bioRxiv

by jackkuo666

9 stars

530 downloads

Not rated

GitHub

About

Provides a specialized interface for searching and retrieving bioRxiv scientific articles through keyword-based searching, advanced parameter filtering, and DOI metadata retrieval using Python's asyncio for asynchronous processing.

Details

Author: jackkuo666
Repository: JackKuo666/bioRxiv-MCP-Server
GitHub stars: 9
Downloads: 530
Categories: AI, Design, Developer Tools, Search, Infrastructure, Security, Other

- 🔎 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 📝

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 bioRxiv

Command (node, npx, python, etc.) python
Arguments
- Argument 1 -m
- Argument 2 biorxiv-mcp-server
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

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-c",
                "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
            ],
            "command": "bash"
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-c",
                "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
            ],
            "command": "bash"
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-c",
                "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
            ],
            "command": "bash"
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-c",
                "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
            ],
            "command": "bash"
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
        }
    }
}

JSON

{
    "mcpServers": {
        "biorxiv": {
            "env": {},
            "args": [
                "-c",
                "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
            ],
            "command": "bash"
        }
    }
}

From the repository

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

To install bioRxiv Server for Claude Desktop automatically via Smithery:

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": []
    }
  }
}

Start the MCP server:

python biorxiv_server.py

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?

`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.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "biorxiv": {
            "cwd": "string",
            "env": {},
            "args": [
                "-m",
                "biorxiv-mcp-server"
            ],
            "shell": false,
            "command": "python"
        }
    }
}

Linux

{
    "env": [],
    "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
    ],
    "command": "bash"
}

Macos

{
    "cwd": "string",
    "env": [],
    "args": [
        "-m",
        "biorxiv-mcp-server"
    ],
    "shell": false,
    "command": "python"
}

Windows

{
    "env": [],
    "args": [
        "-m",
        "biorxiv-mcp-server"
    ],
    "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe"
}

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"
      ]
    }
  }
}

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:

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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About

Details

Jump to

Setting up with Highlight

From the repository

search_biorxiv_key_words

search_biorxiv_advanced

get_biorxiv_metadata

Claude Desktop / Cursor

Linux

Macos

Windows

bioRxiv MCP Server

✨ Core Features

🚀 Quick Start

Prerequisites

Installation

Installing via Smithery

claude

Cursor

Windsurf

CLine

Usage with Claude Desktop

📊 Usage

🛠 MCP Tools

Searching Papers

Getting Paper Details

📁 Project Structure

🔧 Dependencies

🤝 Contributing

📄 License

⚠️ Disclaimer

Install

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`search_biorxiv_key_words`

`search_biorxiv_advanced`

`get_biorxiv_metadata`