Biomni: A General-Purpose Biomedical AI Agent

Summary

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 biomed...