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8 clients · secrets stay placeholders

JSON (mcpServers)Claude CodeCodexOpenCodeCursorVS CodeGemini CLIGoose

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "http",
      "url": "https://biorxiv.caseyjhand.com/mcp"
    }
  }
}

claude mcp add --transport http biorxiv-mcp-server https://biorxiv.caseyjhand.com/mcp

[mcp_servers.biorxiv-mcp-server]
url = "https://biorxiv.caseyjhand.com/mcp"

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "biorxiv-mcp-server": {
      "type": "remote",
      "url": "https://biorxiv.caseyjhand.com/mcp",
      "enabled": true
    }
  }
}

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "http",
      "url": "https://biorxiv.caseyjhand.com/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=biorxiv-mcp-server&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vYmlvcnhpdi5jYXNleWpoYW5kLmNvbS9tY3AifQ%3D%3D"
}

{
  "servers": {
    "biorxiv-mcp-server": {
      "type": "http",
      "url": "https://biorxiv.caseyjhand.com/mcp"
    }
  }
}

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "httpUrl": "https://biorxiv.caseyjhand.com/mcp"
    }
  }
}

extensions:
  "biorxiv-mcp-server":
    enabled: true
    name: "biorxiv-mcp-server"
    type: streamable_http
    uri: "https://biorxiv.caseyjhand.com/mcp"
    timeout: 300

Quality 84 / 100good

protocol88 · weight 25

pass
protocol.modernsupports 2026-07-28 (server/discover)
pass
protocol.statelessanswers without a session
pass
protocol.transportstreamable HTTP
warn
protocol.list_ttltools/list declares ttlMs 0, so clients re-fetch it on every use

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygiene79 · weight 30

pass
tools.descriptionsevery tool has a description
warn
tools.description_length4 tools have descriptions over 1,024 characters, which crowds the context
pass
tools.schemasevery tool has an object input schema
pass
tools.annotations7 of 7 tools declare readOnlyHint or destructiveHint
fail
tools.directory_hintsno tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: biorxiv_list_categories (destructiveHint); biorxiv_list_recent (destructiveHint, idempotentHint); biorxiv_get_published_version (destructiveHint); …
pass
tools.token_costabout 3,939 tokens to load every tool
pass
tools.api_dumptools are not a one-to-one API dump

stability75 · weight 15

warn
stability.changes8 tool changes in 30 days
pass
stability.rug_pullno tool changed its meaning under the same name

dependencies100 · weight 15

pass
deps.known_vulnsno known advisory in 128 resolved packages
pass
deps.mcp_sdk_version@modelcontextprotocol/core 2.3.1, no known advisory
pass
deps.resolvable@cyanheads/[email protected], @cyanheads/[email protected] resolved: 128 packages

7 tools, about 3,939 tokens to load them all · tool set d26421120efd · tools last changed 2026-10-18 · checked 2026-10-20 17:02 UTC

Tool changes

2026-10-18biorxiv_get_fulltextchangedoutput schema
2026-10-18biorxiv_search_preprintschangedinput schema, output schema
2026-10-18biorxiv_list_published_versionschangeddescription, input schema, output schema
before
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. Returns up to 100 publications per server per page (fixed by the API); pass `cursor` as an integer offset (0, 100, 200, …) to step through additional pages. 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.
after · 85% of words in common
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. 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.
2026-10-18biorxiv_get_published_versionchangedoutput schema
2026-10-18biorxiv_get_preprintchangeddescription, input schema, output schema
before
Fetch full metadata, 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. 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. 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.
after · 77% of words in common
Fetch full metadata, 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. 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.
2026-10-15biorxiv_get_fulltextchangeddescription, input schema, output schema
before
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, and references. 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, abstract, and metadata. For a preprint that has been published in a journal, the journal's version may have richer full text elsewhere.
after · 89% of words in common
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, abstract, and metadata. For a preprint that has been published in a journal, the journal's version may have richer full text elsewhere.
2026-10-15biorxiv_search_preprintschangedinput schema, output schema
2026-10-15biorxiv_list_published_versionsadded
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. Returns up to 100 publications per server per page (fixed by the API); pass `cursor` as an integer offset (0, 100, 200, …) to step through additional pages. 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.

Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 94 / 100

provenance80

liveness100

freshness100

hygiene100

+repository +namespace-matches-repo +reachable +uptime-100% +updated-3d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

@cyanheads/[email protected] npm63 dependencies, resolved · MCP SDK @modelcontextprotocol/core 2.3.1 · advisories checked 2026-10-19

No known advisory affects this dependency graph.

@cyanheads/[email protected] npm63 dependencies, resolved · MCP SDK @modelcontextprotocol/core 2.3.1 · advisories checked 2026-10-19

No known advisory affects this dependency graph.

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

remote	auth	reachable	uptime 30d	p50	protocol	last ok
`https://biorxiv.caseyjhand.com/mcp` streamable-http	none	yes	100%	180 ms	2026-07-28	2026-10-20

package	registry	version	runtime	secrets
`@cyanheads/biorxiv-mcp-server`	npm	0.4.1	npx
`@cyanheads/biorxiv-mcp-server`	npm	0.4.1	npx

Tools (7)

`biorxiv_get_fulltext`read-only	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, abstract, and metadata. For a preprint that has been published in a journal, the journal's version may have richer full text elsewhere.
`biorxiv_get_preprint`read-only	Fetch full metadata, 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. 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.
`biorxiv_get_published_version`read-only	Resolve a preprint DOI to its full journal publication record — journal DOI, journal name, published date, and corresponding author details. Use when the preprint's `publishedJournalDoi` field from biorxiv_get_preprint is present and you need the full crosswalk metadata. bioRxiv and medRxiv share their DOI prefixes, so server="both" (the default) checks both in parallel and the response reports which server answered. Works for 10.1101/ and 10.64898/ DOIs alike; 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 only when no server holds the preprint or it lists no journal version at all.
`biorxiv_list_categories`read-only	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.
`biorxiv_list_published_versions`read-only	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. 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.
`biorxiv_list_recent`read-only	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, 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.
`biorxiv_search_preprints`read-only	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".

Schemas: list_tools.

Similar MCP servers

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Official server.json

{
  "name": "io.github.cyanheads/biorxiv-mcp-server",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://biorxiv.caseyjhand.com/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "0.4.1",
  "packages": [
    {
      "version": "0.4.1",
      "transport": {
        "type": "stdio"
      },
      "identifier": "@cyanheads/biorxiv-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "BIORXIV_MAILTO",
          "format": "string",
          "description": "Contact email for User-Agent header — optional, for polite API access."
        },
        {
          "name": "BIORXIV_WEB_BASE_URL",
          "format": "string",
          "default": "https://www.biorxiv.org",
          "description": "bioRxiv website base URL — source of rendered full-text HTML pages for biorxiv_get_fulltext."
        },
        {
          "name": "MEDRXIV_WEB_BASE_URL",
          "format": "string",
          "default": "https://www.medrxiv.org",
          "description": "medRxiv website base URL — source of rendered full-text HTML pages for biorxiv_get_fulltext."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    },
    {
      "version": "0.4.1",
      "transport": {
        "url": "http://localhost:3010/mcp",
        "type": "streamable-http"
      },
      "identifier": "@cyanheads/biorxiv-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_TRANSPORT_TYPE",
          "value": "http",
          "format": "string",
          "description": "Selects the HTTP transport."
        },
        {
          "name": "BIORXIV_MAILTO",
          "format": "string",
          "description": "Contact email for User-Agent header — optional, for polite API access."
        },
        {
          "name": "BIORXIV_WEB_BASE_URL",
          "format": "string",
          "default": "https://www.biorxiv.org",
          "description": "bioRxiv website base URL — source of rendered full-text HTML pages for biorxiv_get_fulltext."
        },
        {
          "name": "MEDRXIV_WEB_BASE_URL",
          "format": "string",
          "default": "https://www.medrxiv.org",
          "description": "medRxiv website base URL — source of rendered full-text HTML pages for biorxiv_get_fulltext."
        },
        {
          "name": "MCP_HTTP_HOST",
          "format": "string",
          "default": "127.0.0.1",
          "description": "The hostname for the HTTP server."
        },
        {
          "name": "MCP_HTTP_PORT",
          "format": "string",
          "default": "3010",
          "description": "The port to run the HTTP server on."
        },
        {
          "name": "MCP_HTTP_ENDPOINT_PATH",
          "format": "string",
          "default": "/mcp",
          "description": "The endpoint path for the MCP server."
        },
        {
          "name": "MCP_AUTH_MODE",
          "format": "string",
          "default": "none",
          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/cyanheads/biorxiv-mcp-server",
    "source": "github"
  },
  "description": "Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP."
}