--> --- name: biomni-general-agent description: Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions. allowed-tools: - read_file - run_shell_command ---
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Added May 30, 2026
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Works with
cli
api
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# COPYRIGHT NOTICE
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# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
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---
name: biomni-general-agent
description: Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.
allowed-tools:
- read_file
- run_shell_command
---
## At-a-Glance
- **description (10-20 chars):** Omni bio agent
- **keywords:** multi-tool, know-how, tutorials, protocols, databases
- **measurable_outcome:** Execute a Biomni workflow that touches ≥2 tool categories and returns a cited research summary or artifact within 15 minutes per request.
## Workflow
1. **Environment:** `cd repo && pip install .` (or follow tutorials env set up). Activate the environment with required GPUs if using heavy models.
2. **Select mode:** Choose Standard (full stack), Light (API-only), or Commercial (license-safe) per task.
3. **Plan tools:** Query the Know-How library for relevant protocols/databases before executing.
4. **Execute notebooks/scripts:** Use `repo/tutorials` or CLI entrypoints to run pipelines; log tool versions.
5. **Summarize:** Provide outputs + citations pulled from the Know-How metadata.
## Guardrails
- Respect tool/data licenses when selecting Light vs Commercial mode.
- Track provenance (tool versions, dataset snapshots) in final response.
- Keep workflows modular—reuse Biomni recipes rather than ad-hoc scripts when possible.
## References
- Full capability list, tool inventory, and tutorial notebooks documented in `README.md` and `repo/tutorials/`.
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
