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
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
Environment:cd repo && pip install . (or follow tutorials env set up). Activate the environment with required GPUs if using heavy models.
Select mode: Choose Standard (full stack), Light (API-only), or Commercial (license-safe) per task.
Plan tools: Query the Know-How library for relevant protocols/databases before executing.
Execute notebooks/scripts: Use repo/tutorials or CLI entrypoints to run pipelines; log tool versions.
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/.
1---2name: biomni-general-agent3description: <!--4---5<!--6# COPYRIGHT NOTICE7# This file is part of the "Universal Biomedical Skills" project.8# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>9# All Rights Reserved.10#11# This code is proprietary and confidential.12# Unauthorized copying of this file, via any medium is strictly prohibited.13#14# Provenance: Authenticated by MD BABU MIA1516-->1718---19name: biomni-general-agent20description: Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.21allowed-tools:22 - read_file23 - run_shell_command24---2526## At-a-Glance27- **description (10-20 chars):** Omni bio agent28- **keywords:** multi-tool, know-how, tutorials, protocols, databases29- **measurable_outcome:** Execute a Biomni workflow that touches ≥2 tool categories and returns a cited research summary or artifact within 15 minutes per request.3031## Workflow321. **Environment:** `cd repo && pip install .` (or follow tutorials env set up). Activate the environment with required GPUs if using heavy models.332. **Select mode:** Choose Standard (full stack), Light (API-only), or Commercial (license-safe) per task.343. **Plan tools:** Query the Know-How library for relevant protocols/databases before executing.354. **Execute notebooks/scripts:** Use `repo/tutorials` or CLI entrypoints to run pipelines; log tool versions.365. **Summarize:** Provide outputs + citations pulled from the Know-How metadata.3738## Guardrails39- Respect tool/data licenses when selecting Light vs Commercial mode.40- Track provenance (tool versions, dataset snapshots) in final response.41- Keep workflows modular—reuse Biomni recipes rather than ad-hoc scripts when possible.4243## References44- Full capability list, tool inventory, and tutorial notebooks documented in `README.md` and `repo/tutorials/`.454647<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add biotender-max/biomni-general-agent in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
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