| name | biomni-research-agent |
| description | Bio-Research Generalist |
| license | MIT |
| metadata | {"author":"Stanford (Snap Lab)","source":"https://github.com/snap-stanford/Biomni","version":"1.0.0"} |
| compatibility | [{"system":"Python 3.9+"}] |
| allowed-tools | ["run_shell_command","web_fetch","python_repl"] |
| keywords | ["biomni","automation","biomedical","reasoning","tools"] |
| measurable_outcome | Execute complex research tasks with >95% success rate and validated tool usage. |
Biomni (General Biomedical Agent)
A general-purpose biomedical AI agent capable of executing complex research workflows using over 150 tools and databases.
Biomni is a "General-Purpose" biomedical agent. Unlike specialized skills (e.g., just for folding proteins), Biomni acts as a high-level orchestrator that can break down complex open-ended research questions into solvable sub-tasks using a vast library of tools.
When to Use This Skill
- Complex Questions: "What are the potential drug targets for Alzheimer's related to mitochondrial dysfunction?"
- Multi-Step Research: Tasks requiring literature search, data retrieval, and analysis in sequence.
- Exploratory Analysis: When the exact path to the answer isn't known and requires "reasoning."
Core Capabilities
- Tool Use: Access to 150+ tools, 105 software packages, and 59 databases.
- Hypothesis Generation: Can formulate scientific hypotheses and plan experiments to test them.
- Plan & Execute: Breaks down queries into a dependency graph of tasks.
- Database QA: High accuracy (74.4%) in querying biomedical databases.
Workflow
- Query Parsing: The agent analyzes the user's natural language request.
- Tool Selection: It selects relevant tools (e.g., "Search GWAS Catalog", "Run GO Enrichment", "Fetch Uniprot Data").
- Execution Loop:
- Step 1: Get data.
- Step 2: Analyze data.
- Step 3: Refine plan based on intermediate results.
- Synthesis: Combines all findings into a comprehensive answer.
Example Usage
User: "Identify genes associated with Type 2 Diabetes that are also expressed in the pancreas and have approved drugs."
Agent Action:
- Tool:
OpenTargets -> Get T2D associated genes.
- Tool:
GTEx -> Filter for high expression in Pancreas.
- Tool:
DrugBank -> Intersect with drug targets.
- Result: Returns a list of genes (e.g., GLP1R, DPP4) and their drugs.
