zrt-bionemo

Local-first protein design loop with deterministic feedback, live comparison artifacts, mock/demo outputs, and a local protein viewer host.

Start Here

1. bionemo_scientist.py
2. protein_viewer_web.py
3. protein_loop_session_index.md
4. protein_loop_status.md
5. protein_loop_runbook.md
6. protein_loop_evidence_matrix.md
7. protein_loop_completion_checklist.md
8. protein_loop_workflow_map.md
9. protein_loop_architecture.md
10. protein_loop.md
11. outputs/openfold3_run_review.md
12. outputs/openfold3_session_index.md

What This Does

• Runs a local-first BioNeMo AI scientist MVP with deterministic tool routing and evidence capture
• Computes dynamic Provenance Confidence scores to measure the auditability of runs
• Embeds a Telemetry Trust Framework directly in the developer logs
• Reuses the current demo protein artifacts in outputs/
• Scores and reweights the MSA / paired-MSA inputs deterministically
• Records comparison deltas, next-step defaults, and a seeded follow-up command
• Generates a compact run review and session index for one-file resumption
• Keeps a root-level landing page and session index for quick restart
• Exposes a root status dashboard with the latest live run state
• Hosts a local browser viewer for the latest protein renders and run artifacts
• Summarizes verified and remaining demo-only items in a checklist
• Shows the workflow map from entrypoint to live handoff artifacts
• Summarizes the architecture and live file roles in one concise note

Status

• BioNeMo scientist MVP: DEMO / LOCAL ONLY
• local viewer host: protein_viewer_web.py
• MOCK / DEMO only
• local-first
• reproducible
• entrypoint: bionemo_scientist.py
• bootstrap: protein_loop_bootstrap.py
• reproducibility check: protein_loop_repro_check.py
• assessor: protein_loop_assess.py
• verifier: protein_loop_verify.py
• root session index: protein_loop_session_index.md
• completion checklist: protein_loop_completion_checklist.md
• runbook: protein_loop_runbook.md
• evidence matrix: protein_loop_evidence_matrix.md
• workflow map: protein_loop_workflow_map.md
• architecture: protein_loop_architecture.md