io.github.cyanheads由 GitHub 帳號 cyanheads 發布v0.5.1更新於 Oct 29, 2026
Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP.
依 DOI、日期區間、關鍵字或作者搜尋並取得 bioRxiv 與 medRxiv 預印本，包含全文與期刊發表紀錄。
Web executable，透過 Streamable HTTP。 遠端服務在工作區中設定後即可從網頁執行環境執行。
把這段提示詞貼上到 Claude Code、Codex、Cursor 等代理程式，或 SourceWeft 對話中。代理程式會讀取該伺服器的安裝指南，先向你展示發布者、端點和登入方式，經你同意後再把它新增到你的客戶端。金鑰不會寫進任何命令。
閱讀 https://sourceweft.com/mcp/io.github.cyanheads%2Fbiorxiv-mcp-server/install.md，並按其中說明把這個 MCP 伺服器接入我的客戶端。修改任何設定之前，先告訴我它的發布者、端點和登入方式，等我確認。不要把 API 金鑰寫進命令或我會提交的檔案；問我金鑰應從哪裡取得。把它新增到你客戶端的 mcpServers 設定中。
{
"mcpServers": {
"biorxiv": {
"type": "http",
"url": "https://biorxiv.caseyjhand.com/mcp"
}
}
}Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. STDIO or Streamable HTTP.
Public Hosted Server: https://biorxiv.caseyjhand.com/mcp
bioRxiv and medRxiv preprints, metadata and full text. Search by keyword and author, browse a date interval (optionally by subject), fetch any preprint by DOI, and see which preprints went on to journal publication.
biorxiv_get_preprint toolhttps://doi.org/…, doi:…, a biorxiv.org/medrxiv.org article URL, a vN or .full suffix), scoped to biorxiv, medrxiv, or both (default both)unprocessed[] to pass in another call. A repeated DOI is looked up once, and every list keeps input orderrevisions[] — title, authors, category, license, awards, jatsxmlUrl, publishedJournalDoi once accepted, and the server it was found on (biorxiv or medrxiv, ready to pass back as server). Funder names are omitted because the upstream API misattributes thembiorxiv_get_fulltext with versionfailed[] with a reason (not_found, invalid_doi_format, upstream_unavailable, rate_limited) and a retryable flag; not_found only when every attempted server answeredbiorxiv_list_recent toolstart_date/end_date interval, server (default both), and optional category (a value from biorxiv_list_categories) and bioRxiv-only funder (a ROR ID) filters; a filter that cannot be applied raises invalid_category or invalid_fundercursor, tracked per server ({ biorxiv: { cursor, total, newPreprints }, medrxiv: { cursor, total, newPreprints } }); a cursor past the last page is marked exhausted: true, and a server that did not answer is named in failed[]total counts every version posted in the interval, while newPreprints counts the preprints whose first version posted in it, as the API reports it (absent when the API sends no count)include_abstract: true adds them. Each is the preprint's latest-revision abstract, even on a row for an earlier revisionbiorxiv_search_preprints toolquery and/or author, optional date_from/date_to and server (default both); up to 100 results per page (default 25; a larger limit returns 100 with a notice), paged with cursor_markbiorxiv_get_preprint; a record left with EuropePMC metadata only carries enriched: false and an enrichment_error (service_error, rate_limited, not_found), with partial_results setinclude_abstract: false drops them for a response about a third the sizebiorxiv_get_published_version toolserver (default both): a preprint DOI (10.1101/, 10.64898/), or a journal article's DOI, which resolves to the preprint it was posted as (10.1016/j.cell.2020.01.001 → 10.1101/614172); 10.64898/ DOIs resolve through the preprint's own journal DOIserver that answered; if no server answers it raises a retryable upstream_unavailable or rate_limited, never doi_not_found10.1101/gr.…, gad.…, lm.…) share the preprint prefix and cannot be resolved by DOIbiorxiv_list_published_versions toolstart_date/end_date interval of journal publication dates and server (default both); each row matches the record biorxiv_get_published_version returns, and may be a preprint posted years earlierlimit rows per server (default 25, up to the API's 100-row page) from an integer cursor, continued at each server's nextCursor; a cursor past the last row is marked exhausted: true, and a server that did not answer is named in failed[]publisher, a journal DOI prefix (10.7554 for eLife), lists only the bioRxiv preprints published under it; server: "both" queries bioRxiv alone, and server: "medrxiv" or a prefix the API does not recognize raises invalid_publisher. These rows carry no journal name, authors, or abstractinclude_abstract: true adds thembiorxiv_get_fulltext toolserver (default both), and an optional version (or a vN suffix; the two must agree, and a version the preprint lacks raises version_not_found); returns Markdown extracted from the rendered HTML article page, naming the answering serveromittedTables names it with the URL that serves its cellsoffset/limit characters (default 20,000), reporting totalChars, remainingChars, hasMore, and wordCount; PDF-only preprints and blocked pages raise fulltext_unavailable, routing to biorxiv_get_preprintbiorxiv_list_categories toolcategory for biorxiv_list_recentBuilt on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.
bioRxiv-specific:
BiorxivApiService wraps api.biorxiv.org (details, publications, and crosswalk endpoints) and EuropePmcService wraps EuropePMC search, both with retry and exponential backoffBiorxivFullTextService extracts Markdown from the article pages on www.biorxiv.org / www.medrxiv.orgbiorxiv and medrxiv in parallel when server="both", each result naming the server that answered; a lookup by DOI stops waiting once the server holding that DOI answersUser-Agent header including a mailto address (BIORXIV_MAILTO env var) per Cold Spring Harbor Lab API guidelinesAgent-friendly output:
failed[] with a typed reason and retryable flag instead of aborting the callreason: "rate_limited" with the parsed retryAfter wait, distinct from upstream_unavailablebiorxiv_search_preprints results carry enriched plus a typed enrichment_error (service_error / rate_limited / not_found){beta}, [≥]) are resolved to plain textConnect to the hosted instance, no install:
Or run it locally:
For other clients, add this to the MCP config file:
A contact email in BIORXIV_MAILTO (-e [email protected], or an env entry) identifies your requests in the User-Agent header, as the Cold Spring Harbor Lab API guidelines ask. For Docker or a source build, see Running the server.
All configuration is validated at startup via Zod schemas in src/config/server-config.ts.
See .env.example for the full list of optional overrides.
Requires Bun v1.4.0 or higher (or Node.js v24+).
Clone and install:
Build and run:
Run checks and tests:
The image defaults to HTTP transport, stateless session mode, and logs to /var/log/biorxiv-mcp-server; the server listens at http://localhost:3010/mcp. To run it over stdio from an MCP client, use "command": "docker" with "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/biorxiv-mcp-server:latest"]. To build locally, docker build -t biorxiv-mcp-server .; OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.
See CLAUDE.md for development guidelines and architectural rules. The short version:
try/catch in tool logicctx.log for request-scoped logging, ctx.state for tenant-scoped storagesrc/mcp-server/tools/definitions/index.tsIssues are welcome. Run checks and tests before submitting:
Apache-2.0 — see LICENSE for details.
來源：README.md，提交 39a91f0
List bioRxiv/medRxiv Categories
List valid subject category strings for bioRxiv and medRxiv — the categories the listing API actually filters on. Use these strings as the `category` filter in biorxiv_list_recent to narrow results to a specific field; case, and "_" or "-" in place of a space, do not matter there. Run this tool before filtering to get the current valid values.
無需輸入參數。
List Recent Preprints
List preprints posted or revised within a date interval, optionally scoped to one server or a subject category. Returns 30 preprints per page (fixed by the API); pass `cursor` as an integer offset (0, 30, 60, …) to step through additional pages. Abstracts are omitted by default to keep the page small — pass include_abstract: true for the whole page (each row carries the latest-revision abstract of its preprint, whichever revision the row is), or call biorxiv_get_preprint (up to 10 DOIs per call) for a few. When server="both" (default), per-server pagination state is returned separately — use each server's `cursor` field for independent advancement. One server failing under server="both" does not abort the call: the other server's page is still returned and the failed one is named in `failed[]`, marking the result set as partial rather than complete. Every attempted server failing is a different case and does abort the call, with a retryable upstream_unavailable (or rate_limited) error — an empty page would otherwise be indistinguishable from an interval that genuinely holds nothing. Call biorxiv_list_categories for valid category strings; a server that answers a category filter with its unfiltered listing is left out with a notice, and invalid_category is raised when no server applied it. `funder` limits the listing to bioRxiv preprints funded by that organization, given its ROR ID; an ID api.biorxiv.org has no funder record for raises invalid_funder rather than returning an empty page.
cursorfunderservercategoryend_date必填start_date必填include_abstractGet Preprint by DOI
Fetch full metadata, the abstract, all revision history, JATS XML full-text links, and published-journal DOI for one or more preprints by DOI. Each DOI returns all revisions in one response, with the abstract on the latest revision only — the API keeps one abstract per preprint. Each call looks up the first 10 distinct DOIs and returns the rest, never looked up, in unprocessed[] — pass that list as dois in another call to continue; a repeated DOI is looked up once and an unparseable entry is reported in failed[], so neither counts toward the 10. When server="both" (default), each DOI is checked against both bioRxiv and medRxiv; the response includes which server the preprint was found on. Failed lookups are reported per-DOI in failed[] rather than aborting the batch, each carrying a reason (not_found, invalid_doi_format, upstream_unavailable, rate_limited) and a retryable flag; a rate_limited entry also carries the wait in seconds the origin asked for. preprints[], failed[], and unprocessed[] follow input order. DOIs must match the pattern 10.NNNN/…; a doi.org or article URL, a doi: label, and a trailing vN / .full suffix are stripped first, and results report the bare DOI.
dois必填serverGet Published Journal Version
Resolve a DOI to its preprint-to-journal crosswalk record — preprint DOI, journal DOI, journal name, published date, and corresponding author details — from either side: a preprint DOI (10.1101/ or 10.64898/) finds the journal article it was published as, and any other DOI is read as a journal article's and finds the bioRxiv or medRxiv preprint it was posted as. Use when biorxiv_get_preprint shows a `publishedJournalDoi` and you need the journal details, or when you hold a journal article and want its preprint. bioRxiv and medRxiv share their DOI prefixes, so server="both" (the default) checks both in parallel and the response reports which server answered. When the crosswalk holds no record for a published preprint, the journal DOI still comes back from the preprint's own record, without journal name or date, and a notice says so. Returns a not-found error when no server holds the preprint, it lists no journal version, or no preprint is recorded for the journal DOI.
doi必填serverList Published Journal Versions
List preprints that appeared as journal articles within a journal publication-date interval, each with its journal DOI, journal name, publication date, and preprint metadata — the same record biorxiv_get_published_version returns for one DOI. The dates filter on journal publication, not preprint posting, so most rows were posted months or years earlier; use biorxiv_list_recent for preprints posted in an interval. `publisher`, a journal DOI prefix such as 10.7554 for eLife, limits the listing to the bioRxiv preprints published under it; those rows carry no journal name, authors, or abstract, and a prefix api.biorxiv.org does not recognize raises invalid_publisher. Returns `limit` publications per server (default 25, up to 100 — the page api.biorxiv.org serves; a larger limit returns 100 and says so). Continue at the `nextCursor` a page returns rather than stepping `cursor` by a fixed amount; `limit: 100` walks an interval in the fewest calls. When server="both" (default), per-server pagination state is returned separately, since one cursor can be past the end of one server and inside the other — to continue a single server, pass its `nextCursor` with `server` set to that server. One server failing under server="both" does not abort the call: the other server's page is still returned and the failed one is named in `failed[]`. Every attempted server failing raises a retryable upstream_unavailable (or rate_limited) error rather than an empty page. Abstracts are omitted by default to keep the page small — pass include_abstract: true for the whole page. Every preprintDoi, 10.1101/ and 10.64898/ alike, is accepted by biorxiv_get_preprint and the other DOI tools.
limitcursorserverend_date必填publisherstart_date必填include_abstractSearch Preprints by Keyword
Search preprints by keyword and/or author using EuropePMC for relevance ranking, then enrich matching DOIs with full bioRxiv/medRxiv metadata. Provide a keyword query, an author name, or both — author maps to an EuropePMC AUTH: field query and is ANDed with the keyword query. Covers both servers by default. EuropePMC indexes new preprints within 1–2 days of posting; for preprints posted within the last day, prefer biorxiv_list_recent. Abstracts are included by default; include_abstract: false omits them from every result for a response about a third the size, and biorxiv_get_preprint returns the abstract for up to 10 DOIs per call. A EuropePMC rate limit (HTTP 429) fails the call with a retryable rate_limited error carrying the wait in seconds — a rate-limited metadata enrichment does not, and instead marks the affected record enrichment_error: "rate_limited".
limitqueryauthorserverdate_todate_fromcursor_markinclude_abstractGet Preprint Full Text
Retrieve a preprint's full text as best-effort Markdown, extracted from its rendered HTML article page. Reads the latest version unless one is requested (the version input, or a vN suffix on the DOI), confirms it via the details API, then fetches and extracts the body — abstract, sections, inline citation labels, and the reference list. Table cells are not on the article page: each table appears as its caption, and omittedTables names it with the URL that serves its cells. bioRxiv and medRxiv share the 10.1101/ DOI prefix, so server="both" (the default) resolves the DOI against both in parallel and the response reports which server answered. This is HTML-to-Markdown extraction, not structured JATS: section structure is approximate and not guaranteed. Long articles exceed a single response, so use offset and limit to page through them (the response reports totalChars, remainingChars, and hasMore); paging is cheap because the extracted article is cached per version for an hour after the first read, so only the first chunk pays for a fetch. Not every preprint has an extractable HTML page — some are PDF-only and some origins block programmatic access — in which case a fulltext_unavailable error routes you to biorxiv_get_preprint for the title, metadata, and current abstract. For a preprint that has been published in a journal, the journal's version may have richer full text elsewhere.
doi必填limitoffsetserverversion已滿足適用檢查項的 90%
該評分衡量此收錄條目的完整程度，依據註冊中心條目、端點與公開來源計算得出。它不是對伺服器本身的評價，也不表示伺服器安全或目前可用：可連通性是帶日期的檢查結果，評分也不包含安裝量或使用者評價。
請在儲存庫或註冊中心條目中宣告授權條款。
claude mcp add --transport http biorxiv-mcp-server https://biorxiv.caseyjhand.com/mcpclaude mcp add biorxiv-mcp-server -- npx -y @cyanheads/biorxiv-mcp-server{ "mcpServers": { "biorxiv-mcp-server": { "command": "npx", "args": ["-y", "@cyanheads/biorxiv-mcp-server"] } }}git clone https://github.com/cyanheads/biorxiv-mcp-server.gitcd biorxiv-mcp-server && bun installcp .env.example .env # optionally set BIORXIV_MAILTO# One-time buildbun run rebuild
# Run the built serverbun run start:stdio# orbun run start:httpbun run devcheck # Lint, format, typecheck, securitybun run test # Vitest test suitebun run lint:mcp # Validate MCP definitions against specdocker run --rm -e [email protected] -p 3010:3010 ghcr.io/cyanheads/biorxiv-mcp-server:latestbun run devcheckbun run test