ToolUniverse: Democratizing AI scientists

Install

[!IMPORTANT] Claude Desktop extension showing "Failed — Server disconnected"? The copy of ToolUniverse in Claude Desktop's built-in Extensions directory is an old build that cannot start. Remove it, then use either option below — both install a working version. Details and status: #585

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

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

The agent will walk you through MCP configuration, API keys, skill installation, and validation.

or set up manually

Add to your MCP config file:

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

--refresh checks PyPI for the newest release on every launch. Drop it ("args": ["tooluniverse"]) to start faster from uv's cache — then upgrade with uv cache clean tooluniverse.

Install agent skills:

npx skills add mims-harvard/ToolUniverse

Claude Code users — one line, no config file:

claude plugin marketplace add mims-harvard/ToolUniverse
claude plugin install tooluniverse@tooluniverse

Python developers — install the SDK. Install uv first and do not use system pip: on a current Mac, pip install tooluniverse fails with externally-managed-environment (PEP 668) and python3 -m venv can fail at ensurepip. uv manages its own Python and avoids both.

curl -LsSf https://astral.sh/uv/install.sh | sh   # if you don't have uv
uv venv --python 3.12 && source .venv/bin/activate
uv pip install tooluniverse

Needs Python 3.10 or newer. On an Apple Silicon Mac it also needs macOS 14 or newer: faiss-cpu, which backs the vector-search tools, publishes no arm64 wheel older than macosx_14_0, so macOS 13 and earlier would have to compile it. Intel Macs, Windows and Linux have no such floor.

The base install covers the API and database tools. Local ML, cheminformatics, and plotting tools need extras — uv pip install 'tooluniverse[all]', or a single group such as [ml], [visualization], [bioinformatics]. Note [all] excludes pdf, singlecell, smolagents, client, and build, which install by name. Run tooluniverse-doctor to see which groups are missing.

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: