FrontierLab v0.10 · BioNeMo scientific-tool preflight
Status: OFFLINE SCHEMA/PROVENANCE INTEGRATION ONLY. No scientific endpoint has been called, no Meta/NVIDIA credits were spent, and no model inference result has been generated by this feature.
Goal
The hackathon uses Meta research reasoning as its core. NVIDIA BioNeMo is strictly an optional, researcher-authorized scientific computation sidecar, not a replacement for required Meta model usage. Existing public HF CPU Basic Space remains Streamlit with no NIM Docker/GPU installation.
Official NVIDIA sources
- Toolkit: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit
- Boltz-2 skill: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/nim-skills/boltz2-nim
- Boltz-2 request/response API: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/blob/main/nim-skills/boltz2-nim/references/api.md
- Scientific validation notes: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/blob/main/nim-skills/boltz2-nim/references/validation.md
Code
frontierlab/bionemo.py exposes four registered tools: boltz2-nim is OFFLINE_PREFLIGHT_ONLY; proteinmpnn-nim, rfdiffusion-nim and openfold3-nim remain NOT_CONNECTED. Skills are documentation + tool instructions; listing them does NOT install a model or authorize a hosted API call.
prepare_boltz2(sequence, source_id=...) validates a canonical uppercase protein sequence of 8–4096 residues, bounded official sampling/recycle parameters, and generates a standard protein-only Boltz-2 request and a separate publishable manifest that omits the raw sequence. The request is never sent to NVIDIA in this version. Output status is always PREPARED_NOT_EXECUTED.
mode='offline_fixture' is for entirely synthetic software tests, and cannot carry a review approval. mode='research' requires researcher_authorized=True and a FrontierLab live literature Run where all claims have human review and at least two distinct papers are marked human-supported. This is authorization for local preflight preparation only, not approval to transfer a sequence externally.
validate_boltz2_response(prepared, response) checks a supplied dictionary against the documented Boltz-2 output shape: requested number of structures, nonempty mmCIF-identified content, and one finite numerical confidence score per structure. It returns structure hashes and confidence scores without inventing missing results. Its status RESPONSE_SHAPE_CHECKED_ORIGIN_UNVERIFIED makes clear that the caller could have supplied a synthetic response. It does not establish that a real hosted request happened, structure predictions are physically correct, scores are pLDDT, binding occurs, or biological activity is confirmed.
Try the local preflight
python -m scripts.bionemo_preflight
python -m pytest -q
The sample is a clearly declared artificial sequence. The script prints sanitized manifest fields, tool status and SHA-256 hashes only, never credentials, private sequence, or fabricated scientific scores.
Live inference is deliberately NOT enabled
- Select a published, safe reference structure/sequence and inspect its license and experimental evidence.
- Review disclosure: NVIDIA hosted Boltz-2 receives the entire full protein sequence and request parameters over HTTPS at https://health.api.nvidia.com/v1/biology/mit/boltz2/predict. Other tools may receive entire PDBs. A private research sequence must never be submitted without explicit data-transfer permission.
- Confirm NVIDIA entitlement, rate limit, current credits/cost and key scope. No assumptions about unlimited free trial.
- Add a separate explicit one-shot transport only after authorization, with timeout, no retries, request limits, redacted logs and model-run receipt.
- Preserve artifacts, controls and runtime metadata, then compare results against independent published reference data. Researcher must review interpretation before publishing.
Explicit limitations
- Full Boltz-2 API supports DNA/RNA/ligands/MSAs/complexes; this intentionally conservative v0.10 adapter handles protein-only preflight and does not claim to implement the full API.
- NVIDIA response confidence_scores are opaque model confidence estimates. No conversion to pLDDT, measured affinity, in-vitro validation or clinical evidence is justified.
- Test fixtures prove deterministic code behavior only. This feature has zero experimentally verified model calls.
- Do not conflate scientific tool output with an independent verdict on the original literature's claim.
- The HF Space needs no restart or upgrade for v0.10 because this adapter is not invoked by its current interface.