BioDSA

BioDSA: Vibe-Prototype AI Agents for Biomedicine

**BioDSA** is an open-source framework for rapidly prototyping, optimizing, and benchmarking AI agents for biomedical tasks — from data analysis and literature research to clinical trial matching and drug discovery.

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Motivation

Building AI agents for biomedicine is hard. A typical agent needs LLM orchestration, access to domain-specific knowledge bases (PubMed, ChEMBL, ClinicalTrials.gov, ...), safe code execution, multi-step reasoning, and structured output — all wired together correctly. Starting from scratch every time is slow and error-prone.

**BioDSA solves this by providing:**

• A BaseAgent foundation with built-in LLM support (OpenAI, Anthropic, Azure, Google), Docker-sandboxed code execution, and retry handling — so you focus on the agent logic, not the plumbing
• LangGraph workflows for composing agent logic as state graphs with conditional edges — supporting ReAct loops, multi-stage pipelines, and multi-agent orchestration
• **17+ biomedical knowledge base integrat