UCSC Cell Browser MCP Server

A Model Context Protocol (MCP) server that provides access to UCSC Cell Browser datasets by parsing the dataset.json file from https://cells.ucsc.edu/dataset.json.

Installation

From Source (Development)

# Clone the repository
git clone https://github.com/MCPmed/UCSCCBmcp
cd ucsccbMCP

# Install in development mode
pip install -e .

From PyPI (when published)

pip install ucsc-cell-browser-mcp

Usage

Command Line

After installation, you can run the MCP server using:

ucsc-mcp

This will start the MCP server and listen for connections via stdio.

As a Python Module

from ucsccbmcp.main import main_cli

# Run the MCP server
main_cli()

Available Tools

The MCP server provides the following tools:

• search_datasets: Search UCSC Cell Browser datasets by various criteria
• get_dataset_details: Get detailed information about a specific dataset
• list_organisms: List all available organisms in the cell browser
• list_body_parts: List all available body parts in the cell browser
• list_diseases: List all available diseases in the cell browser
• list_projects: List all available projects in the cell browser
• refresh_data: Refresh the dataset cache from UCSC Cell Browser

Configuration

The server automatically caches dataset information for 1 hour to improve performance. You can force a refresh using the refresh_data tool.

Dependencies

• Python 3.8+
• httpx>=0.24.0
• mcp>=1.0.0

Development

Setup Development Environment

# Install development dependencies
pip install -e .[dev]

# Run tests
pytest

# Format code
black ucsccbmcp/

# Lint code
flake8 ucsccbmcp/