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mims-harvard/ToolUniverse

A framework that gives LLM-based AI agents standardized access to 1000+ scientific tools, datasets and APIs for research workflows.

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What is it?

ToolUniverse is an ecosystem for building AI scientist systems on top of any large language model. It defines an AI-Tool Interaction Protocol that standardizes how a model discovers tools, issues requests and receives results, and it bundles more than 1000 machine learning models, datasets, APIs and scientific packages for data analysis, knowledge retrieval and experimental design.

The project can be used through a Python SDK, a terminal `tu` CLI, or as a native Model Context Protocol (MCP) server that works with clients such as Claude Desktop and Claude Code. Its compact mode reduces the full tool catalog to a few discovery tools to save context window space, and long-running tasks such as protein docking can run asynchronously with progress tracking. Results are cached in memory and in SQLite.

The repository also ships 68 prebuilt agent skills for research workflows such as drug discovery and pharmacovigilance, and literature search across PubMed, Semantic Scholar, ArXiv, BioRxiv and Europe PMC. New tools can be registered locally or remotely.

Key features

  • 01Standardized AI-Tool Interaction Protocol for tool discovery and calls
  • 02Works with models such as Claude, GPT, Gemini, Qwen and open models
  • 03Native MCP server with configurable transport and tool selection
  • 04Async execution with progress tracking for long-running tasks
  • 05Two-tier result caching with in-memory LRU and SQLite persistence
  • 06Unified literature search across several biomedical and preprint databases

Use cases

  • Building an AI agent that answers drug discovery or genomics questions with real database lookups
  • Letting Claude or another MCP client query scientific APIs such as UniProt or openFDA
  • Searching PubMed and preprint servers from a single interface during literature review
  • Adding custom scientific tools to a shared agent toolkit

Quick start

  1. 1

    Install uv (run the official install script from the README)

  2. 2

    Create and activate a virtual environment with Python 3.12

    uv venv --python 3.12 && source .venv/bin/activate
  3. 3

    Install the ToolUniverse package

    uv pip install tooluniverse

Things to know

  • Apple Silicon Macs need macOS 14 or newer for the vector-search tools.
  • Local ML, cheminformatics and plotting tools require extra installs beyond the base package.

Topics

#ai-agents#mcp-servers#scientific-tools#llm-tools#bioinformatics#drug-discovery#literature-search#agents#ai-communication#ai-for-science

FAQ

What is ToolUniverse?
A framework that gives LLM-based AI agents standardized access to 1000+ scientific tools, datasets and APIs for research workflows. ToolUniverse is an ecosystem for building AI scientist systems on top of any large language model. It defines an AI-Tool Interaction Protocol that standardizes how a model discovers tools, issues requests and receives results, and it bundles more than 1000 machine learning models, datasets, APIs and scientific packages for data analysis, knowledge retrieval and experimental design.
Is ToolUniverse free to use? What license does it have?
ToolUniverse is open source under the Apache-2.0 license. Check the license terms before using it in commercial products.
Is ToolUniverse still maintained?
Actively maintained. The last commit to ToolUniverse was on Oct 19, 2026.
What can I use ToolUniverse for?
Building an AI agent that answers drug discovery or genomics questions with real database lookups Letting Claude or another MCP client query scientific APIs such as UniProt or openFDA Searching PubMed and preprint servers from a single interface during literature review Adding custom scientific tools to a shared agent toolkit
How do I install ToolUniverse?
Install uv (run the official install script from the README) Create and activate a virtual environment with Python 3.12: uv venv --python 3.12 && source .venv/bin/activate Install the ToolUniverse package: uv pip install tooluniverse
Where can I get ToolUniverse?
The source code and installation instructions are on GitHub: https://github.com/mims-harvard/ToolUniverse

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