{"repo":"RyanWangZf/BioDSA","free":true,"listed":false,"github":"https://github.com/RyanWangZf/BioDSA","clone":"git clone https://github.com/RyanWangZf/BioDSA.git","description":"BioDSA: Framework for Vibe Prototyping of AI Agents for Biomedicine","language":"Python","stars":82,"topics":["benchmark","biomedical","code-generation","large-language-models","datascience"],"license":"MIT","category":"dev-tools","readme_excerpt":"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. Describe what you want in natural language. Get a working agent in minutes. --- 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 integrations (PubMed, ChEMBL, UniProt, Open Targets, Ensembl, cBioPortal, Reactome, ...) as plug-and-play tools - 10 benchmarks with 1,900+ tasks for systematic evaluation - Two skill libraries that teach AI coding assistants (Cursor, Claude Code, Codex, Gemini, OpenClaw) to both create new agents and run existing ones — so you can vibe-prototype or execute agents in minutes --- Implemented Agents ","default_branch":null,"files":null,"tree":[],"storefront":"/r/RyanWangZf","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/RyanWangZf/BioDSA/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}