.codex-plugin— mcp server

<div align="center"> <h1>@cyanheads/biorxiv-mcp-server</h1> <p><b>Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. STDIO or Streamable HTTP.</b> <div>5 Tools</div> </p> </div>

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Tools

Five tools for working with bioRxiv and medRxiv preprint data:

biorxiv_get_preprint

Fetch preprint metadata by DOI — all revisions in one call.

• Batch fetch up to 10 DOIs in a single request
• Each DOI returns the full revision history in collection[] — one API call per DOI, no enumeration loop
• Includes title, authors, abstract, category, license, PDF link (jatsxml), and published journal DOI when the preprint has been accepted
• Scope to biorxiv, medrxiv, or both; when both, each DOI fans out in parallel and partial failures report per-DOI in failed[]

biorxiv_list_recent

Page through preprints in a date interval.

• Server-side category filtering via ?category=… — pass a value from biorxiv_list_categories
• Fixed page size of 30 (API constraint); advance with integer cursor (0, 30, 60, …)
• Response includes total count per server for calculating remaining pages
• When server="both", each server paginates independently; response surfaces per-server pagination state ({ biorxiv: { cursor, total }, medrxiv: { cursor, total } })

biorxiv_search_preprints

Keyword search with relevance ranking.

• EuropePMC powers relevance ranking (indexes new preprints within 1–2 days of posting); bioRxiv/medRxiv API provides canonical metadata enrichment
• Covers both servers by default; scope down with server
• Optional date range filters (date_from, date_to)
• Enrichment failures degrade gracefully to EuropePMC-only metadata, surfaced via partial_results

biorxiv_get_published_version

Resolve a preprint DOI to its journal publication crosswalk.

• Uses the /pubs/{server}/{doi} endpoint for richer metadata than the published field in biorxiv_get_preprint
• Returns journal DOI, journal name, published date, and corresponding author institution
• Use when the preprint's published field is non-null and you need the full crosswalk record

biorxiv_list_categories

Return the static subject category taxonomy for both servers.

• No API call — hardcoded static list (~30 bioRxiv + ~50 medRxiv categories)
• Use to validate category strings before passing to biorxiv_list_recent

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool definitions — single file per tool, framework handles registration and validation
• Unified error handling across all tools
• Pluggable auth (none, jwt, oauth)
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• STDIO and Streamable HTTP transports

bioRxiv-specific:

• BiorxivApiService wraps api.biorxiv.org — details, publications, and crosswalk endpoints with retry and exponential backoff
• EuropePmcService wraps the EuropePMC search endpoint for relevance-ranked keyword results
• Two-server fan-out via Promise.allSettled — both biorxiv and medrxiv queried in parallel when server="both", results merged and deduplicated by DOI
• Polite User-Agent header including a mailto address (BIORXIV_MAILTO env var) per Cold Spring Harbor Lab API guidelines
• Pairs with pubmed-mcp-server (post-publication), openalex-mcp-server (citation analytics), and crossref-mcp-server (DOI metadata)

Getting started

Add the following to your MCP client configuration file.

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/biorxiv-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info",
        "BIORXIV_MAILTO": "[email protected]"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/biorxiv-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info",
        "BIORXIV_MAILTO": "[email protected]"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "-e", "[email protected]", "ghcr.io/cyanheads/biorxiv-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 [email protected] bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.3.2 or higher (or Node.js v24+).

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/biorxiv-mcp-server.git

1. Navigate into the directory:

cd biorxiv-mcp-server

1. Install dependencies:

bun install

1. Configure environment:

cp .env.example .env
# optionally set BIORXIV_MAILTO for polite API access

Configuration

All configuration is validated at startup via Zod schemas in src/config/server-config.ts.

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild

  # Run the built server
  bun run start:stdio
  # or
  bun run start:http

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec

Docker

docker build -t biorxiv-mcp-server .
docker run --rm -e [email protected] -p 3010:3010 biorxiv-mcp-server

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/biorxiv-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Development guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools via the barrel in src/mcp-server/tools/definitions/index.ts
• Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.