BioRxivSAFE
🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
🔍 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
- Clone the repository:
git clone https://github.com/JackKuo666/bioRxiv-MCP-Server.git cd bioRxiv-MCP-Server
- 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 th
f2159a2d0152OBSERVED · 2026-10-09Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-server-bioRxiv -- uvx mcp-server-bioRxiv
{
"mcpServers": {
"mcp-server-bioRxiv": {
"command": "uvx",
"args": [
"mcp-server-bioRxiv"
]
}
}
}Exposed tools (3)
3 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
get_biorxiv_metadata | read | logging.info(f |
search_biorxiv_advanced | read | logging.info(f |
search_biorxiv_key_words | read | logging.info(f |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (2 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (2)
requests, bs4, mcp
Gates applied: no_behavioural_pass, no_license.
f2159a2d0152full audit observations/trust-audit/mcp-server/jackkuo666__biorxiv.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-09 | f2159a2d0152 | SAFE | B | 89 | first audit |
Questions
What is the BioRxiv MCP server?
🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.
What tools does BioRxiv expose?
3 in total: 3 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is BioRxiv safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does BioRxiv need?
No credential environment variables were found in its source, so it appears to need none.
How does BioRxiv run?
It speaks stdio, so it runs as a local process your client starts. It is published on PyPI as mcp-server-bioRxiv.
How current is this page?
The grade is for one exact copy of the source (f2159a2d0152), read on 2026-10-09. The repository is watched and re-audited when it changes.