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 latest biomni package:
pip install biomni --upgrade
Or install from the github source version.
Lastly, 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
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" )
🤝 Contributing to Biomni
Biomni is an open-science initiative that thrives on community contributions. We welcome:
🔧 New Tools : Specialized analysis functions and algorithms
: Specialized analysis functions and algorithms 📊 Datasets : Curated biomedical data and knowledge bases
: Curated biomedical data and knowledge bases 💻 Software : Integration of existing biomedical software packages
: Integration of existing biomedical software packages 📋 Benchmarks : Evaluation datasets and performance metrics
: Evaluation datasets and performance metrics 📚 Misc : Tutorials, examples, and use cases
: 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.
(e.g., 10+ significant & integrated tool contributions or equivalent) will be on our upcoming paper in a top-tier journal or conference. All contributors will be acknowledged in our publications.
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
8 Real-world research task benchmark/leaderboard release A tutorial on how to contribute to Biomni
A tutorial on how to contribute to Biomni A tutorial on baseline agents
A tutorial on baseline agents Biomni A1+E1 release
Note
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.
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