Virtual Fly Brain MCP Server v1.6.2

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

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": {
      "type": "http",
      "url": "https://vfb3-mcp.virtualflybrain.org",
      "tools": ["*"]
    }
  }
}

Claude Code Setup

1. Locate your Claude configuration file:
   • macOS/Linux: ~/.claude.json
   • Windows: %USERPROFILE%\.claude.json
2. Add the VFB3-MCP server to your configuration:

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

3. 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
6. Save and restart VS Code if prompted

Other MCP Clients

For any MCP-compatible client that supports HTTP servers:

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

Gemini Setup

To use the Virtual Fly Brain (VFB) Model Context Protocol (MCP) server with Google Gemini, you can connect through custom Python/Node.js clients that support MCP.

Note: Direct Gemini web interface integration with MCP is not currently supported. Developer tools are needed to connect the two.

Using Python

For application development, use the mcp and google-genai libraries to connect.

1. Setup: pip install google-genai mcp
2. Implementation: Use an SSEClientTransport to connect to the VFB URL, list its tools, and pass their schemas to the Gemini model as Function Declarations.

🧪 Testing the Connection

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

Basic Queries:

• "Get information about the neuron VFB_jrcv0i43"
• "Search for terms related to medulla in the fly brain"
• "What neurons are in the antennal lobe?"

Advanced Queries:

• "Find all neurons that connect to the mushroom body"
• "Show me expression patterns for gene repo"
• "What brain regions are involved in olfactory processing?"
• "Run a connectivity analysis for neuron VFB_00101567"

Search Examples:

• "Search for adult neurons in the visual system"
• "Find genes expressed in the central complex"
• "Show me all templates available in VFB"

If you see responses with VirtualFlyBrain data, including neuron names, brain regions, gene expressions, or connectivity information, the setup is successful!

Example Workflow

1. Search for a term: "Search for neurons in the optic lobe"
2. Get detailed info: "Get information about VFB_00101567"
3. Run specific queries: "Show connectivity for VFB_00101567"
4. Explore relationships: "What neurons synapse in the mushroom body?"

🛠️ Available Tools

• get_term_info - Get term information from VirtualFlyBrain using a VFB ID
• run_query - Run a query on VirtualFlyBrain using a VFB ID and query type
• search_terms - Search for VFB terms using the Solr search server with filtering options

🧠 About VirtualFlyBrain

VirtualFlyBrain (VFB) is a comprehensive knowledge base about Drosophila melanogaster neurobiology, integrating neuroanatomical 3D images and models, gene expression data, neural connectivity, and standardized terminology.

📖 Documentation

• Full Documentation on GitHub
• Virtual Fly Brain Website

This server is designed for MCP clients like Claude Desktop, Claude Code, and GitHub Copilot.