README.md

BioModStack Documentation

This directory is the current tracked documentation surface for BioModStack. Canonical docs describe supported source contracts and explicitly identify acceptance boundaries; they are not proof of what is deployed. Active plans are kept separately under docs/plans/ and should not be mistaken for the product truth.

Start Here

• Platform Overview
• Repository Maintenance
• Nonproduction Installation
• Desktop Runtime and Shell Architecture
• Structure Design and Refinement
• Lab Automation, Mol Bio, and Sequencing
• Results and Analysis
• Model Configuration, Operator Control, and Agent Parity

Platform and subsystem references

• API README
• Frontend README
• Electron shell README
• Model Integrations
• FrustraMPNN global configuration and analysis workbench specification
• Remote worker execution, cache, and explicit result retrieval — revision contract; see its explicit software/live acceptance boundaries.

Active plans

• Remote Bridge 1.0 specification — approved design baseline, not a claim of deployed capability; Neurosnap integration deferred.

• Global FrustraMPNN 100% implementation plan

Canonical doc roles

• README.md at the repo root: GitHub landing page and first-run orientation.
• docs/*.md without a date in the filename: operator, workflow, and platform contracts, including explicit limitations. A filename alone is not evidence of live acceptance.
• platform/api/README.md and platform/frontend/README.md: subsystem-specific technical references.
• docs/plans/*.md: active implementation plans and transition notes only; these do not define the canonical product contract.
• Historical planning material belongs in Git history, not an in-tree archive. Keep active plans and explicitly source-bound authority documents until their controlled retirement; do not remove them based on filename age alone.
• docs/ai_guidance/Model_Integrations.md: current model integration guidance. Older AI instruction docs are pruned once stale.

Current scope

The canonical docs set now covers:

• containerized core runtime plus the host-native workflow-adapter boundary
• browser, Electron, GTK, and optional Android thin-shell/update surfaces
• structure design, validation, refinement, and experimental workflow families
• mol bio construct editing and sequence operations
• nanopore/NGS launch and review surfaces
• the bounded BioXP compact control plane and its robot-local authority boundary
• results, lineage, analytics, and persisted runtime-path management
• complete operator and AI-agent control of every relevant model setting through one typed schema
• reusable model data, statistics, visualization, capture, export, and result workbenches

For BioXP, the canonical contract is BioXP Compact Control Plane. BMS does not expose the retired motion, liquid, power, thermal, camera, vision, arbitrary proxy, host-lifecycle, or remote-log families. Robot-local behavior remains authoritative, and unverified normal commands remain disabled.

For the core runtime, the canonical docs distinguish dashboard/control-plane robustness from full scientific workflow readiness. A general Linux host should be able to bring up API/web and show degraded capability states; full workflow readiness still requires host-side Nextflow, Apptainer, GPU/tooling, model, and reference-cache setup.

Older build/implementation planning docs that no longer belong on the repo-facing surface should be pruned instead of left beside the canonical docs as passive clutter.