JackKuo666/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:
2. Install the required dependencies:
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+