Tutorial Navigation

This comprehensive tutorial takes you from basic concepts to advanced AI scientist workflows, with everything you need to democratize AI agents for scientific discovery.

Choose the section that matches your current needs:

💡 For Python API documentation, see the dedicated ../api/index section.

💡 For MCP integration and server setup, see the comprehensive MCP Support guide.

Core Concepts

  • ⚙️ Loading Tools → Tool Loading Tutorial - Complete tutorial to loading tools with Python API and MCP terminal commands

  • 📋 Listing Tools → Tool Listing Tutorial - Discover and filter tools by capability, domain, and IO

  • 🔧 Tool Caller → Tool Caller Tutorial - Primary execution engine with dynamic loading, validation, and MCP server integration

  • 🔗 Tool Composition → Tool Composition Tutorial - Chain ToolUniverse’s 600+ tools into powerful scientific workflows using Tool Composer

  • 🔬 Scientific Workflows → Scientific Workflows - Real-world research scenarios: drug discovery, safety analysis, literature review

  • 📡 MCP Support → MCP Support - Model Context Protocol integration and server setup

  • 🔊 Streaming Tools → Streaming Tools Tutorial - Real-time streaming output and custom tool integration

  • 📝 Logging → Logging Tutorial - Comprehensive logging configuration and debugging

  • 🗃️ Result Caching → Result Caching - Configure in-memory and persistent caches for tool results

  • 🔗 Interaction Protocol → AI-Tool Interaction Protocol - Understanding tool interaction patterns

Tool Discovery & Usage

  • 🔍 Tool Discovery → Tool Finder Tutorial - Tutorial to ToolUniverse’s three tool finder methods: keyword, LLM, and embedding search

  • 📚 Tools Overview → Available Tools Reference - Comprehensive overview of all available tools

Building AI Scientists

  • 🤖 Building AI Scientists → Building AI Scientists - Create AI research assistants from LLMs, reasoning models, and agentic systems

    • 🖥️ Claude Desktop → Claude Desktop - Integrate ToolUniverse with Claude Desktop App through MCP

    • 💻 Claude Code → Claude Code - Build AI scientists using Claude Code environment

    • 🔮 Gemini CLI → Gemini CLI - Command-line based scientific research with Gemini CLI

    • 🧠 Qwen Code → Qwen Code - AI scientist integration with Qwen Code environment

    • ⚡ Codex CLI → GPT Codex CLI - Terminal-based AI scientist with Codex CLI

    • 🎯 ChatGPT API → ChatGPT API - Programmatic scientific research with ChatGPT function calling

Advanced Features

Note

New to ToolUniverse? Start with the Quick Start Tutorial for a 5-minute introduction, then come back here for in-depth learning.

Tool Collections

Specialized tool collections for specific research domains:

  • 🏥 Clinical Guidelines → Clinical Guidelines Tools - Search and extract clinical practice guidelines from NICE, WHO, PubMed, and 5 other authoritative sources

  • 📖 Literature Search → Literature Search Tools Tutorial - Comprehensive literature search across PubMed, arXiv, bioRxiv, and academic databases