ToolUniverse is an open-source ecosystem for building autonomous AI scientist systems from any large language model. Developed by Harvard Medical School, it democratizes scientific research by enabling AI agents to discover, orchestrate, and execute specialized tools for autonomous experimentation and discovery. Key features: - MCP server providing remote and local access to scientific tools for AI scientist workflows - Python SDK for programmatic integration and building custom AI scientist applications - `tu` CLI for discovering, inspecting, running, and testing tools from the terminal - AI agent skills for automated tool selection and execution - Supports scientific research automation across domains including computational biology and biomedical research

ToolUniverse: Democratizing AI scientists

[](https://zitniklab.hms.harvard.edu/ToolUniverse/) [](https://arxiv.org/abs/2509.23426) [](https://badge.fury.io/py/tooluniverse) [](https://registry.modelcontextprotocol.io) [](https://aiscientist.tools) [](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ) [](https://aiscientist.tools/wechat) [](https://www.linkedin.com/in/shanghua-gao-96b0b3168/) [](https://x.com/ScientistTools) [](https://pepy.tech/projects/tooluniverse)

[//]: # (mcp-name: io.github.mims-harvard/tooluniverse)

Install

AI agent (recommended) — open your AI agent and run:

Read https://aiscientist.tools/setup.md and set up ToolUniverse for me.

or set up manually

Add to your MCP config file:

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": ["--refresh", "tooluniverse"],
      "env": {"PYTHONIOENCODING": "utf-8"}
    }
  }
}

Install agent skills:

npx skills add mims-harvard/ToolUniverse

Python developers — install the SDK:

uv pip install tooluniverse

tu CLI — discover, inspect, run, and test tools from the terminal. Python SDK — programmatic access for building AI scientist systems.

Building AI Scientists with ToolUniverse

*Click to watch the demo* (YouTube) (Bilibili)

What is ToolUniverse?

ToolUniverse is an ecosystem for creating AI scientist systems from any large language model. Powered by the AI-Tool Interaction Protocol, it standardizes how LLMs identify and call tools, integrating more than 1000 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design.

Key features: