bioRxiv and medRxiv provide searchable access to biological and medical research preprints. Discover studies by keyword, author, subject, or funder; retrieve abstracts and publication metadata; track preprints published in peer-reviewed journals; and analyze research output statistics.
Hermes is Nous Research's command-line agent. MCP servers are declared in its YAML config and reloaded without a restart.
This guide connects bioRxiv MCP to Hermes through MewCP, so Hermes can use bioRxiv MCP's 7 tools, like search_preprints, get_preprint and get_categories.
bioRxiv MCP needs no credentials, but every call still runs through MewCP: scoped, checked and logged like any other.
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bioRxiv MCP works the same way in every client below. Pick yours for its own guide.
Free to start.
Scope access to the exact bioRxiv MCP tools and accounts you allow, work and personal side by side. Anything outside that scope is refused at call time, even when the model asks for it.
Each call is logged: what ran, on which account, and whether it worked. Failures come back structured, so the agent knows whether to retry instead of guessing.
Every app sits behind one secure MCP URL, and there is no server for you to deploy or keep running. Add an integration in the dashboard and it is live on the next call, with no config to change and no new credentials to wire up. Tools load only when a task needs them, so your agent stays fast and focused however many apps you connect.
Edit config.yaml in your Hermes config directory (~/.hermes).
Put this under the top-level "mcp_servers:" key.
Run /reload-mcp in Hermes, or start a fresh session. Sign in when the browser window opens.
Start a new chat and ask: "List the tools you can use from MewCP." You should see your connected apps.
Search bioRxiv/medRxiv preprints. Returns DOI, title, authors, abstract preview, category. WHEN TO USE: - Literature review and research discovery - Finding recent research in specific fields - Tracking new submissions by date or category SEARCH METHODS (use only ONE): - Date range: date_from + date_to (e.g., '2024-01-01' to '2024-06-30') - RECOMMENDED - Recent days: recent_days=30 (last 30 days) - Recent count: recent_count=50 (searches last ~90 days, returns up to 'limit' results) IMPORTANT: All searches use date ranges internally. recent_count searches a 90-day window. If no search method specified, defaults to last 60 days. SERVERS: - 'biorxiv': Biological sciences (default) - 'medrxiv': Medical/health sciences CATEGORIES (27 available): biochemistry, bioinformatics, cancer biology, cell biology, genetics, genomics, immunology, microbiology, molecular biology, neuroscience, and 17 more. Use get_categories tool for full list. LIMITATIONS: - NO keyword/text search - filter by category and date only - Results are NOT peer-reviewed preprints EXAMPLES: - Last 30 days of neuroscience: recent_days=30, category='neuroscience' - Cancer biology Q1 2024: date_from='2024-01-01', date_to='2024-03-31', category='cancer biology' PAGINATION: Use cursor for next page (cursor=100 for results 100-199) RELATED: get_preprint (full details by DOI), get_categories (list all categories)
Get complete metadata for a specific preprint by DOI. WHEN TO USE: - You have a DOI and need full details - Need abstract, authors, PDF URL, funding info - Checking if preprint was published in a journal RETURNS: title, all authors, corresponding author + institution, full abstract, category, license, version, PDF URL, web URL, funding details, published DOI (if available) DOI FORMATS (all accepted): - '10.1101/2024.01.15.123456' - 'https://doi.org/10.1101/2024.01.15.123456' SERVERS: - 'biorxiv': For bioRxiv preprints (DOI contains biorxiv dates like 2024.01.15) - 'medrxiv': For medRxiv preprints IMPORTANT: Preprints are NOT peer-reviewed RELATED: search_preprints (find DOIs), search_published_articles (find journal version)
List all 27 bioRxiv subject categories for filtering searches. WHEN TO USE: - Before search_preprints to see valid category values - To understand research area classifications RETURNS: Category names and API-compatible format (e.g., 'cancer biology' -> 'cancer_biology') FULL LIST: animal behavior and cognition, biochemistry, bioengineering, bioinformatics, biophysics, cancer biology, cell biology, clinical trials, developmental biology, ecology, epidemiology, evolutionary biology, genetics, genomics, immunology, microbiology, molecular biology, neuroscience, paleontology, pathology, pharmacology and toxicology, physiology, plant biology, scientific communication and education, synthetic biology, systems biology, zoology
Find preprints that have been published in peer-reviewed journals. WHEN TO USE: - Track which preprints became journal articles - Find the peer-reviewed version of a preprint - Analyze preprint-to-publication patterns - Filter articles by whether they were published by a specific journal SEARCH METHODS (use only ONE): - Date range: date_from + date_to - Recent count: recent_count=50 - Recent days: recent_days=30 FILTERS: - include_details: True for full metadata (slower), False for summary (faster) - publisher: Filter by DOI prefix (e.g., '10.1038' for Nature) - see below COMMON PUBLISHER PREFIXES: - '10.1038' - Nature Publishing Group - '10.1126' - Science/AAAS - '10.1016' - Elsevier - '10.1371' - PLOS - '10.7554' - eLife - '10.1073' - PNAS EXAMPLE: Find recently published medRxiv papers: server='medrxiv', recent_days=30
Search for preprints funded by a specific organization using ROR ID. WHEN TO USE: - Track research output from specific funding bodies - Analyze funder-specific publication patterns - Monitor grant-funded research areas REQUIRES: funder_ror_id (9-character ROR ID) COMMON FUNDER ROR IDS: - '021nxhr62' - NIH (National Institutes of Health) - '01cwqze88' - NSF (National Science Foundation) - '02mhbdp94' - European Commission - '029chgv08' - Wellcome Trust - '05a28rw58' - HHMI (Howard Hughes Medical Institute) - '006wxqw41' - MRC (Medical Research Council UK) - '00f54p054' - BBSRC (UK) - '01s5ya894' - Chan Zuckerberg Initiative Find more ROR IDs at: https://ror.org/search RETURNS: DOI, title, authors, abstract preview, category (same as search_preprints) IMPORTANT: Date range required. Earliest date is 2025-04-10 (funder metadata inception) SERVERS: 'biorxiv' or 'medrxiv'
Get bioRxiv submission statistics over time. WHEN TO USE: - Analyze bioRxiv growth trends - Track submission patterns (new vs revised papers) - Generate platform statistics reports RETURNS (per month/year): new_papers, revised_papers, new_authors, cumulative_papers, cumulative_authors, period (YYYY-MM or YYYY) INTERVALS: 'monthly' (default) or 'yearly' NOTE: Returns all historical data from bioRxiv inception to present
Get bioRxiv usage/engagement statistics over time. WHEN TO USE: - Analyze readership trends - Track engagement metrics (views, downloads) - Compare abstract vs full-text vs PDF engagement RETURNS (per month/year): abstract_views, full_text_views, pdf_downloads, cumulative_abstract, cumulative_full_text, cumulative_pdf, period (YYYY-MM or YYYY) INTERVALS: 'monthly' (default) or 'yearly' NOTE: Returns all historical data from bioRxiv inception to present
