BioPilot Prototype

Reference prototype for local-first protein-computing workflows using OpenSciFlow manifests and workflow templates.

Current status

Early prototype scaffold. This repository should demonstrate the first OpenSciFlow reference workflow:

Protein MD Stability Report Lite

MVP demo

Input:

• protein topology/structure file;
• trajectory file;
• optional ligand identifier.

Output:

• RMSD/RMSF/Rg metrics;
• plots;
• run logs;
• artifact list;
• reproducibility manifest;
• Markdown/HTML report.

MVP acceptance criteria

See:

• docs/mvp-acceptance-criteria.md
• docs/run-record-spec.md
• docs/protocol-compliance-plan.md
• docs/minimal-runner-contract.md
• docs/skill-run-record-projection.md
• schema/opensciflow-run-record.schema.json
• schema/biopilot-demo-request.schema.json
• schema/biopilot-plan-response.schema.json
• schema/biopilot-artifact-resolution.schema.json
• docs/api-draft.md
• docs/sample-data-policy.md
• docs/manifest-workflow-loading.md
• docs/local-readiness-check.md
• docs/demo-runbook.md
• templates/report.md.j2
• examples/protein-md-stability/sample-run-manifest.json
• examples/protein-md-stability/demo-run-request.json
• examples/protein-md-stability/plan-response.blocked.json
• examples/protein-md-stability/artifact-resolution.local.json
• examples/protein-md-stability/sample-data-checklist.md
• examples/protein-md-stability/sample-data-metadata-template.md

Validate the sample run record:

python scripts\validate_demo_request.py
python scripts\validate_plan_response.py
python scripts\validate_artifact_resolution.py
python scripts\validate_run_records.py

Generate a review-only planning response:

python scripts\plan_demo_run.py

Resolve declared workflow and manifest artifacts without execution:

python scripts\resolve_demo_artifacts.py

Check the local Python environment before dry runs:

python scripts\check_local_readiness.py

Intentionally out of scope

• General autonomous science.
• Full plugin marketplace.
• Automatic arbitrary package installation.
• Clinical or drug-development decision support.

Safety rule

The Local Agent must execute only reviewed plugin commands. It must not execute arbitrary shell generated by an LLM.