Cell protocol compiler

Machine-readable research checklists for three published pluripotent-cell workflows, plus a validator that rejects missing QC gates, absurd well volumes, hood collisions, and small-molecule values outside the window encoded from the paper.

This is a protocol formalization exercise. It is not a lab and it does not authorize one.

Workflows

id	What it abridges	Source
e8_feeder_free_maintenance	Feeder-free maintenance on the academic E8 formulation (Chen 2011), EDTA passage context, ROCK inhibitor for 24 h	10.1038/nmeth.1593
dual_smad_neural	Adherent neural induction, 10 µM SB431542 + 200 ng/mL Noggin, SRM toward N2	10.1038/nbt.1529
giwi_cardiac	Wnt activation then Wnt inhibition. CHIR defaults to 6 µM inside 2–12, not to the paper's 12 µM example	10.1038/nprot.2012.150
hepatocyte_differentiation	4-stage differentiation into functional hepatocyte-like cells: Activin A, BMP4/FGF2, HGF, Oncostatin M / Dex	10.1038/nprot.2012.153

LDN-193189 is a parameter on the neural checklist and defaults to 0. Later protocols use ~100 nM as a substitute for Noggin. This compiler does not stack them.

Non-goals

• GMP batch records, IND text, or biosafety approval
• Instructions for putting cells, genes, or media into a person
• A claim that a concentration inside the published window will work on your line
• Proprietary medium recipes beyond the academic formulation printed in Chen et al. 2011. "Essential 8" is a commercial trademark; the table in this repo is the paper's list

Run

make test
PYTHONPATH=src python3 -m protocolcompiler.cli giwi_cardiac --markdown
PYTHONPATH=src python3 -m protocolcompiler.cli hepatocyte_differentiation --json
PYTHONPATH=src python3 -m protocolcompiler.cli dual_smad_neural

Python 3.10+. No third-party packages.

The validator's feed-gap rule is there because a checklist that skips from day 0 to day 7 without a medium change is how cultures die. It is not a new biological finding.

Where this sits

Pair it with brightfield-colony-qc for a morphology gate and diffmedia-loop when the next plate of doses is the actual question. The compiler does not search doses. It refuses ones outside the encoded window.

License

MIT.

Reproducible validation (v0.2)

Install with python -m pip install -e .. Compiled JSON now contains a canonical protocol_sha256 over the complete input dataclass. Archive it with a review so the reviewed checklist can be identified exactly.

Validation rejects nonfinite schedule/parameter/formulation values, duplicate parameter names and invalid feed-gap limits. It checks the interval from the last feed to the endpoint as well as intervals between feeds. It also requires exactly one endpoint, no active step after it, and an explicit QC gate on an executable step. Gates must be lists of nonblank strings. A narrative note, blank gate label, or empty qc step does not count as a gate.

This checks encoded consistency, not the accuracy of a source transcription. Programmatically changing a parameter does not rewrite the narrative steps; review them together. No new biological protocol or parameter range was added in this revision.