biomni 0.0.7

Biomni

Biomni: A General-Purpose Biomedical AI Agent

Overview

Biomni is a general-purpose biomedical AI agent designed to autonomously execute a wide range of research tasks across diverse biomedical subfields. By integrating cutting-edge large language model (LLM) reasoning with retrieval-augmented planning and code-based execution, Biomni helps scientists dramatically enhance research productivity and generate testable hypotheses.

Quick Start

Installation

Our software environment is massive and we provide a single setup.sh script to setup. Follow this file to setup the env first.

Then activate the environment E1:

conda activate biomni_e1

then install the biomni official pip package:

pip install biomni --upgrade

For the latest update, install from the github source version, or do:

pip install git+https://github.com/snap-stanford/Biomni.git@main

Lastly, configure your API keys using one of the following methods:

Click to expand

Option 1: Using .env file (Recommended)

Create a .env file in your project directory:

# Copy the example file
cp .env.example .env

# Edit the .env file with your actual API keys

Your .env file should look like:

# Required: Anthropic API Key for Claude models
ANTHROPIC_API_KEY=your_anthropic_api_key_here

# Optional: OpenAI API Key (if using OpenAI models)
OPENAI_API_KEY=your_openai_api_key_here

# Optional: Azure OpenAI API Key (if using Azure OpenAI models)
OPENAI_API_KEY=your_azure_openai_api_key
OPENAI_ENDPOINT=https://your-resource-name.openai.azure.com/

# Optional: AI Studio Gemini API Key (if using Gemini models)
GEMINI_API_KEY=your_gemini_api_key_here

# Optional: groq API Key (if using groq as model provider)
GROQ_API_KEY=your_groq_api_key_here

# Optional: Set the source of your LLM for example:
#"OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "Groq", "Custom"
LLM_SOURCE=your_LLM_source_here

# Optional: AWS Bedrock Configuration (if using AWS Bedrock models)
AWS_BEARER_TOKEN_BEDROCK=your_bedrock_api_key_here
AWS_REGION=us-east-1

# Optional: Custom model serving configuration
# CUSTOM_MODEL_BASE_URL=http://localhost:8000/v1
# CUSTOM_MODEL_API_KEY=your_custom_api_key_here

# Optional: Biomni data path (defaults to ./data)
# BIOMNI_DATA_PATH=/path/to/your/data

# Optional: Timeout settings (defaults to 600 seconds)
# BIOMNI_TIMEOUT_SECONDS=600

Option 2: Using shell environment variables

Alternatively, configure your API keys in bash profile ~/.bashrc:

export ANTHROPIC_API_KEY="YOUR_API_KEY"
export OPENAI_API_KEY="YOUR_API_KEY" # optional if you just use Claude
export OPENAI_ENDPOINT="https://your-resource-name.openai.azure.com/" # optional unless you are using Azure
export AWS_BEARER_TOKEN_BEDROCK="YOUR_BEDROCK_API_KEY" # optional for AWS Bedrock models
export AWS_REGION="us-east-1" # optional, defaults to us-east-1 for Bedrock
export GEMINI_API_KEY="YOUR_GEMINI_API_KEY" #optional if you want to use a gemini model
export GROQ_API_KEY="YOUR_GROQ_API_KEY" # Optional: set this to use models served by Groq
export LLM_SOURCE="Groq" # Optional: set this to use models served by Groq

⚠️ Known Package Conflicts

Some Python packages are not installed by default in the Biomni environment due to dependency conflicts. If you need these features, you must install the packages manually and may need to uncomment relevant code in the codebase. See the up-to-date list and details in docs/known_conflicts.md.

Basic Usage

Once inside the environment, you can start using Biomni:

from biomni.agent import A1

# Initialize the agent with data path, Data lake will be automatically downloaded on first run (~11GB)
agent = A1(path='./data', llm='claude-sonnet-4-20250514')

# Execute biomedical tasks using natural language
agent.go("Plan a CRISPR screen to identify genes that regulate T cell exhaustion, generate 32 genes that maximize the perturbation effect.")
agent.go("Perform scRNA-seq annotation at [PATH] and generate meaningful hypothesis")
agent.go("Predict ADMET properties for this compound: CC(C)CC1=CC=C(C=C1)C(C)C(=O)O")

If you plan on using Azure for your model, always prefix the model name with azure- (e.g. llm='azure-gpt-4o').

Configuration Management

Biomni includes a centralized configuration system that provides flexible ways to manage settings. You can configure Biomni through environment variables, runtime modifications, or direct parameters.

from biomni.config import default_config
from biomni.agent import A1

# RECOMMENDED: Modify global defaults for consistency
default_config.llm = "gpt-4"
default_config.timeout_seconds = 1200

# All agents AND database queries use these defaults
agent = A1()  # Everything uses gpt-4, 1200s timeout

Note: Direct parameters to A1() only affect that agent's reasoning, not database queries. For consistent configuration across all operations, use default_config or environment variables.

For detailed configuration options, see the Configuration Guide.

PDF Generation

Generate PDF reports of execution traces:

from biomni.agent import A1

# Initialize agent
agent = A1(path='./data', llm='claude-sonnet-4-20250514')

# Run your task
agent.go("Your biomedical task here")

# Save conversation history as PDF
agent.save_conversation_history("my_analysis_results.pdf")

PDF Generation Dependencies:

For optimal PDF generation, install one of these packages:

# Option 1: WeasyPrint (recommended for best layout control)
# Conda environment (recommended)
conda install weasyprint

# System installation
brew install weasyprint  # macOS
apt install weasyprint   # Linux

# See [WeasyPrint Installation Guide](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html) for detailed instructions.

# Option 2: markdown2pdf (Rust-based, fast and reliable)
# macOS:
brew install theiskaa/tap/markdown2pdf

# Windows/Linux (using Cargo):
cargo install markdown2pdf

# Or download prebuilt binaries from:
# https://github.com/theiskaa/markdown2pdf/releases/latest

# Option 3: Pandoc (pip installation)
pip install pandoc

MCP (Model Context Protocol) Support

Biomni supports MCP servers for external tool integration:

from biomni.agent import A1

agent = A1()
agent.add_mcp(config_path="./mcp_config.yaml")
agent.go("Find FDA active ingredient information for ibuprofen")

Built-in MCP Servers: For usage and implementation details, see the MCP Integration Documentation and examples in tutorials/examples/add_mcp_server/ and tutorials/examples/expose_biomni_server/.

🤝 Contributing to Biomni

Biomni is an open-science initiative that thrives on community contributions. We welcome:

• 🔧 New Tools: Specialized analysis functions and algorithms
• 📊 Datasets: Curated biomedical data and knowledge bases
• 💻 Software: Integration of existing biomedical software packages
• 📋 Benchmarks: Evaluation datasets and performance metrics
• 📚 Misc: Tutorials, examples, and use cases
• 🔧 Update existing tools: many current tools are not optimized - fix and replacements are welcome!

Check out this Contributing Guide on how to contribute to the Biomni ecosystem.

If you have particular tool/database/software in mind that you want to add, you can also submit to this form and the biomni team will implement them.

🔬 Call for Contributors: Help Build Biomni-E2

Biomni-E1 only scratches the surface of what’s possible in the biomedical action space.

Now, we’re building Biomni-E2 — a next-generation environment developed with and for the community.

We believe that by collaboratively defining and curating a shared library of standard biomedical actions, we can accelerate science for everyone.

Join us in shaping the future of biomedical AI agent.

• Contributors with significant impact (e.g., 10+ significant & integrated tool contributions or equivalent) will be invited as co-authors on our upcoming paper in a top-tier journal or conference.
• All contributors will be acknowledged in our publications.
• More contributor perks...

Let’s build it together.

Tutorials and Examples

Biomni 101 - Basic concepts and first steps

More to come!

🌐 Web Interface

Experience Biomni through our no-code web interface at biomni.stanford.edu.

Release schedule

• 8 Real-world research task benchmark/leaderboard release
• A tutorial on how to contribute to Biomni
• A tutorial on baseline agents
• MCP support
• Biomni A1+E1 release

Important Note

• Security warning: Currently, Biomni executes LLM-generated code with full system privileges. If you want to use it in production, please use in isolated/sandboxed environments. The agent can access files, network, and system commands. Be careful with sensitive data or credentials.
• This release was frozen as of April 15 2025, so it differs from the current web platform.
• Biomni itself is Apache 2.0-licensed, but certain integrated tools, databases, or software may carry more restrictive commercial licenses. Review each component carefully before any commercial use.

Cite Us

@article{huang2025biomni,
  title={Biomni: A General-Purpose Biomedical AI Agent},
  author={Huang, Kexin and Zhang, Serena and Wang, Hanchen and Qu, Yuanhao and Lu, Yingzhou and Roohani, Yusuf and Li, Ryan and Qiu, Lin and Zhang, Junze and Di, Yin and others},
  journal={bioRxiv},
  pages={2025--05},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}