biomni-general-agent

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/.