Setup Tooluniverse

This walks you through installing ToolUniverse, the open-source gateway to 2,000+ scientific databases like PubMed, UniProt, and ChEMBL. You get three access patterns: MCP server for chat-based queries in Claude Desktop or Cursor, a CLI with nine subcommands (tu find, tu run, tu test), or a Python SDK with typed imports and JSON-based calls. The guide is explicitly step-by-step and language-aware, covering uv setup, config file locations for a dozen AI clients, API key setup, and the difference between the 1,200+ tools in compact mode versus direct execution. Use this when someone asks how to install ToolUniverse, which mode to pick, or needs MCP troubleshooting for scientific tooling.

skills.sh installs: 448
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

$ npx -y skills add mims-harvard/tooluniverse --skill setup-tooluniverse --agent claude-code

Installs into .claude/skills of the current project.

Files

Setup ToolUniverse

Guide the user step-by-step through setting up ToolUniverse.

Agent Behavior

Detect language from user's first message. Respond in their language; keep commands/URLs in English.
Go one step at a time. Ask before proceeding.
Use AskQuestion for structured choices.
Explain briefly in plain language. Celebrate small wins.
When something goes wrong, help troubleshoot before moving on.

Internal Notes (do not show)

ToolUniverse has 2,700+ tools. The tooluniverse command enables compact mode automatically, exposing only 5 core MCP tools (list_tools, grep_tools, get_tool_info, execute_tool, find_tools) while keeping all tools accessible via execute_tool.

What is ToolUniverse?

Always explain first, in plain language:

ToolUniverse is free, open-source software connecting to 2,000+ scientific databases (PubMed, UniProt, ChEMBL, FAERS, ClinicalTrials.gov, etc.). Instead of visiting each website, you search from one place. Think of it like a universal remote for scientific databases.

SKILL.md on GitHub