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BioRxiv MCP Server

@JackKuo666

Repository

Basic information

Category

Other

Transports

stdio

Author

JackKuo666

Submitted by

lyonlin

About BioRxiv MCP Server

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.

#biorxiv#bioinformatics#research-assistant

BioRxiv MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "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": []
    }
  }
}

BioRxiv MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is BioRxiv MCP Server?

The BioRxiv MCP Server bridges 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 programmatically. It is designed for researchers and AI users who need to query bioRxiv content.

How to use BioRxiv MCP Server?

Install the server by cloning the repository and running pip install -r requirements.txt, or use Smithery for Claude/Cursor/Windsurf/CLine. Start the server with python biorxiv_server.py and add the MCP configuration to your client’s config file. Ask the AI assistant to search papers using keywords or to retrieve metadata by DOI.

Key features of BioRxiv MCP Server

  • Paper search with keywords or advanced queries
  • Fast retrieval of paper metadata
  • Access detailed metadata for specific papers
  • Download and read full paper content
  • Local storage of papers for faster access
  • Specialized prompts for paper analysis

Use cases of BioRxiv MCP Server

  • Search for recent bioRxiv papers about a specific topic
  • Retrieve full metadata for a known preprint DOI
  • Download papers for offline reading and analysis
  • Automate literature surveys with AI assistance

Frequently asked questions

1

What are the prerequisites to run the server?

Python 3.10 or higher and the FastMCP library are required.

2

How can I install the server automatically via Smithery?

Run the Smithery CLI command for your client (e.g., `npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client claude --config "{}"`).

3

What MCP tools does the server provide?

Three tools: `search_biorxiv_key_words`, `search_biorxiv_advanced`, and `get_biorxiv_metadata` (using a DOI).

4

Where are downloaded papers stored?

Papers are saved locally on your machine for faster subsequent access.

5

Is this tool intended for commercial use?

No – the disclaimer states the tool is for research purposes only, and users must respect bioRxiv’s terms of service.

Comments

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