medRxiv MCP Server
About
🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.
Details
- Author
- JackKuo666
- GitHub stars
- 25
- Downloads
- 311
- Categories
- Other
Jump to
- Paper search with keywords or advanced parameters
- Fast retrieval of paper metadata
- Download and read full paper content
- List all locally stored papers
- Local storage for faster subsequent access
- Specialized prompts for paper analysis
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
medRxiv MCP ServerCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Requires Python 3.10+ and the FastMCP library. Clone the repository, install dependencies, then start the server with python biorxiv_server.py. Alternatively, install via Smithery for Claude Desktop, Cursor, Windsurf, or CLine by adding the appropriate configuration to the client's MCP settings.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"medrxiv mcp server": {
"mcp-server-bioRxiv": {
"command": "npx",
"args": [
"-y",
"@smithery/cli@latest",
"install",
"@JackKuo666/biorxiv-mcp-server",
"--client",
"claude",
"--config",
"{}"
]
}
}
}
}McpServers
{
"mcp-server-bioRxiv": {
"command": "npx",
"args": [
"-y",
"@smithery/cli@latest",
"install",
"@JackKuo666/biorxiv-mcp-server",
"--client",
"claude",
"--config",
"{}"
]
}
}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:
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"
]
}
}
}
{
"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:
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.
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