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Provenance registry of datasets, outcome models and simulators linked to each task #65

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# Datasets, outcome models and simulators linked to each task

Generated by `scripts/check_linked_resources.py` from `sources/linked_resources.json`. Links and metadata only;
nothing third-party is stored here. **Direct** = from the task's own source paper; **related** = same method, different study.
"Pinned" is what the host reported on the checked date (Zenodo checksum count, Hugging Face or GitHub commit, PyPI version).

Found: Web search plus Zenodo, Hugging Face, PyPI, Crossref and GitHub API queries, 2026-10-13.

## `a1-a12-100ul`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [LiqTransferOptimizer](https://doi.org/10.5281/zenodo.10847234) | dataset, outcome_model | related | Code and collected data for optimising liquid-handling parameters for viscous liquid transfers on pipetting robots (gravimetric transfer accuracy). | mit-license | yes | v1.0.0 | 2026-10-13 |
| [labos-sim/real_human_pipetting_lerobot_anonymized](https://huggingface.co/datasets/labos-sim/real_human_pipetting_lerobot_anonymized) | dataset | related | Multi-camera recordings of humans pipetting, with success/failure annotations (LeRobot format). | not stated | unknown | 56972c4038 | 2026-10-13 |
| [lerobotForScienceEdu/AgarBadge_v1_1st_Liquid-Handling_100_20251203](https://huggingface.co/datasets/lerobotForScienceEdu/AgarBadge_v1_1st_Liquid-Handling_100_20251203) | dataset | related | Robot liquid-handling demonstrations in LeRobot format. | apache-2.0 | yes | 9cd05b4950 | 2026-10-13 |

## `colony-pcr-screening`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [pydna](https://github.com/pydna-group/pydna) | outcome_model | related | In-silico PCR (primers + template -> product), restriction digestion, ligation, Gibson and Golden Gate assembly. | BSD | yes | v5.5.16 | 2026-10-13 |
| [Sequence-specific PCR amplification efficiency prediction (1D CNN)](https://doi.org/10.1038/s41467-025-64221-4) | outcome_model | related | Deep-learning model predicting amplification efficiency from sequence in multi-template PCR. | CC BY 4.0 (paper) | unknown | 2025 | 2026-10-13 |
| [PrimerCast](https://github.com/broadinstitute/PrimerCast) | dataset, outcome_model | related | Experimental dataset of primer-target PCR reactions with amplification-efficiency labels (reported as 50,760 reactions) and a predictive model (NeurIPS 2025). | MIT | yes | 50d357b43a | 2026-10-13 |

## `colony-pcr-screening-hard`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [pydna](https://github.com/pydna-group/pydna) | outcome_model | related | In-silico PCR (primers + template -> product), restriction digestion, ligation, Gibson and Golden Gate assembly. | BSD | yes | v5.5.16 | 2026-10-13 |
| [Sequence-specific PCR amplification efficiency prediction (1D CNN)](https://doi.org/10.1038/s41467-025-64221-4) | outcome_model | related | Deep-learning model predicting amplification efficiency from sequence in multi-template PCR. | CC BY 4.0 (paper) | unknown | 2025 | 2026-10-13 |
| [PrimerCast](https://github.com/broadinstitute/PrimerCast) | dataset, outcome_model | related | Experimental dataset of primer-target PCR reactions with amplification-efficiency labels (reported as 50,760 reactions) and a predictive model (NeurIPS 2025). | MIT | yes | 50d357b43a | 2026-10-13 |

## `golden-gate-assembly`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [T4 DNA ligase four-base overhang fidelity profile and NEBridge design tools](https://www.neb.com/en-us/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning/golden-gate-assembly/ligase-fidelity) | dataset, outcome_model | related | Measured ligation frequency for all 256 four-base overhangs; drives tools that predict Golden Gate assembly fidelity for a chosen overhang set (Ligase Fidelity Viewer, GetSet, SplitSet). | ACS AuthorChoice (paper); data in the paper's supporting information | unknown | 2018 | 2026-10-13 |
| [DNA Cauldron](https://github.com/Edinburgh-Genome-Foundry/DnaCauldron) | outcome_model | related | Cloning simulation: given parts and an enzyme, predicts the constructs a Golden Gate (or Gibson, BASIC, BioBrick) assembly yields and reports assembly flaws. | MIT | yes | v2.0.12 | 2026-10-13 |
| [pydna](https://github.com/pydna-group/pydna) | outcome_model | related | In-silico PCR (primers + template -> product), restriction digestion, ligation, Gibson and Golden Gate assembly. | BSD | yes | v5.5.16 | 2026-10-13 |
| [AssemblyTron v0.0.8 archive](https://doi.org/10.5281/zenodo.7250273) | software | direct | The archived release of the code behind the task's source paper. Software, not a results dataset. | Apache-2.0 | yes | v0.0.8 | 2026-10-13 |

## `golden-gate-assembly-hard`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [T4 DNA ligase four-base overhang fidelity profile and NEBridge design tools](https://www.neb.com/en-us/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning/golden-gate-assembly/ligase-fidelity) | dataset, outcome_model | related | Measured ligation frequency for all 256 four-base overhangs; drives tools that predict Golden Gate assembly fidelity for a chosen overhang set (Ligase Fidelity Viewer, GetSet, SplitSet). | ACS AuthorChoice (paper); data in the paper's supporting information | unknown | 2018 | 2026-10-13 |
| [DNA Cauldron](https://github.com/Edinburgh-Genome-Foundry/DnaCauldron) | outcome_model | related | Cloning simulation: given parts and an enzyme, predicts the constructs a Golden Gate (or Gibson, BASIC, BioBrick) assembly yields and reports assembly flaws. | MIT | yes | v2.0.12 | 2026-10-13 |
| [pydna](https://github.com/pydna-group/pydna) | outcome_model | related | In-silico PCR (primers + template -> product), restriction digestion, ligation, Gibson and Golden Gate assembly. | BSD | yes | v5.5.16 | 2026-10-13 |
| [AssemblyTron v0.0.8 archive](https://doi.org/10.5281/zenodo.7250273) | software | direct | The archived release of the code behind the task's source paper. Software, not a results dataset. | Apache-2.0 | yes | v0.0.8 | 2026-10-13 |

## `opentrons-rna-extraction`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [Source paper results: Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection](https://doi.org/10.1371/journal.pone.0246302) | dataset | direct | Ct comparisons of the in-house OT-2 protocol against a commercial kit, reported in the paper. | CC BY 4.0 | yes | 2021 | 2026-10-13 |
| [RNA extraction alternative method for SARS-CoV-2 molecular diagnosis](https://doi.org/10.5281/zenodo.5616875) | dataset | related | Data from a different study evaluating an alternative RNA extraction method for SARS-CoV-2 diagnosis. | cc-by-4.0 | yes | 1 files | 2026-10-13 |
| [Comparison of two RNA extraction methods for the molecular detection of SARS-CoV-2 from nasopharyngeal swab samples](https://doi.org/10.5281/zenodo.6477268) | dataset | related | Raw data of a study comparing two RNA extraction methods. | not stated | unknown | | 2026-10-13 |

## `opentrons-rna-extraction-hard`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [Source paper results: Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection](https://doi.org/10.1371/journal.pone.0246302) | dataset | direct | Ct comparisons of the in-house OT-2 protocol against a commercial kit, reported in the paper. | CC BY 4.0 | yes | 2021 | 2026-10-13 |
| [RNA extraction alternative method for SARS-CoV-2 molecular diagnosis](https://doi.org/10.5281/zenodo.5616875) | dataset | related | Data from a different study evaluating an alternative RNA extraction method for SARS-CoV-2 diagnosis. | cc-by-4.0 | yes | 1 files | 2026-10-13 |
| [Comparison of two RNA extraction methods for the molecular detection of SARS-CoV-2 from nasopharyngeal swab samples](https://doi.org/10.5281/zenodo.6477268) | dataset | related | Raw data of a study comparing two RNA extraction methods. | not stated | unknown | | 2026-10-13 |

## `split-200ul-two-wells`

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [LiqTransferOptimizer](https://doi.org/10.5281/zenodo.10847234) | dataset, outcome_model | related | Code and collected data for optimising liquid-handling parameters for viscous liquid transfers on pipetting robots (gravimetric transfer accuracy). | mit-license | yes | v1.0.0 | 2026-10-13 |
| [labos-sim/real_human_pipetting_lerobot_anonymized](https://huggingface.co/datasets/labos-sim/real_human_pipetting_lerobot_anonymized) | dataset | related | Multi-camera recordings of humans pipetting, with success/failure annotations (LeRobot format). | not stated | unknown | 56972c4038 | 2026-10-13 |
| [lerobotForScienceEdu/AgarBadge_v1_1st_Liquid-Handling_100_20251203](https://huggingface.co/datasets/lerobotForScienceEdu/AgarBadge_v1_1st_Liquid-Handling_100_20251203) | dataset | related | Robot liquid-handling demonstrations in LeRobot format. | apache-2.0 | yes | 9cd05b4950 | 2026-10-13 |

## All tasks (robot-level datasets and simulators)

| Resource | Kind | Relation | What it is | Licence | Redistributable | Pinned | Checked |
|---|---|---|---|---|---|---|---|
| [Opentrons/PhysicalAI](https://huggingface.co/datasets/Opentrons/PhysicalAI) | dataset | related | Opentrons' own robot dataset on Hugging Face (reported as Flex teleoperation episodes). | not stated | unknown | b4d34687f5 | 2026-10-13 |
| [AutoBio](https://huggingface.co/papers/2505.14030) | simulator, dataset | related | MuJoCo-based simulation and benchmark for robot manipulation in a biology lab (pipette aspiration, tube handling, centrifuge loading); task datasets on Hugging Face under autobio-bench. | mit | yes | dcd1ba6d6f | 2026-10-13 |
| [Pipette: embodied simulation platform and benchmark for wet-lab robotics](https://arxiv.org/abs/2606.12936) | simulator | related | Embodied simulation platform with 12 wet-lab tasks (sample handling, instrument interaction, lid operation, alignment). | not stated | unknown | | 2026-10-13 |

## Gaps

- **ecoli-heat-shock-transformation, ecoli-heat-shock-transformation-hard:** No outcome model and no public dataset of transformation efficiency found; only small experimental studies. The APEX paper reports its results in the text with no data deposit recorded.
- **ampure-bead-cleanup:** No quantitative model or dataset for SPRI bead clean-up found; only vendor rules of thumb (bead ratio versus retained fragment size), which vary by bead lot.
- **colony-pcr-screening, colony-pcr-screening-hard:** The Slowpoke paper has no data deposit recorded; the PCR resources listed are for the method in general.
- **all:** Nothing relevant found on Kaggle.

## Notes on individual resources

- **T4 DNA ligase four-base overhang fidelity profile and NEBridge design tools:** Location and format of the raw overhang table not checked; read the supporting information before using it in a grader.
- **DNA Cauldron:** Candidate for outcome-aware grading: does the model's fragment and overhang choice assemble into the intended plasmid?
- **pydna:** Candidate check for colony PCR: do the primers amplify the intended product from the template?
- **AssemblyTron v0.0.8 archive:** Already recorded in sources/assemblytron/record.json.
- **Sequence-specific PCR amplification efficiency prediction (1D CNN):** Code and training-data location not checked.
- **PrimerCast:** Dataset size is from the conference abstract, not counted here.
- **LiqTransferOptimizer:** The closest public data on how accurately a robot delivers a commanded volume, which the Opentrons simulator does not model.
- **Opentrons/PhysicalAI:** No licence stated on the dataset card. Contents not inspected.
- **labos-sim/real_human_pipetting_lerobot_anonymized:** Real-world failure labels: relevant to physical faults a simulator cannot see.
- **AutoBio:** Models robot manipulation, not the biology. arXiv 2505.14030.
- **Pipette: embodied simulation platform and benchmark for wet-lab robotics:** Code location not found.
- **Source paper results: Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection:** Data-availability section and supporting files not opened. The task instruction gives this paper a different title; Crossref's is the one used here.
- **RNA extraction alternative method for SARS-CoV-2 molecular diagnosis:** Not the task's protocol; useful only as outcome data for the same kind of experiment.
- **Comparison of two RNA extraction methods for the molecular detection of SARS-CoV-2 from nasopharyngeal swab samples:** Not the task's protocol. The record exists but lists no public files (restricted or embargoed).
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