bioRxiv

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.

python

21

GitHub Stars

python

Language

6 months ago

First Indexed

2 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "jackkuo666-biorxiv-mcp-server": {
      "command": "python",
      "args": [
        "biorxiv_server.py"
      ]
    }
  }
}

The bioRxiv MCP Server lets AI assistants search bioRxiv preprints, fetch metadata, and download papers through a lightweight MCP interface. It connects your AI workflows to biology literature so you can query, compare, and analyze recent preprints efficiently.

How to use

You will interact with the server through an MCP client. Start by launching the local server, then issue MCP actions such as searching for papers by keywords or retrieving metadata for a specific DOI. You can request a list of downloaded papers and download full paper content for reading. Use the provided tools to perform keyword searches, run advanced queries, and fetch structured metadata to feed your AI prompts.

How to install

Prerequisites are Python 3.10 or higher and the FastMCP library.

Step 1: Clone the repository and navigate into the project directory.

git clone https://github.com/JackKuo666/bioRxiv-MCP-Server.git
cd bioRxiv-MCP-Server

Step 2: Install the required dependencies.

pip install -r requirements.txt

Optional Step: If you want to install via Smithery for various clients, use the provided installation commands for your client. The server can be run locally as a Python module or script after installation.

Additional notes

Usage starts with running the server locally. The basic start command shown is to run the server as a Python script.

If you plan to integrate with Claude Desktop or other MCP clients, you can configure an MCP server entry that points to the local Python process. This enables clients to send MCP requests to your running server and receive paper search results, metadata, and content.

Tools and capabilities

The bioRxiv MCP Server provides several tools to interact with bioRxiv data:

Troubleshooting and tips

Ensure Python 3.10+ is installed and the virtual environment (if used) is activated when running the server. - If the server cannot be started, verify that the working directory contains the script biorxiv_server.py and that required dependencies are installed. - When using MCP clients, make sure the client configuration points to the correct command and arguments for launching the local server.

Available tools

search_biorxiv_key_words

Search bioRxiv papers using keywords and retrieve matching results with metadata.

search_biorxiv_advanced

Perform an advanced search with multiple parameters to refine results.

get_biorxiv_metadata

Fetch detailed metadata for a bioRxiv article identified by its DOI.