bioRxiv-MCP-Server

# 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 📝 ## 🚀 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](https://smithery.ai/server/@JackKuo666/biorxiv-mcp-server): #### claude ```bash 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 ```s npx -y @smithery/cli@latest run @JackKuo666/biorxiv-mcp-server --client cursor --config "{}" ``` #### Windsurf ```sh npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client windsurf --config "{}" ``` #### CLine ```sh 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) ```json { "mcpServers": { "biorxiv": { "command": "python", "args": ["-m", "biorxiv-mcp-server"] } } } ``` (Windows version): ```json { "mcpServers": { "biorxiv": { "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe", "args": [ "-m", "biorxiv-mcp-server" ] } } } ``` Using with Cline ```json { "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: ```bash 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? ``` ## 📁 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.