base on Biomni: a general-purpose biomedical AI agent <p align="center"> <img src="./figs/biomni_logo.png" alt="Biomni Logo" width="600px" /> </p> <p align="center"> <a href="https://join.slack.com/t/biomnigroup/shared_invite/zt-38dat07mc-mmDIYzyCrNtV4atULTHRiw"> <img src="https://img.shields.io/badge/Join-Slack-4A154B?style=for-the-badge&logo=slack" alt="Join Slack" /> </a> <a href="https://biomni.stanford.edu"> <img src="https://img.shields.io/badge/Try-Web%20UI-blue?style=for-the-badge" alt="Web UI" /> </a> <a href="https://x.com/ProjectBiomni"> <img src="https://img.shields.io/badge/Follow-on%20X-black?style=for-the-badge&logo=x" alt="Follow on X" /> </a> <a href="https://www.linkedin.com/company/project-biomni"> <img src="https://img.shields.io/badge/Follow-LinkedIn-0077B5?style=for-the-badge&logo=linkedin" alt="Follow on LinkedIn" /> </a> <a href="https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1"> <img src="https://img.shields.io/badge/Read-Paper-green?style=for-the-badge" alt="Paper" /> </a> </p> # 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](biomni_env/README.md) to setup the env first. Then activate the environment E1: ```bash conda activate biomni_e1 ``` then install the biomni official pip package: ```bash pip install biomni --upgrade ``` For the latest update, install from the github source version, or do: ```bash pip install git+https://github.com/snap-stanford/Biomni.git@main ``` Lastly, configure your API keys in bash profile `~/.bashrc`: ```bash export ANTHROPIC_API_KEY="YOUR_API_KEY" export OPENAI_API_KEY="YOUR_API_KEY" # optional if you just use Claude 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 ``` ### Basic Usage Once inside the environment, you can start using Biomni: ```python 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 - **📊 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](CONTRIBUTION.md)** 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](https://forms.gle/nu2n1unzAYodTLVj6) 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](./tutorials/biomni_101.ipynb)** - Basic concepts and first steps More to come! ## 🌐 Web Interface Experience Biomni through our no-code web interface at **[biomni.stanford.edu](https://biomni.stanford.edu)**. [](https://youtu.be/E0BRvl23hLs) ## Release schedule - [ ] 8 Real-world research task benchmark/leaderboard release - [ ] A tutorial on how to contribute to Biomni - [ ] A tutorial on baseline agents - [x] 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. ## 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} } ``` ", Assign "at most 3 tags" to the expected json: {"id":"14248","tags":[]} "only from the tags list I provide: [{"id":77,"name":"3d"},{"id":89,"name":"agent"},{"id":17,"name":"ai"},{"id":54,"name":"algorithm"},{"id":24,"name":"api"},{"id":44,"name":"authentication"},{"id":3,"name":"aws"},{"id":27,"name":"backend"},{"id":60,"name":"benchmark"},{"id":72,"name":"best-practices"},{"id":39,"name":"bitcoin"},{"id":37,"name":"blockchain"},{"id":1,"name":"blog"},{"id":45,"name":"bundler"},{"id":58,"name":"cache"},{"id":21,"name":"chat"},{"id":49,"name":"cicd"},{"id":4,"name":"cli"},{"id":64,"name":"cloud-native"},{"id":48,"name":"cms"},{"id":61,"name":"compiler"},{"id":68,"name":"containerization"},{"id":92,"name":"crm"},{"id":34,"name":"data"},{"id":47,"name":"database"},{"id":8,"name":"declarative-gui "},{"id":9,"name":"deploy-tool"},{"id":53,"name":"desktop-app"},{"id":6,"name":"dev-exp-lib"},{"id":59,"name":"dev-tool"},{"id":13,"name":"ecommerce"},{"id":26,"name":"editor"},{"id":66,"name":"emulator"},{"id":62,"name":"filesystem"},{"id":80,"name":"finance"},{"id":15,"name":"firmware"},{"id":73,"name":"for-fun"},{"id":2,"name":"framework"},{"id":11,"name":"frontend"},{"id":22,"name":"game"},{"id":81,"name":"game-engine "},{"id":23,"name":"graphql"},{"id":84,"name":"gui"},{"id":91,"name":"http"},{"id":5,"name":"http-client"},{"id":51,"name":"iac"},{"id":30,"name":"ide"},{"id":78,"name":"iot"},{"id":40,"name":"json"},{"id":83,"name":"julian"},{"id":38,"name":"k8s"},{"id":31,"name":"language"},{"id":10,"name":"learning-resource"},{"id":33,"name":"lib"},{"id":41,"name":"linter"},{"id":28,"name":"lms"},{"id":16,"name":"logging"},{"id":76,"name":"low-code"},{"id":90,"name":"message-queue"},{"id":42,"name":"mobile-app"},{"id":18,"name":"monitoring"},{"id":36,"name":"networking"},{"id":7,"name":"node-version"},{"id":55,"name":"nosql"},{"id":57,"name":"observability"},{"id":46,"name":"orm"},{"id":52,"name":"os"},{"id":14,"name":"parser"},{"id":74,"name":"react"},{"id":82,"name":"real-time"},{"id":56,"name":"robot"},{"id":65,"name":"runtime"},{"id":32,"name":"sdk"},{"id":71,"name":"search"},{"id":63,"name":"secrets"},{"id":25,"name":"security"},{"id":85,"name":"server"},{"id":86,"name":"serverless"},{"id":70,"name":"storage"},{"id":75,"name":"system-design"},{"id":79,"name":"terminal"},{"id":29,"name":"testing"},{"id":12,"name":"ui"},{"id":50,"name":"ux"},{"id":88,"name":"video"},{"id":20,"name":"web-app"},{"id":35,"name":"web-server"},{"id":43,"name":"webassembly"},{"id":69,"name":"workflow"},{"id":87,"name":"yaml"}]" returns me the "expected json"