Helix Technical Documentation

Helix is software-only, in silico decision infrastructure for genome engineering workflows. It produces replayable evidence bundles, schema-versioned artifacts, provenance receipts, checksum indexes, and offline verification paths so reviewers can inspect the computational record without trusting a hosted service.

Desktop app: Download Omnis Helix
Fast local evaluation: 5-Minute Proof + 14-Day Evaluation Quickstart
Trust proof: Helix Trust Kit
Release verification: Release Verification
Positioning and boundaries: Positioning and Language System

Start Here

Use these paths based on the job you need to complete:

Goal	Start with	Then read
Evaluate Helix locally	Getting Started	Proof Bundles, Audit Walkthrough
Verify a received bundle	Audit Walkthrough	Trust Kit, Artifacts & Provenance
Understand the trust model	Helix Hub Trust Model	Threat Model, Reference Validation Bundle
Integrate headless verification	Headless CLI	CLI, CLI Config Schema
Review release integrity	Release Verification	Release Provenance Policy, Security Policy
Build against schemas	Schema Reference	Artifacts, Schemas

Core Operating Loop

Helix documentation is organized around the same loop the platform enforces:

Design intent
  -> authoring and constraints
  -> simulation and evidence
  -> policy review
  -> replay verification
  -> signed export bundle
  -> offline audit

The important distinction: Helix verifies computational provenance and artifact integrity. It does not establish biological truth, clinical suitability, or real-world execution readiness.

Trust And Evidence

Helix Trust Kit - two-minute proof path for auditors, partner engineers, and reviewers.
Proof Bundles - portable bundles, replay receipts, and verification commands.
Audit Walkthrough - non-engineer checklist for validating a bundle.
Scientific Contract v1 - determinism classes, verification boundaries, and contract semantics.
Reference Validation Bundle - reference evidence layout and verifier expectations.
Helix Hub Trust Model - what Hub can and cannot lie about when offline verification passes.
Threat Model - adversarial assumptions and designed failure modes.
Release Verification - offline release checks for hashes, SBOMs, provenance, and demo bundles.

Product And Workflow

Download - desktop app and access paths.
Getting Started - local proof, Studio evaluation, pilot package, and verifier install.
Omnis Helix Tour - product walkthrough.
Omnis Helix Strategy - product strategy and market position.
Product Manual - broad product reference.
Teams v0 - shared review and approval layer.
Helix Hub - local-first DecisionOps control plane.

CLI And Automation

CLI - command overview.
Headless CLI - CI, batch, and offline verification usage.
CLI Config Schema - configuration contract.
CLI Workflows - workflow runner.
CLI Schema Tools - schema inspection and diffing.
CLI Visualization - visualization commands.
CI Verify Gate Template - verification gate pattern.
CI Verify Reason Codes - machine-readable failure categories.

Concepts And Contracts

Artifacts & Provenance - hashes, manifests, receipts, and artifact lineage.
Schemas - contracts for JSON and visualization payloads.
Workflows - YAML pipelines and schema hooks.
Artifacts - artifact classes and expectations.
Governance Contract - policy and evidence boundaries.
Enzyme Program Contract - contract-scoped artifact model.
HelixSpec MVP and HelixSpec Quickstart - compile, lower, execute, verify.

Validation And Performance

Validation Pack - public validation pack overview.
CRISPR Efficiency Panel - in silico evaluation panel.
CRISPR Off-target Panel - scoring panel.
Prime Panel - prime-editing evaluation panel.
Benchmarks - reproducible benchmark harness and trends.
Conformance Policy - conformance packs and enforcement.
External Attestation - third-party attestation policy.

Studio, Visualization, And UI

Studio Core Features - primary Studio surfaces.
Studio Plugins - plugin system overview.
Snapshot Spec v1 - reproducible visual snapshot contract.
Edit DAG Overview - edit DAG internals.
Edit DAG Visualization - visualization surface.
Alignment Ribbon, RNA Dot-Plot, Motif Logo, Distance Heatmap, and Minimizer Density - visualization gallery.