "ok": false,
+    "url": "https://europepmc.org/articles/PMC12215622?pdf=render"
+   },
+   {
+    "http": 200,
+    "manual": false,
+    "ok": true,
+    "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12215622.1/PMC12215622.1.pdf"
+   }
+  ],
+  "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12215622.1/PMC12215622.1.pdf"
+ },
+ "pmcid": "PMC12215622",
+ "readiness": "partial",
+ "robot_platform": "scheduling",
+ "simulator": "not run",
+ "slug": "experimental/zhao-autonomous-enzyme",
+ "title": "A generalized platform for artificial intelligence-powered autonomous enzyme engineering (iBioFAB)",
+ "year": "2025"
+}