VFB3-MCP Server

A Model Context Protocol (MCP) server for interacting with VirtualFlyBrain (VFB) APIs. This server provides tools to query VFB data, run queries, and search for terms.

🚀 Quick Start

Use the Live Service (Recommended)

The easiest way to use VFB3-MCP is through our hosted service at https://vfb3-mcp.virtualflybrain.org. This requires no installation or setup on your machine.

#### Claude Desktop Setup

1. Open Claude Desktop and go to Settings
2. Navigate to the MCP section
3. Add a new MCP server with these settings:

• Server Name: virtual-fly-brain (or any name you prefer)
• Type: HTTP
• Server URL: https://vfb3-mcp.virtualflybrain.org

Configuration JSON (alternative method):

{
  "mcpServers": {
    "virtual-fly-brain": {
      "url": "https://vfb3-mcp.virtualflybrain.org"
    }
  }
}

#### Claude Code Setup

1. Locate your Claude configuration file:

• macOS/Linux: ~/.claude.json
• Windows: %USERPROFILE%\.claude.json

1. Add the VFB3-MCP server to your configuration:

{
  "mcpServers": {
    "virtual-fly-brain": {
      "url": "https://vfb3-mcp.virtualflybrain.org"
    }
  }
}

1. Restart Claude Code for changes to take effect

#### GitHub Copilot Setup

1. Open VS Code with GitHub Copilot installed
2. Open Settings (Ctrl/Cmd + ,)
3. Search for "MCP" in the settings search
4. Find the MCP Servers setting
5. Add the server URL: https://vfb3-mcp.virtualflybrain.org
6. Give it a name like "Virtual Fly Brain"

#### Visual Studio Code (with MCP Extension)

1. Install the MCP extension for VS Code from the marketplace
2. Open the Command Palette (Ctrl/Cmd + Shift + P)
3. Type "MCP: Add server" and select it
4. Choose "HTTP" as the server type
5. Enter the server details:

• Name: virtual-fly-brain
• URL: https://vfb3-mcp.virtualflybrain.org

1. Save and restart VS Code if prompted

#### Other MCP Clients

For any MCP-compatible client that supports HTTP servers:

{
  "mcpServers": {
    "virtual-fly-brain": {
      "url": "https://vfb3-mcp.virtualflybrain.org",
      "type": "http"
    }
  }
}

#### Testing the Connection

Once configured, you can test that VFB3-MCP is working by asking your AI assistant to:

• "Get information about the term VFB_jrcv0i43"
• "Search for terms related to medulla"
• "Run a PaintedDomains query for VFB_00101567"

If you see responses with VirtualFlyBrain data, the setup is successful!

🛠️ Local Installation

Prerequisites

• Node.js 18 or higher
• npm or yarn

Step-by-Step Installation

1. Clone the repository:

   git clone https://github.com/Robbie1977/VFB3-MCP.git
   cd VFB3-MCP

1. Install dependencies:

   npm install

1. Build the project:

   npm run build

1. Start the server:

   npm start

Platform-Specific Setup

#### Claude Desktop (Local Development)

For local development with Claude Desktop, add this to your MCP configuration:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "vfb3-mcp": {
      "command": "node",
      "args": ["/absolute/path/to/VFB3-MCP/dist/index.js"]
    }
  }
}

#### Claude Code

Add to your claude.json file:

{
  "mcpServers": {
    "vfb3-mcp": {
      "command": "node",
      "args": ["/absolute/path/to/VFB3-MCP/dist/index.js"]
    }
  }
}

#### Visual Studio Code

1. Install the MCP extension for VS Code
2. Press Cmd + Shift + P (macOS) or Ctrl + Shift + P (Windows/Linux)
3. Select MCP: Add server…
4. Choose Command type
5. Enter:

• Name: vfb3-mcp
• Command: node
• Arguments: /absolute/path/to/VFB3-MCP/dist/index.js

#### GitHub Copilot

Configure the MCP server URL in your Copilot settings to point to your local server:

http://localhost:3000

For HTTP mode testing:

MCP_MODE=http PORT=3000 node dist/index.js

Docker Installation

Using Docker Compose (Recommended):

docker-compose up --build

Manual Docker Build:

# Build the image
docker build -t vfb3-mcp .

# Run the container
docker run -p 3000:3000 vfb3-mcp

Pull Pre-built Image:

docker pull virtualflybrain/vfb3-mcp:latest
docker run -p 3000:3000 virtualflybrain/vfb3-mcp:latest

Available Tools

get_term_info

Retrieve detailed information about VFB terms using their IDs.

Parameters:

• id (string): VFB ID (e.g., "VFB_jrcv0i43")

run_query

Execute predefined queries on VFB data.

Parameters:

• id (string): VFB ID (e.g., "VFB_00101567")
• query_type (string): Type of query (e.g., "PaintedDomains")

search_terms

Search for VFB terms using the Solr search server.

Parameters:

• query (string): Search query (e.g., "medulla")

🧠 About VirtualFlyBrain

VirtualFlyBrain (VFB) is a comprehensive knowledge base about Drosophila melanogaster neurobiology, providing 3D images, gene expression data, neural connectivity information, and standardized terminology for fly brain research.

📖 Documentation

• [LLM Guidance](LLM_GUIDANCE.md): Guide for AI assistants on using this MCP effectively
• [Examples](examples.md): Usage examples and integration guides
• [Technical Documentation](TECHNICAL.md): Infrastructure, deployment, and development details

📄 License

MIT