The biology of the future will be built on proof.
Not just results that look right, but results that can prove where they came from.
Veri-Helix is an open-source Python toolkit that turns reproducibility into a first-class feature.
Every workflow, schema, and figure you generate carries cryptographic provenance and versioned validation — no more mystery plots or lost notebooks.
✳️ Why it matters
Most bioinformatics projects are a maze of scripts and notebooks.
A small tweak in data or dependencies can silently change your output.
Veri-Helix keeps you honest by stamping every artifact — from a FASTA triage plot to a motif logo — with:
✅ Schema validation (Pydantic-based) for every JSON artifact
🔖 Versioned spec manifests (spec_version = 1.0) so outputs stay compatible
🧾 Provenance metadata (tool version, timestamp, and input SHA-256) baked into each .viz.json and figure footer
If you can see it, you can verify it.
🧬 What’s inside
Unified CLI: one command (helix) for analysis, plotting, and schema inspection
Schema-verified visualization: RNA dot-plots, motif logos, distance heatmaps, alignment ribbons, and more
Validated workflows: YAML pipelines that log schema kind, version, and hash for every step
Reproducible demos: all screenshots on docs.verihelix.org come straight from helix demo viz
⚙️ Try it in a minute
pip install veri-helix[viz,schema,protein]
helix demo viz --all
Each command leaves a .viz.json next to your figure:
{
"kind": "motif_logo",
"spec_version": "1.0",
"input_sha256": "...",
"helix_version": "0.2.0",
"timestamp": "2025-11-11T18:23Z"
}
That JSON is your proof — a portable, machine-readable trail of how your science was made.
💡 Get started
Docs: https://omniscoder.github.io/Helix
PyPI: pypi.org/project/veri-helix
GitHub: github.com/omniscoder/Helix
🧠 For educators & researchers
Veri-Helix notebooks drop cleanly into Jupyter and Binder, letting students explore validated results without hidden state.
Every command can export a manifest that journals and repositories (like Zenodo) can archive alongside your paper.
🚀 Join us
Help shape the future of reproducible biology — contribute examples, workflows, or new schema definitions:
git clone https://github.com/omniscoder/Helix
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