bioRxiv MCP Server

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?