\n\n[](https://github.com/cyanheads/biorxiv-mcp-server/releases/latest/download/biorxiv-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=biorxiv-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvYmlvcnhpdi1tY3Atc2VydmVyIl19) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22biorxiv-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/biorxiv-mcp-server%22%5D%7D)\n\n[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)\n\n
\n\n---\n\n## Tools\n\nSix tools for working with bioRxiv and medRxiv preprint data:\n\n| Tool | Description |\n|:---|:---|\n| `biorxiv_get_preprint` | Fetch full metadata, abstract, revision history, and journal crosswalk for one or more preprints by DOI |\n| `biorxiv_list_recent` | List preprints posted or updated within a date interval, with optional server and category filters |\n| `biorxiv_search_preprints` | Search preprints by keyword and/or author via EuropePMC for relevance ranking, enriched with bioRxiv/medRxiv metadata |\n| `biorxiv_get_published_version` | Resolve a preprint DOI to its journal publication record (journal DOI, name, published date) |\n| `biorxiv_get_fulltext` | Retrieve a preprint's full text as best-effort Markdown extracted from its rendered HTML article page |\n| `biorxiv_list_categories` | List valid subject category strings for bioRxiv and medRxiv |\n\n### `biorxiv_get_preprint`\n\nFetch preprint metadata by DOI — all revisions in one call.\n\n- Batch fetch up to 10 DOIs in a single request\n- Each DOI returns the full revision history in `collection[]` — one API call per DOI, no enumeration loop\n- Includes title, authors, abstract, category, license, JATS XML full-text link (`jatsxml`), and published journal DOI when the preprint has been accepted\n- Scope to `biorxiv`, `medrxiv`, or `both`; when `both`, each DOI fans out in parallel and partial failures report per-DOI in `failed[]`\n- Each `failed[]` entry carries a `reason` (`not_found`, `invalid_doi_format`, `upstream_unavailable`, `rate_limited`) and a `retryable` flag — a DOI is only reported as not found when every attempted server answered\n- A lookup the origin rate-limited (HTTP 429) reports as `rate_limited` rather than folding into `upstream_unavailable`, and carries `retryAfter` — the wait in seconds `api.biorxiv.org` asked for\n\n---\n\n### `biorxiv_list_recent`\n\nPage through preprints in a date interval.\n\n- Server-side category filtering via `?category=…` — pass a value from `biorxiv_list_categories`\n- Fixed page size of 30 (API constraint); advance with integer `cursor` (0, 30, 60, …)\n- Response includes `total` count per server for calculating remaining pages\n- When `server=\"both\"`, each server paginates independently; response surfaces per-server pagination state (`{ biorxiv: { cursor, total }, medrxiv: { cursor, total } }`)\n- A server whose cursor is past its last page is marked `exhausted: true` — the API reports `total: 0` for an out-of-range cursor, so that count is an artifact rather than the interval total\n- One server not answering under `server=\"both\"` is named in `failed[]` rather than dropped; the other server's page is still returned, and a non-empty `failed[]` marks the result set as partial\n- Every attempted server failing raises a retryable `upstream_unavailable` (or `rate_limited`) error instead of returning an empty page — nothing answered, so an empty interval was never established\n\n---\n\n### `biorxiv_search_preprints`\n\nKeyword and/or author search with relevance ranking.\n\n- EuropePMC powers relevance ranking (indexes new preprints within 1–2 days of posting); bioRxiv/medRxiv API provides canonical metadata enrichment\n- Optional `author` maps to an EuropePMC `AUTH:\"…\"` field query, ANDed with the keyword query — supply `query`, `author`, or both\n- Covers both servers by default; scope down with `server`\n- Optional date range filters (`date_from`, `date_to`)\n- Enriched results carry the same latest-revision fields `biorxiv_get_preprint` returns — including `type`, `license`, `funder`, and `authorCorrespondingInstitution`\n- Enrichment failures degrade gracefully to EuropePMC-only metadata, surfaced via `partial_results` and a per-record `enrichment_error` (`service_error`, `rate_limited`, or `not_found`)\n- A EuropePMC rate limit (HTTP 429) raises a retryable `rate_limited` error carrying the origin's `Retry-After` wait — the search is the primary call and has no metadata to fall back on, unlike the enrichment step\n\n---\n\n### `biorxiv_get_published_version`\n\nResolve a preprint DOI to its journal publication crosswalk.\n\n- Uses the `/pubs/{server}/{doi}` endpoint for richer metadata than the `publishedJournalDoi` field in `biorxiv_get_preprint`\n- Returns journal DOI, journal name, published date, and corresponding author institution\n- Use when the preprint's `publishedJournalDoi` field is present and you need the full crosswalk record\n- Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix, and the output `server` field names the one that answered\n- No server answering raises a retryable `upstream_unavailable`, or `rate_limited` with the origin's wait when the failure was an HTTP 429 — never `doi_not_found`, which would assert an absence nothing established\n\n---\n\n### `biorxiv_get_fulltext`\n\nRetrieve a preprint's full text as best-effort Markdown.\n\n- Fetches the rendered HTML article page (`www.{server}.org/content/{doi}v{N}.full`) and extracts Markdown — there is no keyless JATS source\n- Resolves the latest version via the details API first, for the URL version and clean not-found handling\n- Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix. Only the DOI resolution fans out — the full-text fetch targets the single server that answered, named in the output `server` field\n- Long articles page via `offset`/`limit` character chunking (`totalChars`, `remainingChars`, `hasMore`); the extracted article is cached per version, so paging costs one origin fetch rather than one per chunk\n- PDF-only preprints and blocked/challenge pages return a typed `fulltext_unavailable` error routing to `biorxiv_get_preprint`\n- An origin rate limit (HTTP 429) returns a retryable `rate_limited` error carrying the origin's `Retry-After` wait, rather than a bare fetch failure. Both origins this tool touches can hit it — the article page during the full-text fetch, `api.biorxiv.org` during version resolution — and the recovery hint names which of them are limiting, since `biorxiv_get_preprint` is only a useful fallback while the metadata origin is answering\n\n---\n\n### `biorxiv_list_categories`\n\nReturn the static subject category taxonomy for both servers.\n\n- No API call — hardcoded static list (~30 bioRxiv + ~50 medRxiv categories)\n- Use to validate category strings before passing to `biorxiv_list_recent`\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):\n\n- Declarative tool definitions — single file per tool, framework handles registration and validation\n- Unified error handling across all tools\n- Pluggable auth (`none`, `jwt`, `oauth`)\n- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`\n- Structured logging with optional OpenTelemetry tracing\n- STDIO and Streamable HTTP transports\n\nbioRxiv-specific:\n\n- `BiorxivApiService` wraps `api.biorxiv.org` — details, publications, and crosswalk endpoints with retry and exponential backoff. An origin rate limit (HTTP 429) is classified as a retryable `rate_limited` error carrying the parsed `Retry-After` wait; the upstream response body never reaches the error payload\n- `EuropePmcService` wraps the EuropePMC search endpoint for relevance-ranked keyword and/or author results. An origin rate limit (HTTP 429) is classified the same way as the JSON API's — a retryable `rate_limited` error carrying the parsed `Retry-After` wait, with the upstream response body kept out of the error payload\n- `BiorxivFullTextService` fetches and extracts Markdown from the rendered HTML article pages on `www.biorxiv.org` / `www.medrxiv.org` — a distinct origin from the JSON API\n- Two-server fan-out via `Promise.allSettled` — both `biorxiv` and `medrxiv` queried in parallel when `server=\"both\"`, results merged and deduplicated by DOI\n- Polite `User-Agent` header including a mailto address (`BIORXIV_MAILTO` env var) per Cold Spring Harbor Lab API guidelines\n- Pairs with **pubmed-mcp-server** (post-publication), **openalex-mcp-server** (citation analytics), and **crossref-mcp-server** (DOI metadata)\n\n## Getting started\n\nAdd the following to your MCP client configuration file.\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/biorxiv-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\",\n \"BIORXIV_MAILTO\": \"your@email.com\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/biorxiv-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\",\n \"BIORXIV_MAILTO\": \"your@email.com\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\"run\", \"-i\", \"--rm\", \"-e\", \"MCP_TRANSPORT_TYPE=stdio\", \"-e\", \"BIORXIV_MAILTO=your@email.com\", \"ghcr.io/cyanheads/biorxiv-mcp-server:latest\"]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 BIORXIV_MAILTO=your@email.com bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\n### Prerequisites\n\n- [Bun v1.3.0](https://bun.sh/) or higher (or Node.js v24+).\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/biorxiv-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd biorxiv-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n4. **Configure environment:**\n\n```sh\ncp .env.example .env\n# optionally set BIORXIV_MAILTO for polite API access\n```\n\n## Configuration\n\nAll configuration is validated at startup via Zod schemas in `src/config/server-config.ts`.\n\n| Variable | Description | Default |\n|:---|:---|:---|\n| `BIORXIV_MAILTO` | Email address included in the `User-Agent` header for polite API access per Cold Spring Harbor Lab guidelines. Optional, but recommended. | — |\n| `BIORXIV_API_BASE_URL` | Override the bioRxiv API base URL. | `https://api.biorxiv.org` |\n| `EUROPEPMC_API_BASE_URL` | Override the EuropePMC base URL. | `https://www.ebi.ac.uk/europepmc/webservices/rest` |\n| `BIORXIV_WEB_BASE_URL` | Override the bioRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.biorxiv.org` |\n| `MEDRXIV_WEB_BASE_URL` | Override the medRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.medrxiv.org` |\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |\n| `MCP_HTTP_PORT` | HTTP server port. | `3010` |\n| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path. | `/mcp` |\n| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |\n| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.). | `info` |\n| `LOGS_DIR` | Directory for log files (Node.js only). | `/logs` |\n| `OTEL_ENABLED` | Enable OpenTelemetry instrumentation. | `false` |\n\n## Running the server\n\n### Local development\n\n- **Build and run:**\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:stdio\n # or\n bun run start:http\n ```\n\n- **Run checks and tests:**\n\n ```sh\n bun run devcheck # Lint, format, typecheck, security\n bun run test # Vitest test suite\n bun run lint:mcp # Validate MCP definitions against spec\n ```\n\n### Docker\n\n```sh\ndocker build -t biorxiv-mcp-server .\ndocker run --rm -e BIORXIV_MAILTO=your@email.com -p 3010:3010 biorxiv-mcp-server\n```\n\nThe 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.\n\n## Project structure\n\n| Directory | Purpose |\n|:---|:---|\n| `src/index.ts` | `createApp()` entry point — registers tools and initializes services. |\n| `src/config` | Server-specific environment variable parsing and validation with Zod. |\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Six tools across bioRxiv and medRxiv. |\n| `src/services/biorxiv` | `BiorxivApiService` — details, publications, and crosswalk endpoint wrappers with retry. |\n| `src/services/biorxiv-fulltext` | `BiorxivFullTextService` — rendered HTML article page fetch and Markdown extraction. |\n| `src/services/europe-pmc` | `EuropePmcService` — preprint keyword/author search endpoint wrapper. |\n| `tests/` | Unit and integration tests mirroring the `src/` structure. |\n\n## Development guide\n\nSee [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage\n- Register new tools via the barrel in `src/mcp-server/tools/definitions/index.ts`\n- Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields\n\n## Contributing\n\nIssues and pull requests are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nApache-2.0 — see [LICENSE](./LICENSE) for details.\n",
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