bioRxiv MCP Server

🔍 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.

🤝 Contribute • 📝 Report Bug

✨ 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 📝

Related MCP server: mcp-simple-arxiv

🚀 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

Cursor

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

• Mac/Linux

Windsurf

CLine

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

(Windows version):

Using with Cline

📊 Usage

Start the MCP server:

🛠 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:

Getting Paper Details

Once you have a DOI, you can ask for more details:

📁 Project Structure

• biorxiv_server.py: The main MCP server implementation using FastMCP

• biorxiv_web_search.py: Contains the web scraping logic for searching bioRxiv

🔧 Dependencies

• Python 3.10+

• FastMCP

• asyncio

• logging

🤝 Contributing

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

📄 License

This project is licensed under the MIT License.

⚠️ Disclaimer

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