mims-harvard__tooluniverse/docs/dev_docs/overview.md

TxAgent Documentation

This directory contains documentation for TxAgent and guides on integrating with MCP (Model Context Protocol) servers and ToolUniverse.

Available Documentation

<EFBFBD>️ Adding Tools Tutorial

NEW! Complete Tutorial for adding custom tools to ToolUniverse:

• Decorator-based auto-registration system
• Step-by-step examples with real code
• Configuration best practices
• Troubleshooting and testing guides
• Multiple registration methods

<EFBFBD> MCP Server Tutorial

A comprehensive Tutorial that covers:

• Converting your Python program into an MCP server
• Creating ToolUniverse configuration files
• Integration best practices
• Troubleshooting common issues
• Complete working examples

Overview

TxAgent is an AI agent for precision therapeutics and personalized treatment recommendations. This documentation helps you:

1. Add Custom Tools: Create your own tools using the decorator-based system
2. Expose TxAgent as an MCP Server: Make TxAgent accessible via the Model Context Protocol
3. Integrate with ToolUniverse: Use TxAgent tools within the ToolUniverse framework
4. Create Your Own MCP Tools: Convert any Python program into an MCP server

Key Components

MCP Server

• Purpose: Standardized way to expose AI tools and functions
• Protocol: HTTP-based communication
• Benefits: Remote access, scalability, standardization

ToolUniverse Integration

• Auto-discovery: Automatically finds and registers MCP tools
• Unified Interface: Single API for multiple tool types
• Configuration: JSON-based tool definitions

FastMCP Framework

• Library: Python framework for creating MCP servers
• Features: Easy decorator-based tool definition
• Transport: HTTP and other protocols supported

Getting Started

1. Want to add your own tools? Start with the Adding Tools Tutorial
2. New to MCP? Check out the MCP Server Tutorial
3. Need quick optimization? Use the Tool Description Optimizer Quick Start

Example Files

In the parent directory, you'll find:

• run_mcp.py - TxAgent MCP server implementation
• tooluni_client.py - Example of using TxAgent through ToolUniverse
• txagent_client_tools.json - ToolUniverse configuration for TxAgent

Architecture Overview

┌─────────────────┐    HTTP/MCP     ┌──────────────────┐
│   Your Client   │ ◄─────────────► │   MCP Server     │
│  (ToolUniverse) │                 │  (Your Program)  │
└─────────────────┘                 └──────────────────┘
       │                                    │
       │                                    │
       ▼                                    ▼
┌─────────────────┐                 ┌──────────────────┐
│ Configuration   │                 │  Tool Functions  │
│ JSON File       │                 │  (@server.tool)  │
└─────────────────┘                 └──────────────────┘

Support

If you encounter issues:

1. Check the troubleshooting sections in the tutorials
2. Verify your configuration matches the examples
3. Ensure all dependencies are properly installed
4. Test MCP server functionality independently

Contributing

When adding new documentation:

1. Follow the existing markdown structure
2. Include practical examples
3. Test all code snippets
4. Update this README if adding new files

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For questions about TxAgent specifically, refer to the main project README in the parent directory.