RESEARCH USE ONLY - not clinically validated.
Full-stack, autonomous single-cell omics: from "run this assay on N cells" all the way to a result. Cheap, fast, autonomous, with molecule counting (UMIs), aimed at expert-level benchmarks on commodity hardware (Hamilton + PyLabRobot + on-deck thermocycler + BioTek Synergy H1).
Each assay is a self-contained module that runs end to end: purchase, instrument bring-up, liquid-handling readiness, automated execution, and fastq-to-analysis. Everything runs in the PyLabRobot simulator with no hardware attached.
| Module | Assay | Status |
|---|---|---|
autonomous-scRNAseq/ |
FLASH-seq UMI v3 (low-input full-length scRNA-seq + UMIs) | v0.1: 4 stages + Rhodamine B readiness QC + human/humanoid operator + fastq-to-analysis (scanpy), all wired end to end in the PyLabRobot simulator |
autonomous-scWGS/ |
single-cell WGS: ResolveDNA PTA WGA + NEBNext Ultra II (FACS Melody sort up front) | v0.1: sort + WGA + library prep + Rhodamine readiness + human/humanoid operator + BJ-WGS sequencing analysis, end to end in the PyLabRobot simulator (10/10 tests) |
autonomous-scRNAseq/ is the FLASH-seq scRNA-seq pipeline. It delivers, all runnable
with no hardware: procurement (BOM to IDT/browser/PO channels to one human approval),
a printable bench manual, instrument-readiness QC (Rhodamine B pipetting precision on
a Synergy H1), the full FLASH-seq automation in the simulator with QC gates and tacit
guards, a swappable human or humanoid operator, and a fastq-to-analysis pipeline
(bcl2fastq to umi_tools to STAR to featureCounts to umi_tools count to scanpy).
autonomous-scWGS/ is the single-cell whole-genome sequencing pipeline: a BD FACS Melody
sort into ResolveDNA Cell Buffer, ResolveDNA PTA whole-genome amplification, post-WGA
dsDNA QC on the Synergy H1, NEBNext Ultra II library prep (exact SPRI ratios, do-not-
over-dry guards), pool, and a fastq-to-variants analysis via the BaseJumper BJ-WGS
Nextflow pipeline (Sentieon BWA MEM to Dedup to BQSR to DNAScope to SnpEff/ClinVar/dbSNP
to MultiQC). It shares the Rhodamine B readiness QC and human/humanoid operator with the
scRNAseq module. The underlying kits are proprietary (RESEARCH USE ONLY), not CC-BY;
values are sourced from the vendor guides and never invented. The FACS Melody control
plane is being reverse-engineered (owner's TODO); sorting is simulated until wired.
- Procurement - resolve reagents to SKUs, route to IDT API / browser carts / PO, one human approval, schedule the run on lead times.
- Instrument bring-up - controller kit (Raspberry Pi + PyLabRobot) and a connectivity registry that emits exact cabling. Includes reverse-engineering the cell sorter.
- Readiness - Rhodamine B liquid-handling CV check: READY or NEEDS_CALIBRATION.
- Execution - the assay on a Hamilton deck + on-deck thermocycler + Synergy H1.
- Ops - a human or an (experimental) humanoid robot sets up the deck, presses run, collects output.
- Analysis - fastq to count matrix to clustered result (UMI molecule counting).
The single-cell sort (cells into lysis buffer) depends on a BD FACS Melody, which has no open automation API, so programmatic control has to be reverse-engineered. Tracked per module. Nothing about that interface is invented; unknowns stay TODO.
- Never invent a value: source from the protocol; unknowns are
# TODO, OCR-ambiguous items areverify, tuning knobs are# expert-tunable. - One human approval before any purchase; fail closed on readiness.
- Swappable backends: everything runs in simulation with no hardware.
Code: MIT (LICENSE). Each module credits its source protocol under that
protocol's own license (FLASH-seq UMI v3 is CC-BY; see the module's ATTRIBUTION).