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Autonomously executes complex biomedical research tasks in genomics, drug discovery, molecular biology, and clinical analysis using LLM reasoning, code execution, and integrated databases. For CRISPR screening, scRNA-seq analysis, ADMET prediction, GWAS, rare disease diagnosis.
npx claudepluginhub logauaengstrom/claude-scientific-skills --plugin scientific-skillsThis skill uses the workspace's default tool permissions.
Biomni is an open-source biomedical AI agent framework from Stanford's SNAP lab that autonomously executes complex research tasks across biomedical domains. Use this skill when working on multi-step biological reasoning tasks, analyzing biomedical data, or conducting research spanning genomics, drug discovery, molecular biology, and clinical analysis.
Autonomously executes complex biomedical research tasks in genomics, drug discovery, molecular biology, and clinical analysis using LLM reasoning, code execution, and integrated databases. For CRISPR screening, scRNA-seq analysis, ADMET prediction, GWAS, rare disease diagnosis.
Autonomously executes multi-step biomedical research tasks across genomics, drug discovery, molecular biology, and clinical analysis using LLM reasoning, code execution, and integrated databases. For CRISPR screening, scRNA-seq analysis, ADMET prediction, GWAS, and rare disease diagnosis.
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Biomni is an open-source biomedical AI agent framework from Stanford's SNAP lab that autonomously executes complex research tasks across biomedical domains. Use this skill when working on multi-step biological reasoning tasks, analyzing biomedical data, or conducting research spanning genomics, drug discovery, molecular biology, and clinical analysis.
Biomni excels at:
Use biomni for:
Install Biomni and configure API keys for LLM providers:
uv pip install biomni --upgrade
Configure API keys (store in .env file or environment variables):
export ANTHROPIC_API_KEY="your-key-here"
# Optional: OpenAI, Azure, Google, Groq, AWS Bedrock keys
Use scripts/setup_environment.py for interactive setup assistance.
from biomni.agent import A1
# Initialize agent with data path and LLM choice
agent = A1(path='./data', llm='claude-sonnet-4-20250514')
# Execute biomedical task autonomously
agent.go("Your biomedical research question or task")
# Save conversation history and results
agent.save_conversation_history("report.pdf")
The A1 class is the primary interface for biomni:
from biomni.agent import A1
from biomni.config import default_config
# Basic initialization
agent = A1(
path='./data', # Path to data lake (~11GB downloaded on first use)
llm='claude-sonnet-4-20250514' # LLM model selection
)
# Advanced configuration
default_config.llm = "gpt-4"
default_config.timeout_seconds = 1200
default_config.max_iterations = 50
Supported LLM Providers:
claude-sonnet-4-20250514, claude-opus-4-20250514gpt-4, gpt-4-turbogemini-2.0-flash-expllama-3.3-70b-versatileSee references/llm_providers.md for detailed LLM configuration instructions.
Biomni follows an autonomous agent workflow:
# Step 1: Initialize agent
agent = A1(path='./data', llm='claude-sonnet-4-20250514')
# Step 2: Execute task with natural language query
result = agent.go("""
Design a CRISPR screen to identify genes regulating autophagy in
HEK293 cells. Prioritize genes based on essentiality and pathway
relevance.
""")
# Step 3: Review generated code and analysis
# Agent autonomously:
# - Decomposes task into sub-steps
# - Retrieves relevant biological knowledge
# - Generates and executes analysis code
# - Interprets results and provides insights
# Step 4: Save results
agent.save_conversation_history("autophagy_screen_report.pdf")
agent.go("""
Design a genome-wide CRISPR knockout screen for identifying genes
affecting [phenotype] in [cell type]. Include:
1. sgRNA library design
2. Gene prioritization criteria
3. Expected hit genes based on pathway analysis
""")
agent.go("""
Analyze this single-cell RNA-seq dataset:
- Perform quality control and filtering
- Identify cell populations via clustering
- Annotate cell types using marker genes
- Conduct differential expression between conditions
File path: [path/to/data.h5ad]
""")
agent.go("""
Predict ADMET properties for these drug candidates:
[SMILES strings or compound IDs]
Focus on:
- Absorption (Caco-2 permeability, HIA)
- Distribution (plasma protein binding, BBB penetration)
- Metabolism (CYP450 interaction)
- Excretion (clearance)
- Toxicity (hERG liability, hepatotoxicity)
""")
agent.go("""
Interpret GWAS results for [trait/disease]:
- Identify genome-wide significant variants
- Map variants to causal genes
- Perform pathway enrichment analysis
- Predict functional consequences
Summary statistics file: [path/to/gwas_summary.txt]
""")
See references/use_cases.md for comprehensive task examples across all biomedical domains.
Biomni integrates ~11GB of biomedical knowledge sources:
Data is automatically downloaded to the specified path on first use.
Extend biomni with external tools via Model Context Protocol:
# MCP servers can provide:
# - FDA drug databases
# - Web search for literature
# - Custom biomedical APIs
# - Laboratory equipment interfaces
# Configure MCP servers in .biomni/mcp_config.json
Benchmark agent performance on biomedical tasks:
from biomni.eval import BiomniEval1
evaluator = BiomniEval1()
# Evaluate on specific task types
score = evaluator.evaluate(
task_type='crispr_design',
instance_id='test_001',
answer=agent_output
)
# Access evaluation dataset
dataset = evaluator.load_dataset()
⚠️ Important: Biomni executes LLM-generated code with full system privileges. For production use:
default_config.timeout_seconds for complex tasksmax_iterations to prevent runaway loops# Always save conversation history for reproducibility
agent.save_conversation_history("results/project_name_YYYYMMDD.pdf")
# Include in reports:
# - Original task description
# - Generated analysis code
# - Results and interpretations
# - Data sources used
Detailed documentation available in the references/ directory:
api_reference.md - Complete API documentation for A1 class, configuration, and evaluationllm_providers.md - LLM provider setup (Anthropic, OpenAI, Azure, Google, Groq, AWS)use_cases.md - Comprehensive task examples for all biomedical domainsHelper scripts in the scripts/ directory:
setup_environment.py - Interactive environment and API key configurationgenerate_report.py - Enhanced PDF report generation with custom formattingData download fails
# Manually trigger data lake download
agent = A1(path='./data', llm='your-llm')
# First .go() call will download data
API key errors
# Verify environment variables
echo $ANTHROPIC_API_KEY
# Or check .env file in working directory
Timeout on complex tasks
from biomni.config import default_config
default_config.timeout_seconds = 3600 # 1 hour
Memory issues with large datasets
For issues or questions:
references/ files for detailed guidance