PlugWiki
tooluniverse logo

ToolUniverse MCP Server: Setup for Claude, Cursor and Other Apps

OfficialLocal
GetPyPItooluniversemims-harvard/tooluniverse
Tools
5
4 read · 1 change
Works in
12
apps
Risk
High
can write
Auth
None
Version
1.5.7
last commit Oct 2026

Gives Claude, Cursor and other assistants a catalog of 2,700+ science tools for biology, medicine and research literature.

ToolUniverse is a research project from Harvard's Zitnik lab. Its server shows your assistant five search-and-run tools by default. The assistant uses them to find the science tool it needs and run it, so your context window is not filled with thousands of tool descriptions.

It runs on your computer through uvx. What a call does depends on which catalog tool the assistant picks, so check each call.

Good for

  • Life-science researchers who want an assistant to query biomedical databases
  • Bioinformatics developers building AI scientist workflows
  • Students doing literature and data lookups across many sources

Works in

12 should work

Tap an app to see how to set it up and any known problems.

Install tooluniverse MCP

Claude Code

  1. 1

    Copy this prompt.

    Add the tooluniverse MCP server to Claude Code. Run this command:

claude mcp add tooluniverse -- uvx tooluniverse

Then check that it loaded and tell me if I need to sign in or restart.
  2. 2

    Paste it into Claude Code. It shows the change and asks before running it.

Requires uv (Python).

Built from the package data we hold. Not yet tested by us.

Tools

  • Lists the tools in the ToolUniverse catalog

    Lists tool names by default, or categories and other views. The big views return very large payloads, so the assistant should filter or page through them.

    Try: “List the categories of tools you can use.”

    Read · list_tools

  • Searches the catalog by text or pattern

    Finds tools whose names or descriptions match plain text or a regular expression, without any AI ranking.

    Try: “Find tools with 'protein' in the name.”

    Read · grep_tools

  • Shows what a tool does and what it needs

    Returns a tool's description, or its full definition with parameters, for one tool or a list of them.

    Try: “Show me the full definition of the UniProt lookup tool.”

    Read · get_tool_info

  • Runs any tool in the catalog by name

    Runs the tool you name with the arguments you give. This is how every one of the 2,700+ catalog tools is reached, including the ones that run Python code, so what it does depends on the tool called.

    Try: “Run the PubMed search tool for 'CRISPR off-target'.”

    Runs code · execute_tool

  • Finds tools from a plain-language request

    Searches the catalog for tools that fit a description, with an optional category filter. Its annotation marks it read-only.

    Try: “Which tools can help me look up drug targets?”

    Read · find_tools

Read from the source code

Permissions

high risk · 5 things to watch

High risk

The assistant can run any tool in a 2,700-tool science catalog, including tools that run Python code on your machine. Those calls also send your queries to outside services.

What it can do

  • Read your data
  • Create and change things
  • Delete things
  • Read-only mode

Watch out for

  • The catalog includes tools that run Python code on your computer

    Two catalog tools, python_code_executor and python_script_runner, run Python code or script files you pass to them, and execute_tool can call both. The code executor limits imports and time, and the script runner uses a subprocess with a timeout, but neither is a read-only mode. Both can install pip packages when the call asks for it. The project marks them as destructive. github.com

  • One tool runs anything in a 2,700-tool catalog

    execute_tool runs any catalog tool by name, so the real reach depends on which tool is called. The catalog was not reviewed tool by tool for this page, so keep per-call approval on. zitniklab.hms.harvard.edu

  • Tools call outside services

    Catalog tools query external databases and APIs, so your prompts and parameters leave your computer for those services. github.com

  • Large catalog views use a lot of context

    list_tools in its larger modes returns very large payloads. Ask for names or categories first, as its description advises. zitniklab.hms.harvard.edu

  • Compact mode is the default for the uvx command

    The default tooluniverse command adds compact mode, which exposes only the discovery tools plus execute_tool. pypi.org

Security advisories

No published security advisories as of Nov 1, 2026.

Technical details
Turning on read-onlyNo read-only mode is documented. The search tools are read-only, but execute_tool can run any catalog tool, including the Python code runners.
Talks toExternal science databases and APIs the chosen tool calls
Sign-in and keysThe server itself needs no account. Individual catalog tools may need their own API keys, which this page did not check.

Questions

Is it official?

Yes. It is the ToolUniverse project's own server, from the mims-harvard GitHub organization, whose README names Marinka Zitnik of Harvard Medical School as a project leader. It serves that project's own tool catalog.

Is it free?

The code is Apache-2.0 licensed. Some catalog tools may need their own API keys or accounts, which this page does not list.

How many tools does it have?

The server shows five by default, and those reach a catalog the project counts as 2,700+ tools. The README and docs give that number, and it may change between releases.

What does compact mode mean?

It exposes only the discovery tools and execute_tool, so the catalog does not fill your context window. The docs recommend it for MCP use, and the default tooluniverse command turns it on.

What do I need to run it?

uv, so that uvx can fetch the package, and Python 3.10 or newer. On an Apple Silicon Mac the README says macOS 14 or later is needed for the vector-search tools.

Can I set it up without editing a config file?

Yes. The README offers an agent-led setup, and a Claude Code plugin you add with two commands. Use the install box above for the manual route.

Can it run read-only?

No. No read-only mode is documented. The four search tools are read-only, but execute_tool can run any catalog tool, including python_code_executor and python_script_runner, which run Python code on your machine.

Does it work in Claude Desktop?

The README warns that Claude Desktop's built-in Extensions directory version is old and cannot start, and tells you to use a manual or agent-led setup instead.

Information

updated Nov 2, 2026

Publisher
Official
Package
tooluniverse
Registry
PyPI
Transport
stdio
Auth
None
Version
1.5.7
License
Apache-2.0
Last commit
Oct 31, 2026
Open issues
9
Listed in
Official MCP registry

WebsiteGitHubPyPIOfficial MCP RegistryChangelogIssues

Sources

Docs, issue trackers and discussions this page is built from. Issues, quotes and findings above link to their own source.

Show all 4
  1. ToolUniverse README · github.com
  2. Compact Mode guide · zitniklab.hms.harvard.edu
  3. tooluniverse on PyPI · pypi.org
  4. ToolUniverse python_executor_tools.json · github.com

Facts from the official MCP registry, GitHub, npm, PyPI and the Docker catalog. Updated Nov 2, 2026.