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biostudies-mcp-server

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Overview

biostudies-mcp-server is a proof-of-concept (POC) implementation for a Model Context Protocol (MCP) server designed for BioStudies search, facilitating the integration of bioinformatics data.

To use biostudies-mcp-server, install Node.js and follow the instructions provided at https://modelcontextprotocol.io/quickstart/user. Alternatively, you can install it using Python with the following commands: pip install mcp mcp install server.py

  • POC implementation for BioStudies search - Integration capabilities with Claude Desktop - Easy installation via Node.js or Python
  1. Searching and retrieving bioinformatics data from BioStudies.
  2. Integrating bioinformatics tools with MCP for enhanced data handling.
  3. Facilitating research collaboration through shared bioinformatics resources.

Add to your AI client

Use these steps to connect biostudies-mcp-server in Cursor, Claude, VS Code, and other MCP-compatible apps. The same JSON appears in the Use with menu above for one-click copy.

Cursor

Add this to your .cursor/mcp.json file in your project root, then restart Cursor.

.cursor/mcp.json

{
  "mcpServers": {
    "biostudies-mcp-server-ebibiostudies": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

Claude Desktop

Add this server entry to the mcpServers object in your Claude Desktop config, then restart the app.

~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows)

{
  "mcpServers": {
    "biostudies-mcp-server-ebibiostudies": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

Claude Code

Add this to your project's .mcp.json file. Claude Code will detect it automatically.

.mcp.json (project root)

{
  "mcpServers": {
    "biostudies-mcp-server-ebibiostudies": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

VS Code (Copilot)

Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.

.vscode/mcp.json

{
  "servers": {
    "biostudies-mcp-server-ebibiostudies": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

Windsurf

Add this to your Windsurf MCP config file, then restart Windsurf.

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "biostudies-mcp-server-ebibiostudies": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

Cline

Open Cline settings, navigate to MCP Servers, and add this server configuration.

Cline MCP Settings (via UI)

{
  "mcpServers": {
    "biostudies-mcp-server-ebibiostudies": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-biostudies-mcp-server-ebibiostudies"
      ]
    }
  }
}

FAQ

What is the purpose of biostudies-mcp-server?

It serves as a POC for integrating bioinformatics data using the Model Context Protocol.

Is there a specific programming language required?

Yes, it is implemented in Python and requires Node.js for certain functionalities.

Where can I find more information?

Detailed instructions and documentation are available at https://modelcontextprotocol.io/quickstart/user.

Research and data