# tooluniverse Connects AI agents to research literature, scientific databases, and computational biology tools. Useful for running automated research workflows in agent sessions. - MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed · ★ 1759 - Author: mims-harvard - License: Apache-2.0 · policy=link-only · description only; the file stays with the author - Source: https://github.com/mims-harvard/ToolUniverse - Updated: 2026-10-24 - HTML: https://affpapa.org/en/nevibecode/mcp/tooluniverse ## What it does The server gives coding agents direct access to scientific papers from sources like PubMed and ArXiv. It connects models to specialized biology packages and experimental pipelines. To preserve context space, compact mode swaps the large tool catalog for four or five discovery functions. That keeps the prompt lean. The system includes a two-tier cache using memory and SQLite storage. Tasks like molecular docking run in the background through async calls. Developers can inspect tools via the `tu` command-line interface, and `tooluniverse-doctor` flags missing extra dependencies. Running the server requires Python 3.10 or later. On Apple Silicon Macs, macOS 14 or newer is necessary because `faiss-cpu` lacks precompiled arm64 wheels for older releases. ## Requirements - Needs: Python and uv (commands run via uvx) - Environment variables: `OPENAI_API_KEY`, `ANTHROPIC_API_KEY`, `GEMINI_API_KEY`, `OPENROUTER_API_KEY`, `AZURE_OPENAI_API_KEY`, `HF_TOKEN`, `NCBI_API_KEY`, `SEMANTIC_SCHOLAR_API_KEY`, `BIOGRID_API_KEY`, `DISGENET_API_KEY` — keys and tokens: ask the human for the values, never commit them or put them in shared files. ## Install ### Claude Code (native platform) **Platform CLI** ```bash claude mcp add --env OPENAI_API_KEY= --env ANTHROPIC_API_KEY= --env GEMINI_API_KEY= --env OPENROUTER_API_KEY= --env AZURE_OPENAI_API_KEY= --transport stdio tooluniverse -- uvx tooluniverse ``` Replace <…> with your own values. 12 more environment variables are in the server README. uvx runs the command named after the package; if the README names another one, use uvx --from tooluniverse ### Codex **Platform CLI** ```bash codex mcp add tooluniverse --env OPENAI_API_KEY= --env ANTHROPIC_API_KEY= --env GEMINI_API_KEY= --env OPENROUTER_API_KEY= --env AZURE_OPENAI_API_KEY= -- uvx tooluniverse ``` Replace <…> with your own values. 12 more environment variables are in the server README. uvx runs the command named after the package; if the README names another one, use uvx --from tooluniverse ### Cursor **Config file** File `.cursor/mcp.json`: ```json { "mcpServers": { "tooluniverse": { "command": "uvx", "args": [ "tooluniverse" ], "env": { "OPENAI_API_KEY": "", "ANTHROPIC_API_KEY": "", "GEMINI_API_KEY": "", "OPENROUTER_API_KEY": "", "AZURE_OPENAI_API_KEY": "" } } } } ``` Replace <…> with your own values. 12 more environment variables are in the server README. uvx runs the command named after the package; if the README names another one, use uvx --from tooluniverse ### GitHub Copilot **Config file** File `.vscode/mcp.json`: ```json { "servers": { "tooluniverse": { "type": "stdio", "command": "uvx", "args": [ "tooluniverse" ], "env": { "OPENAI_API_KEY": "", "ANTHROPIC_API_KEY": "", "GEMINI_API_KEY": "", "OPENROUTER_API_KEY": "", "AZURE_OPENAI_API_KEY": "" } } } } ``` Replace <…> with your own values. 12 more environment variables are in the server README. uvx runs the command named after the package; if the README names another one, use uvx --from tooluniverse ### Gemini CLI **Platform CLI** ```bash gemini mcp add -e OPENAI_API_KEY= -e ANTHROPIC_API_KEY= -e GEMINI_API_KEY= -e OPENROUTER_API_KEY= -e AZURE_OPENAI_API_KEY= tooluniverse uvx tooluniverse ``` Replace <…> with your own values. 12 more environment variables are in the server README. uvx runs the command named after the package; if the README names another one, use uvx --from tooluniverse ## When to use it - query biomedical literature across PubMed and ArXiv - execute protein docking and molecular simulations asynchronously - reduce context token consumption using compact discovery mode - diagnose missing package dependencies with `tooluniverse-doctor` ## Example prompts - Search PubMed for recent clinical trials on rare genetic diseases and summarize them. - Run an ArXiv search for protein folding papers and extract the top citations. - Check missing extras and tool dependencies using `tooluniverse-doctor`. ## Similar - [Zotero MCP](https://affpapa.org/en/nevibecode/mcp/zotero-mcp.md) — MCP server · ★ 5548 - [arxiv-mcp-server](https://affpapa.org/en/nevibecode/mcp/arxiv-mcp-server.md) — MCP server · ★ 3231 - [PaperBanana](https://affpapa.org/en/nevibecode/mcp/paperbanana.md) — MCP server · ★ 2417 - [MATLAB MCP Server](https://affpapa.org/en/nevibecode/mcp/matlab-mcp-server.md) — MCP server · ★ 1716 - [Hex Research](https://affpapa.org/en/nevibecode/mcp/hex-research.md) — MCP server · ★ 583 - [DocsAgent — Zotero, Obsidian & Apple Notes MCP Server](https://affpapa.org/en/nevibecode/mcp/docsagent-zotero-obsidian-apple-notes-mcp-server.md) — MCP server · ★ 578 From the same set: [mims-harvard/tooluniverse](https://affpapa.org/en/nevibecode/by/mims-harvard/tooluniverse.md) — 55 cards --- NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md