What is Biorxiv Mcp Server

bioRxiv-MCP-Server is a tool that enables AI assistants to search and access bioRxiv papers through a simple Model Context Protocol (MCP) interface, facilitating programmatic access to biology preprints and their metadata.

Use cases

Use cases include academic research, literature reviews, and data analysis in biological sciences, allowing researchers to quickly find and access relevant preprints.

How to use

To use bioRxiv-MCP-Server, clone the repository, install the required dependencies, and start the MCP server. You can then query papers using keywords or DOIs through your AI assistant.

Key features

Key features include paper search with keywords, efficient retrieval of metadata, access to detailed paper information, local storage for faster access, and specialized prompts for research analysis.

Where to use

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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.

🤝 Contribute • 📝 Report Bug

✨ 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.