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

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

search_biorxiv_key_words: Search for articles on bioRxiv using keywords.
search_biorxiv_advanced: Perform an advanced search for articles on bioRxiv with multiple parameters.
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?

📁 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.

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Resources

GitHub Repository

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Related Servers

bioRxiv-MCP-Server