Enables communication between AI assistants and the bioRxiv preprint repository through the Model Context Protocol, allowing AI models to search biological preprints and programmatically access their metadata.

Installation

From Source Code

git clone https://github.com/JackKuo666/bioRxiv-MCP-Server.git
cd bioRxiv-MCP-Server
pip install -r requirements.txt

Smithery (Claude)

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

Smithery (Cursor)

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

Smithery (Windsurf)

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

Smithery (CLine)

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

Configuration

Claude Desktop (Mac OS)

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

Claude Desktop (Windows)

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

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": []
    }
  }
}

Available Tools

Tool	Description
search_biorxiv_key_words	Search for articles on bioRxiv by keywords
search_biorxiv_advanced	Advanced search for articles on bioRxiv with multiple parameters
get_biorxiv_metadata	Retrieve metadata for a bioRxiv article by its DOI

Features

• Article Search: Query bioRxiv articles by keywords or advanced search
• Efficient Data Retrieval: Fast access to article metadata
• Metadata Access: Obtain detailed metadata for specific articles
• Research Support: Facilitate research and analysis in biological sciences
• Article Access: Download and read article content
• Article List: View all downloaded articles
• Local Storage: Articles are stored locally for faster access
• Research Prompts: A set of specialized prompts for article analysis

Usage Examples

Can you search bioRxiv for recent papers about genomics?

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

Notes

Requires Python 3.10+ and the FastMCP library. This tool is intended for research purposes only—please respect bioRxiv's terms of use and use responsibly.