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Helix — Deterministic, auditable genome-editing simulation (CRISPR/Prime/PCR)

PyPI Scientific Contract CI VeriBiota CI Verified by VeriBiota Reproducible Viz (spec v1.0)

Helix is a deterministic, auditable genome editing simulator and reporting system for pre-clinical, in-silico CRISPR, Prime, and PCR workflows — a computational system of record for genome editing design decisions.

Helix does not claim biological truth. It guarantees computational reproducibility, explicit modeling boundaries, and verifiable decision artifacts (reports, manifests, schema-versioned evidence bundles).

Pre-clinical, in-silico simulation only. See docs/positioning.

Migration note (veri-helix → helix-governance)

Helix is now published on PyPI as helix-governance (Python module namespace and CLI entrypoints are unchanged).

python -m pip uninstall -y veri-helix
python -m pip install -U helix-governance

Omnis Helix Outcome Explorer overlay

Choose your path

AUROC (in silico evaluation packs)

Helix computes AUROC for a scoring function against a frozen in silico evaluation pack, and emits offline-verifiable evidence bundles that include the metric, its provenance, and integrity checks.

The buyer demo (make demo-auroc-delta) runs two edit programs (baseline + candidate) against the same evaluation pack and prints Baseline AUROC, Candidate AUROC, and Δ AUROC. Results are comparable only when the evaluation pack id matches.

Important: AUROC reported by Helix is computed only against a declared in silico evaluation pack. It is not a claim of biological validation or real‑world performance/accuracy. The metric is meaningful only within the scope, labels, and versioned provenance of the evaluation pack.

See demo/auroc_delta/README and docs/enterprise_proof/auroc_delta_demo.

First Run

Install, run a deterministic demo, and open the exported report:

python -m venv .venv
source .venv/bin/activate
pip install "helix-governance"

helix --version
helix-cli --version

helix demo run --demo-id crispr --outdir out/demo_crispr --zip
python -m http.server --directory out/demo_crispr/reports 8000

helix-cli is a compatibility alias of helix; both commands should report the same version.

Prime demo:

helix demo run --demo-id prime --outdir out/demo_prime --zip

Evaluator Loop

For the actual MVP evaluator flow, use Studio for the proof and pilot handoff, then verify the generated package offline:

python -m pip install -U helix-governance
omnis-helix --help
python -m pip install "helix-governance[studio]"
omnis-helix
helix-pilot-verify /path/to/helix_run_17_pilot_request_package.zip --json

If you are working from a source checkout instead of an installed package, the repo-local fallback is:

python tools/verify_pilot_package.py /path/to/helix_run_17_pilot_request_package.zip --json

The full proof-first evaluator path is documented in docs/getting-started.

Enzyme Program Contract v1.0.0 (quickstart)

Contract status:

  • Contract: Enzyme Program Contract v1.0.0
  • Tag (contract freeze): enzyme-contract-v1.0.0
  • Tag (docs/quickstart): enzyme-contract-v1.0.2
  • Golden vector: golden_bundle.zip (+ golden_bundle.zip.sha256)
  • Compatibility: COMPATIBILITY.md

One-command verify (60 seconds):

pip install helix-governance==1.1.5

curl -L -O https://github.com/omniscoder/Helix/releases/download/enzyme-contract-v1.0.2/golden_bundle.zip
curl -L -O https://github.com/omniscoder/Helix/releases/download/enzyme-contract-v1.0.2/golden_bundle.zip.sha256

EXPECTED_SHA="$(awk '{print $1}' golden_bundle.zip.sha256)"
helix-cli enzyme verify golden_bundle.zip --expected-bundle-sha256 "$EXPECTED_SHA"

Build the golden bundle yourself:

curl -L -O https://github.com/omniscoder/Helix/releases/download/enzyme-contract-v1.0.2/golden_config.json
curl -L -O https://github.com/omniscoder/Helix/releases/download/enzyme-contract-v1.0.2/golden_policy.json

helix-cli enzyme artifacts build --config golden_config.json --policy golden_policy.json --outdir out_bundle --backend cpu --zip
helix-cli enzyme verify out_bundle.zip

Access and licensing

  • Free local proof: Omnis Helix desktop, CLI replay, diff, and offline verification are free for exploratory evaluation and technical review.
  • Licensed decision-grade authoring: signed bundles and decision-grade assertions require an offline license file.
  • Governance Workspace: Teams/Hub/Registry is the shared review and approval layer for RBAC, proof links, audit export, and durable decision state.
  • Private deployment: this means the customer runs the Teams/Hub/Registry layer inside its own VPC, private cloud, or on-prem environment. It does not mean downloading the desktop app.
  • Verification is always free + offline: helix verify <bundle_dir_or_zip> validates signatures and lineage, and never reads your local license.

Dynamic CRISPR simulation (resource-aware)

Copy/paste quickstart (Python API):

from helix.crispr.dynamic import CrisprDynamicSimConfig, simulate_crispr_dynamic

# Key mental model: `delivery` shapes Cas(t) (availability over time), not a static cut probability.
# `population.seed` makes the stochastic simulation reproducible.
cfg = CrisprDynamicSimConfig.from_yaml("""
time: {dt_h: 0.25, t_end_h: 48.0}
population: {n_cells: 2000, seed: 1}
delivery: {mode: RNP, params: {C0: 1.0}}
cas_kinetics: {k_deg: 0.35, k_dil: 0.0}
engagement: {k_eff: 0.55}
grnas: [{id: g1, abundance: 1.0, load_efficiency: 1.0}, {id: g2, abundance: 1.0, load_efficiency: 1.0}]
targets: [{id: t1, grna_id: g1, chr: chr1, pos: 1000, accessibility: 1.0}, {id: t2, grna_id: g2, chr: chr1, pos: 2000, accessibility: 1.0}]
ploidy: {loci: [{locus_id: t1, copies: 2, allele_accessibility: [1.0, 0.5]}, {locus_id: t2, copies: 2, allele_accessibility: [1.0, 1.0]}]}
measurement: {amplicons: [{id: amp1, chr: chr1, start: 900, end: 1100, locus_id: t1}]}
""")
result = simulate_crispr_dynamic(cfg)

print("edited_fraction(t1) =", result.edited_fraction("t1"))
print("edited_fraction(t2) =", result.edited_fraction("t2"))
print("amp1 truth =", result.measurement.amplicons[0].truth_counts)
print("amp1 observed =", result.measurement.amplicons[0].observed_counts)

Want the GUI? pip install "helix-governance[studio]" then run omnis-helix.

Who this is for

  • Genome editing researchers who need reproducible CRISPR/Prime outcome enumeration and comparisons
  • Auditors/reviewers who need deterministic replays and verifiable artifacts
  • Contributors building policies, verifiers, and visualization/reporting pipelines

Docs