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bioRxiv-MCP-Server

bioRxiv-MCP-Server

Public
JackKuo666/bioRxiv-MCP-Server

Enable AI assistants to search, retrieve, and access detailed metadata and full content of biology preprints from bioRxiv efficiently via the Model Context Protocol for enhanced research and analysis.

python
0 tools
May 29, 2025
Updated Jun 4, 2025

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bioRxiv MCP Server

šŸ” 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.

šŸ¤ Contribute • šŸ“ Report Bug

✨ Core Features

  • šŸ”Ž Paper Search: Query bioRxiv papers with keywords or advanced search āœ…
  • šŸš€ Efficient Retrieval: Fast access to paper metadata āœ…
  • šŸ“Š Metadata Access: Retrieve detailed metadata for specific papers āœ…
  • šŸ“Š Research Support: Facilitate biological sciences research and analysis āœ…
  • šŸ“„ Paper Access: Download and read paper content šŸ“
  • šŸ“‹ Paper Listing: View all downloaded papers šŸ“
  • šŸ—ƒļø Local Storage: Papers are saved locally for faster access šŸ“
  • šŸ“ Research Prompts: A set of specialized prompts for paper analysis šŸ“

šŸš€ 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": [] } } }

šŸ“Š Usage

Start the MCP server:

python biorxiv_server.py

šŸ›  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?

šŸ“ Project Structure

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

šŸ”§ Dependencies

  • Python 3.10+
  • FastMCP
  • asyncio
  • logging

šŸ¤ Contributing

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

šŸ“„ License

This project is licensed under the MIT License.

āš ļø Disclaimer

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

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