# 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.
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## ✨ 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.