bioRxiv MCP server

The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol. This tool allows AI models to search for biology preprints and access their metadata in a structured format, making it easier to retrieve and work with scientific papers.

Installation Options

Standard 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

For automatic installation using Smithery, choose the option matching your AI assistant:

For Claude Desktop

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

For Cursor

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

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

For Windsurf

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

For CLine

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

Configuration

Claude Desktop Configuration

Add this to your claude_desktop_config.json:

For macOS:

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

For Windows:

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

CLine Configuration

{
  "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": []
    }
  }
}

Starting the Server

Run the server with:

python biorxiv_server.py

Available Tools

The bioRxiv MCP Server provides three main tools:

1. Simple Paper Search

Use the search_biorxiv_key_words tool to search for articles using keywords.

Example query to your AI assistant:

Can you search bioRxiv for recent papers about CRISPR gene editing?

2. Advanced Paper Search

Use the search_biorxiv_advanced tool to perform more targeted searches with multiple parameters.

Example query:

Can you do an advanced search on bioRxiv for papers about machine learning in genomics published in the last year?

3. Paper Metadata Retrieval

Use the get_biorxiv_metadata tool to retrieve detailed information about a specific paper using its DOI.

Example query:

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

Practical Usage Tips

• The server needs to be running for the AI assistant to access bioRxiv papers
• Use specific keywords for better search results
• For advanced searches, you can specify parameters like date range, authors, and subject areas
• When asking about a specific paper, always include the DOI if you have it

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "biorxiv" '{"command":"python","args":["-m","biorxiv-mcp-server"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

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

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

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

3. Restart Claude Desktop for the changes to take effect