mims-harvard/ToolUniverse

記録された最新のソース活動: 2026年10月25日 12:09

SkillsMP カタログ更新: 2026年11月2日 18:02

収集済み skills: 439

GitHub スター: 1,771
GitHub フォーク: 267

AI アシスタントでインストール

このプロンプトをコピーして、使用中の AI アシスタントに送ってください。

Follow https://skillsmp.com/skill-install/prompt.md to install Agent Skills from https://github.com/mims-harvard/ToolUniverse.

リポジトリの README

README の元ファイル：README.md

README の元ファイルを読む

README 全文を表示

# <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists [![Documentation](https://img.shields.io/badge/Documentation-Available-green)](https://zitniklab.hms.harvard.edu/ToolUniverse/) [![Paper](https://img.shields.io/badge/Paper-Arxiv-blue)](https://arxiv.org/abs/2509.23426) [![PyPI version](https://badge.fury.io/py/tooluniverse.svg)](https://badge.fury.io/py/tooluniverse) [![MCP Registry](https://img.shields.io/badge/MCP_Registry-Listed-blue)](https://registry.modelcontextprotocol.io) [![Website](https://img.shields.io/badge/Website-aiscientist.tools-blue)](https://aiscientist.tools) [![Slack](https://img.shields.io/badge/Slack-Join_Community-orange)](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ) [![WeChat](https://img.shields.io/badge/WeChat-Community-07C160)](https://aiscientist.tools/wechat) [![LinkedIn](https://img.shields.io/badge/LinkedIn-Follow-0077B5)](https://www.linkedin.com/in/shanghua-gao-96b0b3168/) [![X](https://img.shields.io/badge/X-Follow-000000)](https://x.com/ScientistTools) [![PyPI Downloads](https://static.pepy.tech/personalized-badge/tooluniverse?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=BLACK&left_text=downloads)](https://pepy.tech/projects/tooluniverse) [//]: # (mcp-name: io.github.mims-harvard/tooluniverse) ## 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](https://github.com/mims-harvard/ToolUniverse/issues/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. <details> <summary>or set up manually</summary> Add to your MCP config file: ```json { "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: ```bash npx skills add mims-harvard/ToolUniverse ``` </details> **Claude Code users** — one line, no config file: ```bash claude plugin marketplace add mims-harvard/ToolUniverse claude plugin install tooluniverse@tooluniverse ``` **Python developers** — install the SDK. Install [`uv`](https://docs.astral.sh/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. ```bash 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](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tu_cli.html)** — discover, inspect, run, and test tools from the terminal. **[Python SDK](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/python_guide.html)** — programmatic access for building AI scientist systems. ## Building AI Scientists with ToolUniverse <p align="center"> <a href="https://www.youtube.com/watch?v=fManSJlSs60"> <img src="https://github.com/user-attachments/assets/13ddb54c-4fcc-4507-8695-1c58e7bc1e68" width="600" /> </a> </p> *Click to watch the demo* [(YouTube)](https://www.youtube.com/watch?v=fManSJlSs60) [(Bilibili)](https://www.bilibili.com/video/BV1GynhzjEos/?share_source=copy_web&vd_source=b398f13447281e748f5c41057a2c6858) ## 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 **2,700 machine learning models, datasets, APIs, and scientific packages** for data analysis, knowledge retrieval, and experimental design. **Key features:** - [**AI-Tool Interaction Protocol**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/interaction_protocol.html): Standardized interface governing how AI scientists issue tool requests and receive results - [**Universal AI Model Support**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html): Works with Claude, GPT, Gemini, Qwen, Deepseek, and open models - [**MCP Integration**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/mcp_support.html): Native Model Context Protocol server with configurable transport and tool selection - [**Async Operations**](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/async_tools_guide.html): Long-running tasks (protein docking, molecular simulations) with progress tracking and parallel execution - [**Tool Composition**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_composition.html): Chain tools for sequential or parallel execution in self-directed workflows - [**Compact Mode**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/compact_mode.html): Reduces 2,700+ tools to 4-5 core discovery tools, saving ~99% context window - [**CLI (`tu`)**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tu_cli.html): Discover, inspect, run, and test tools directly from the terminal — 14 subcommands for interactive and scripted workflows - [**Agent Skills**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/skills_showcase.html): 68 pre-built research workflows for drug discovery, precision oncology, rare disease diagnosis, pharmacovigilance, and more - [**Literature Search**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/literature_search_tools_tutorial.html): Unified search across PubMed, Semantic Scholar, ArXiv, BioRxiv, Europe PMC, and more - [**Two-Tier Result Caching**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/cache_system.html): In-memory LRU + SQLite persistence with per-tool fingerprinting for 10x speedup, offline support, and reproducibility - [**Continuous Expansion**](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/index.html): Register new tools locally or remotely without additional configuration <p align="center"> <img src="https://github.com/user-attachments/assets/eb15bd7c-4e73-464b-8d65-733877c96a51" width="888" /> </p> ## AI Scientists Powered by ToolUniverse *Building your project with ToolUniverse? Submit via [GitHub Pull Request](https://github.com/mims-harvard/ToolUniverse/pulls) or contact us.* **TxAgent: AI Agent for Therapeutic Reasoning** [[Project]](https://zitniklab.hms.harvard.edu/TxAgent) [[Paper]](https://arxiv.org/pdf/2503.10970) [[PyPI]](https://pypi.org/project/txagent/) [[GitHub]](https://github.com/mims-harvard/TxAgent) [[HuggingFace]](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c) > TxAgent leverages ToolUniverse's scientific tool ecosystem to solve complex therapeutic reasoning tasks. --- **Medea: An Omics AI Agent for Therapeutic Discovery** [[Project]](https://medea.openscientist.ai) [[Paper]](https://www.biorxiv.org/content/early/2026/01/20/2026.01.16.696667) [[GitHub]](https://github.com/mims-harvard/Medea) > Medea integrates ToolUniverse tools for multi-omics analysis to identify therapeutic targets and predict drug responses across cancer, autoimmune, and other diseases. ## Workshops and Education **[Building AI Co-Scientists with ToolUniverse](https://github.com/ccb-hms/tooluniverse-ai-workshop)** > Materials from the October 8, 2026 workshop in the Core for Computational Biomedicine (CCB) AI Seminar & Workshop Series at Harvard Medical School. Includes the ToolUniverse workshop slides, CCB introduction slides, and a follow-along Markdown guide for using ToolUniverse live with clinical and genetics examples. ## Documentation Full documentation: [zitniklab.hms.harvard.edu/ToolUniverse](https://zitniklab.hms.harvard.edu/ToolUniverse/) - [CLI Reference (`tu`)](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tu_cli.html) - [Python Developer Guide](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/python_guide.html) - [AI Agent Setup](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html) - [Agent Skills](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/skills_showcase.html) - [Expand ToolUniverse](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/index.html) - [API Reference](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html) ## Community **[Shanghua Gao](https://shgao.site)**, the lead creator of this project, is currently on the job market. [Slack](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ) · [GitHub Issues](https://github.com/mims-harvard/ToolUniverse/issues) · [Shanghua Gao](mailto:shanghuagao@gmail.com) · [Marinka Zitnik](mailto:marinka@hms.harvard.edu) **Leaders:** [Shanghua Gao](https://shgao.site) · [Marinka Zitnik](https://zitniklab.hms.harvard.edu/) **Contributors:** [Shanghua Gao](https://shgao.site) · [Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/) · [Pengwei Sui](https://psui3905.github.io/) · [Zhenglun Kong](https://zlkong.github.io/homepage/) · [Sufian Aldogom](mailto:saldogom@mit.edu) · [Yepeng Huang](https://yepeng.notion.site/Yepeng-Huang-16ad8dd1740080c28d4bd3e3d7c1080c) · [Ayush Noori](https://www.ayushnoori.com/) · [Reza Shamji](mailto:reza_shamji@hms.harvard.edu) · [Krishna Parvataneni](mailto:krishna_parvataneni@hms.harvard.edu) · [Theodoros Tsiligkaridis](https://sites.google.com/view/theo-t) · [Marinka Zitnik](https://zitniklab.hms.harvard.edu/) ## Privacy Policy ToolUniverse runs locally and collects nothing: no telemetry, no analytics, no conversation data. When you run a tool, that tool's arguments are sent to that tool's data provider (UniProt, openFDA, Open Targets and so on) so it can answer, and nothing else leaves your machine. API keys stay local and are sent only to the service they belong to. Full policy: https://github.com/mims-harvard/ToolUniverse/blob/main/PRIVACY.md ## Citation ``` @article{gao2025democratizingaiscientistsusing, title={Democratizing AI scientists using ToolUniverse}, author={Shanghua Gao and Richard Zhu and Pengwei Sui and Zhenglun Kong and Sufian Aldogom and Yepeng Huang and Ayush Noori and Reza Shamji and Krishna Parvataneni and Theodoros Tsiligkaridis and Marinka Zitnik}, year={2025}, eprint={2509.23426}, archivePrefix={arXiv}, primaryClass={cs.AI}, url={https://arxiv.org/abs/2509.23426}, } ```

リポジトリの README を読み込んでいます…

このリポジトリの skills

その他の生物科学者医学科学者（疫学者除く）その他コンピュータ職生化学者・生物物理学者

22 件の職業カテゴリ · 36% 分類済み

skill

職業分類

説明

更新

setup-bioemu2-remote-tool

未分類

Set up, launch, validate, and troubleshoot the BioEmu-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

原文の言語: 英語

2026-10-25

setup-rfd4-proteina-remote-tool

未分類

Set up, launch, validate, and troubleshoot the RFD4-Proteina ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

原文の言語: 英語

2026-10-25

tooluniverse-protein-design-campaign

未分類

Run and review iterative protein binder design campaigns with multiple model families, structural and glycan checks, conditional pH hypotheses, resource-aware computation, and competition submission preparation. Use for ongoing candidate optimization or…

原文の言語: 英語

2026-10-22

tooluniverse-protein-design-campaign

未分類

原文の言語: 英語

2026-10-22

未分類

原文の言語: 英語

2026-10-19

未分類

How to use ToolUniverse Connect (connect.aiscientist.tools), the hosted ToolUniverse service, and when to use it instead of ToolUniverse installed on this computer. Use when the user asks how to use ToolUniverse or ToolUniverse Connect, how to connect Claude,…

原文の言語: 英語

2026-10-15

収集済み skill 439 件中 40 件を表示しています。