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Democratizing AI Scientists for Science
---------------------------



ToolUniverse is a unified ecosystem that transforms any large language model (LLM)—open or closed—into a powerful AI scientist. By standardizing how LLMs identify and call tools, it integrates over 600 scientific resources, including machine learning models, datasets, APIs, and analysis packages.

With its **AI-Tool Interaction Protocol**, ToolUniverse provides a common interface for seamless communication between LLMs and tools, ensuring compatibility across platforms such as GPT, Claude, Gemini, and open-source models.


Building your AI Scientists
---------------------------

Transform any LLM/Reasoning Model/Agent into a powerful research scientist with ToolUniverse's comprehensive integration guides:

📖 **Complete Tutorial**: `Building AI Scientists Overview <guide/building_ai_scientists/index.html>`_


- **Claude Desktop**: `Claude Desktop Integration <guide/building_ai_scientists/claude_desktop.html>`_
- **Claude Code**: `Claude Code Integration <guide/building_ai_scientists/claude_code.html>`_
- **Gemini CLI**: `Gemini CLI Integration <guide/building_ai_scientists/gemini_cli.html>`_
- **Qwen Code**: `Qwen Code Integration <guide/building_ai_scientists/qwen_code.html>`_
- **Codex CLI**: `Codex CLI Integration <guide/building_ai_scientists/codex_cli.html>`_
- **ChatGPT API**: `ChatGPT API Integration <guide/building_ai_scientists/chatgpt_api.html>`_

🌍 Ecosystem & Community
------------------------
**Open Science**

- Open-source ecosystem encouraging community contributions
- Standardized tool specifications for agentic AI
- Integration with heterogeneous scientific workflows

**Join the Community**

- **Web Service**: `aiscientist.tools <https://aiscientist.tools>`_
- **GitHub Repository**: `mims-harvard/ToolUniverse <https://github.com/mims-harvard/ToolUniverse>`_
- **Report Issues**: `GitHub Issues <https://github.com/mims-harvard/ToolUniverse/issues>`_
- **Discussions**: `Join our Slack community <https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ>`_

📚 Documentation Structure
-------------------------

.. toctree::
   :maxdepth: 1
   :caption: 🚀 Getting Started

   quickstart
   installation
   getting_started

.. toctree::
   :maxdepth: 3
   :caption: 🤖 Building AI Scientists

   guide/building_ai_scientists/index

.. toctree::
   :maxdepth: 1
   :caption: 💡 Use ToolUniverse

   guide/index
   guide/interaction_protocol
   guide/loading_tools
   guide/listing_tools
   tutorials/finding_tools
   guide/tool_caller
   guide/mcp_support
   guide/compact_mode
   guide/toolspace
   guide/coding_api
   tutorials/tooluniverse_case_study
   tutorials/agentic_tools_tutorial
   tutorials/literature_search_tools_tutorial
   tutorials/literature_search_web_ui_tutorial
   guide/clinical_guidelines_tools
   guide/tool_composition
   guide/scientific_workflows
   tutorials/expert_feedback
   guide/hooks/index

.. toctree::
   :maxdepth: 3
   :caption: 🔨 Add Tools to ToolUniverse

   expand_tooluniverse/index
   expand_tooluniverse/quick_start
   expand_tooluniverse/local_tools/index
   expand_tooluniverse/remote_tools/index
   expand_tooluniverse/contributing/index
   expand_tooluniverse/architecture
   deployment

.. toctree::
   :maxdepth: 1
   :caption: 🔧 Tools

   tools/tools_config_index
   tools/remote_tools


.. toctree::
   :maxdepth: 1
   :caption: 🔌 API

   api/modules

.. toctree::
   :maxdepth: 1
   :caption: ❓ Reference

   reference/data_sources