bioRxiv MCP Server

Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.

The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv’s preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their metadata in a programmatic way.

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Core Features

• Paper Search: Query bioRxiv papers with keywords or advanced search
• Efficient Retrieval: Fast access to paper metadata
• Metadata Access: Retrieve detailed metadata for specific papers
• Research Support: Facilitate biological sciences research and analysis
• Paper Access: Download and read paper content
• Paper Listing: View all downloaded papers
• Local Storage: Papers are saved locally for faster access
• Research Prompts: A set of specialized prompts for paper analysis

Quick Start

Prerequisites

• Python 3.10+
• FastMCP library

Installation

1. Clone the repository:

   git clone https://github.com/JackKuo666/bioRxiv-MCP-Server.git
   cd bioRxiv-MCP-Server
   

2. Install the required dependencies:

   pip install -r requirements.txt
   

Installing via Smithery

To install bioRxiv Server for Claude Desktop automatically via Smithery:

claude

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client claude --config "{}"

Cursor

Paste the following into Settings → Cursor Settings → MCP → Add new server:

• Mac/Linux

npx -y @smithery/cli@latest run @JackKuo666/biorxiv-mcp-server --client cursor --config "{}" 

Windsurf

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client windsurf --config "{}"

CLine

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client cline --config "{}"

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

{
  "mcpServers": {
    "biorxiv": {
      "command": "python",
      "args": ["-m", "biorxiv-mcp-server"]
      }
  }
}

(Windows version):

{
  "mcpServers": {
    "biorxiv": {
      "command": "C:\Users\YOUR_USERNAME\AppData\Local\Programs\Python\Python311\python.exe",
      "args": [
        "-m",
        "biorxiv-mcp-server"
      ]
    }
  }
}

Using with Cline

{
  "mcpServers": {
    "biorxiv": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

Usage

Start the MCP server:

python biorxiv_server.py

MCP Tools

The bioRxiv MCP Server provides the following tools:

1. search_biorxiv_key_words: Search for articles on bioRxiv using keywords.
2. search_biorxiv_advanced: Perform an advanced search for articles on bioRxiv with multiple parameters.
3. get_biorxiv_metadata: Fetch metadata for a bioRxiv article using its DOI.

Searching Papers

You can ask the AI assistant to search for papers using queries like:

Can you search bioRxiv for recent papers about genomics?

Getting Paper Details

Once you have a DOI, you can ask for more details:

Can you show me the metadata for the paper with DOI 10.1101/123456?

Project Structure

• biorxiv_server.py: The main MCP server implementation using FastMCP
• biorxiv_web_search.py: Contains the web scraping logic for searching bioRxiv

Dependencies

• Python 3.10+
• FastMCP
• asyncio
• logging

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License.

Disclaimer

This tool is for research purposes only. Please respect bioRxiv’s terms of service and use this tool responsibly.