CASRAI Dictionary

Tag: biorxiv author area

  • How bioRxiv Versioning Works (v1, v2, v3)

    bioRxiv versioning works by assigning every preprint a version number starting at v1 on first posting; authors can submit revisions at any time before journal acceptance, each becoming v2, v3 and so on under the same DOI, with every prior version preserved and independently citable via the “Info/History” tab. Unlike a journal correction process, there is no editor gatekeeping a revision, and nothing is ever deleted from the record.

    A bioRxiv version is a distinct, permanently archived snapshot of a preprint’s PDF, HTML and XML files, numbered sequentially (v1, v2, v3…) and linked to one persistent DOI that never changes across revisions. Understanding this versioning system — what triggers a new version, what stays fixed, and how to cite a specific one — matters for authors tracking revision history and readers who need to know exactly which version of a claim they are reading.

    What happens when a preprint first posts as v1?

    When a manuscript clears bioRxiv’s screening process — typically within 72 hours of submission, according to bioRxiv’s own FAQ — it is posted as version 1 (v1). The PDF appears first; full-text HTML and XML conversion follows 24–48 hours later.

    Each version, from v1 onward, is independently available in PDF, HTML and XML — the XML format exists for text-mining and machine-readable indexing, a detail most competing explainers omit. Once v1 is live, it is immediately assigned a DOI (via Crossref) and indexed by Google Scholar, Europe PubMed Central and the Preprint Citation Index connected to Web of Science: v1 is citable and part of the permanent scientific record from the moment it posts, not a provisional draft.

    How do authors submit a v2 or later revision?

    Authors submit revisions through the “Submit a Revision” option in their bioRxiv Author Area, locating their existing submission ID and selecting “Submit a revised manuscript.” bioRxiv’s policy states a manuscript “can be revised at any time until it is published in a journal” — there is no fixed revision window and no limit on the number of versions.

    The revision mechanism is intended for substantive changes: new datasets, re-analyses, expanded discussion, or additional supplemental information. A revision is posted under the same DOI, and — critically — the prior version is not overwritten. It remains permanently accessible through the article’s Info/History tab, so a reader can always compare what changed between v1 and v2, or v2 and v3.

    One detail rarely covered elsewhere: if a preprint was originally submitted indirectly via a journal’s own pipeline (journal-to-bioRxiv, or “J2B”), the corresponding author must first register a bioRxiv account using the same email address used at journal submission before they can access the Author Area to file a revision.

    Does the DOI change between versions, and how do you cite one?

    The DOI stays fixed across every version of a bioRxiv preprint. v1, v2 and v3 of the same manuscript all resolve through one DOI — a reader following an older citation lands on whatever version is current, with the option to step back through history.

    To cite a specific version rather than “whatever is current,” bioRxiv appends a version-specific URL to the DOI. Its FAQ gives this exact pattern:

    Element Format Example
    Standard DOI citation doi: 10.1101/[identifier] doi: 10.1101/2019.12.11.123456
    Version-specific citation DOI + version-specific URL doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2

    This matters for reference managers such as EndNote: the DOI field should carry the persistent identifier, while the version number belongs in the URL or a note field if the citing author wants to pin the exact revision read, rather than whichever version happens to be live later.

    One exception: if a revision alters the manuscript so substantially that bioRxiv considers it a genuinely different article, the author must submit it as a new manuscript — which receives its own, separate DOI rather than becoming v2 of the original.

    What does NOT require a new version?

    Three specific cases are worth flagging because they trip up first-time bioRxiv authors and are absent from most general explainers:

    • Metadata typos. If the title, author names, affiliations or abstract in the submission form contain an error but the PDF is correct, bioRxiv auto-replaces the site metadata with text extracted from the PDF within roughly 48 hours — authors are told not to submit a full revision solely to fix this.
    • Author name changes. bioRxiv permits a “silent” first/last name update — for example after a legal name change — by direct email request, without a new version or correction notice. This excludes author removal or reordering, which need a standard revision.
    • Supplemental-file-only changes. If only supplemental files change, bioRxiv still requires them submitted together with the article file as part of a new version; a supplemental-only upload cannot be filed alone.

    What happens if an author withdraws a preprint?

    bioRxiv preprints cannot be deleted once posted, because each version carries a DOI and is indexed externally by Google Scholar and Crossref, creating a permanent footprint independent of bioRxiv’s own servers. If authors no longer stand behind their findings, the remedy is a formal withdrawal, not removal.

    To withdraw, the corresponding author uses “Submit a Withdrawal Statement” inside the same Author Area used for revisions. A withdrawal adds a “Withdrawn” watermark to the PDF of every version ever posted and posts an explanatory statement on the article page — but the original manuscript remains viewable via the Info/History tab. It is a labelled correction, not an erasure. bioRxiv notes outright removal happens only in “extremely rare cases,” for legal or safety reasons.

    Once a preprint is published in a peer-reviewed journal, no further author action is usually needed: bioRxiv automatically adds a link to the published version within approximately two weeks, and all preprint versions — v1 through the final revision — remain live alongside it.

    Common questions about bioRxiv versioning

    Can I upload a new version or replace a bioRxiv preprint?

    Authors cannot replace or delete a posted version, but they can add a new one. Using “Submit a Revision” in the Author Area at any point before journal acceptance creates the next sequential version (v2, v3…) while every earlier version stays permanently visible in the Info/History tab.

    Why does bioRxiv take so long to post a new version?

    Both initial posting and revisions go through the same screening step, which usually completes within 72 hours. Delays typically occur over weekends or holidays, or when a submission needs extra scrutiny for scope, plagiarism or safety-related content before the new version is approved.

    Does bioRxiv count as published once it has multiple versions?

    No. Additional versions do not confer peer-reviewed status. bioRxiv is explicit that it “is not a journal” and has no Impact Factor; every version, however many revisions deep, carries the standard disclaimer that the content has not been certified by peer review.

    Are previous bioRxiv versions still readable after a revision posts?

    Yes. Every prior version remains permanently accessible through the Info/History tab on the preprint’s landing page after a new version is submitted, so readers can compare v1 against later revisions rather than losing access to earlier text.

    Implications for research administrators and institutions

    For institutions tracking preprint outputs in repository or CRIS systems, the persistent-DOI-plus-version model means a single DOI can legitimately correspond to several distinct texts over time. Metadata harvesting workflows that snapshot “the” abstract or author list at ingestion risk becoming stale if a later version changes those fields — administrators should record which version number was harvested, not just the DOI.

    For funders, the NIH has stated it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and preprints of NIH-funded studies are indexed in PubMed regardless of version count. Citing the version actually reviewed — using the version-specific URL pattern above — gives reviewers an unambiguous audit trail rather than a moving target.

    As preprint volume grows, the version history itself is becoming part of the evidentiary record: it documents how a finding evolved in response to community comment before formal peer review.

  • bioRxiv License Update: What Changed for Authors and Reuse

    bioRxiv’s licence update, live via the platform’s Author Area since January 2026, lets authors request a change to a less-restrictive Creative Commons licence on a preprint already posted — without submitting a new version. The change can only move in one direction, towards more permissive reuse, and it exists chiefly to help authors bring older preprints into line with funder mandates that require CC BY.

    bioRxiv is a free preprint server for the life sciences, operated by the non-profit organisation openRxiv, which also runs the companion server medRxiv for health-sciences preprints.

    Contents

    What is the bioRxiv licence update, and why was it introduced?

    The bioRxiv licence update is a self-service feature that lets a preprint’s corresponding or submitting author switch its Creative Commons licence to a less restrictive option after posting, without triggering a full revision. openRxiv documented the mechanics in a step-by-step guide published on 7 January 2026, and followed up with a policy explainer on 20 May 2026 setting out the rationale.

    The trigger is compliance drift. Openrxiv’s own explainer states that a growing number of funders “require their grantees to apply specific licenses to their preprints, typically CC BY,” but that “many authors are unaware of this” and post under a more restrictive option by default. Before this update, the only remedy was submitting an entirely new version of the preprint and re-selecting a licence — a heavier process that also generates a fresh revision record. This is distinct from an earlier, smaller change in January 2025, when bioRxiv and medRxiv reordered their licence-selection menus to place CC BY at the top of the list; the 2026 update is the first mechanism that lets authors retroactively fix the licence on preprints they have already posted.

    How do authors request a licence change?

    The workflow runs entirely through the bioRxiv submission system’s Author Area and does not require re-uploading a manuscript. It applies only to the most recent version of a preprint, and only to preprints posted within the past two years.

    • Log into the Author Area from the bioRxiv submit page.
    • Locate the “Request License Update” box on the right-hand side of the page.
    • Select “Update license choice on previously posted papers.”
    • Choose the eligible preprint by its manuscript ID (only papers where the requester was corresponding or submitting author are listed).
    • Select a new, less restrictive licence and submit the request; a confirmation email follows.

    Two constraints apply strictly. First, the feature is unavailable if an incomplete revision is already in the submission system, or if a previous licence request is still pending. Second, a request can even be made after the preprint has been formally published in a journal, since the licence sits on the preprint record independently of the journal’s own copyright terms.

    Licence options compared: what actually changed

    bioRxiv preprints have long offered a choice of Creative Commons licences plus a “no licence” (all rights reserved) default, and a CC0 public-domain option for US federal employees such as NIH intramural researchers. What changed in 2026 is not the menu of options — it is that authors can now move an already-posted preprint from a more restrictive option to a less restrictive one after the fact.

    Licence Commercial reuse Attribution required Text-and-data mining / AI training Typical funder fit
    CC BY Permitted Yes Unrestricted, including commercial use HHMI, Gates Foundation, most cOAlition S funders
    CC BY-ND Permitted (no derivatives) Yes Mining permitted; no adapted/derivative outputs distributed Rarely funder-compliant
    CC BY-NC Not permitted Yes Restricted to non-commercial use Non-compliant with CC BY mandates
    CC BY-NC-ND Not permitted Yes Most restrictive; non-commercial, no derivatives Rarely funder-compliant
    CC0 Permitted (public domain) No Unrestricted US federal/NIH intramural authors only
    No licence selected Not permitted without separate permission N/A Reuse requires author permission Non-compliant with most funder mandates

    Because Creative Commons licences are irrevocable once attached to a public copy of a work, the update only runs in the permissive direction. An author can move from CC BY-NC to CC BY; the system rejects a request to move from CC BY to a more restrictive licence, since existing downloaded and archived copies would remain under the original, broader terms regardless.

    What this means for CC-BY reuse, text-and-data mining, and AI training

    bioRxiv’s baseline terms of use already permit text-and-data mining of posted content, which is the legal hook that has made preprint corpora attractive training data for machine-learning systems. The licence attached to an individual preprint then determines the scope of onward reuse beyond that baseline — and this is where the 2026 update has practical bite.

    Under CC BY, any party — including a commercial AI developer — may reproduce, adapt, and redistribute the work, provided the original authors are credited. Under CC BY-NC or CC BY-NC-ND, commercial reuse (which covers most AI model training conducted by for-profit developers) is not licensed, regardless of the platform-level text-mining consent. That gap is precisely what several funders have moved to close: the Howard Hughes Medical Institute’s preprint requirement, effective 1 January 2026, and the Bill & Melinda Gates Foundation’s preprint mandate, in force since 1 January 2025, both require grantee preprints to carry CC BY. The licence-update feature exists to let authors already out of step with those mandates fix a specific preprint without a full resubmission.

    For institutions and research-integrity offices, the practical implication is that a preprint’s licence — not merely its posting on an open server — is the operative variable for downstream reuse and AI-training permissions. Auditing grantee preprints for licence compliance, not just for the fact of preprint deposit, is now a distinct compliance step.

    Answer-first Q&A

    How do I update a bioRxiv?

    Authors can request a licence update from the Author Area of the bioRxiv submission system, using the “Request License Update” box, without submitting a full revision. The change applies only to preprints posted in the past two years and only to the most recent version, moving to a less restrictive licence.

    What are the licence options for bioRxiv?

    bioRxiv authors can choose CC BY, CC BY-ND, CC BY-NC, CC BY-NC-ND, or leave the preprint with no licence (all rights reserved). A CC0 public-domain option is also available specifically for US federal employees, such as NIH intramural researchers.

    Does bioRxiv count as published?

    No. A bioRxiv preprint is not peer reviewed and does not constitute formal journal publication; it is a publicly posted manuscript with its own DOI. Authors remain free to submit the same work to a journal afterward, and the preprint record persists independently of that later publication.

    Who maintains bioRxiv?

    bioRxiv is operated by openRxiv, a non-profit organisation dedicated to advancing science communication, which also runs the companion health-sciences server medRxiv. openRxiv is supported by institutions including Cold Spring Harbor Laboratory, the Chan Zuckerberg Initiative, and the Sergey Brin Family Foundation.

    Implications for institutions, funders, and authors

    Research-administration offices tracking open-access compliance should treat the licence update as a remediation tool, not a substitute for correct licence selection at submission. It closes a specific gap — preprints posted before an author understood their funder’s CC BY requirement — but it does not apply to preprints older than two years, to superseded versions, or where a revision is already mid-process.

    For anyone advising authors on authorship rights and responsibilities, the clearest guidance is to check funder licensing terms before first posting, since fixing a mismatched licence later depends on the preprint still being within the two-year eligibility window. Related open-research terminology, including licensing and reuse definitions, is tracked in the CASRAI open-research dictionary.

    Expect other preprint servers to face similar pressure as CC BY mandates spread across research funders. The direction of travel — author-initiated, platform-mediated licence correction rather than manuscript resubmission — is a practical template other repositories are likely to adopt as funder compliance checks tighten.

  • BioRxiv Submission Guidelines: A 5-Step Process for First-Time Authors

    BioRxiv submission guidelines require a single PDF (or Word file plus separate figure files), a free author-area registration, an article-category selection, and a two-step in-house-plus-Affiliate screening that typically clears in 24-48 hours. There is no submission fee, no mandatory template, and no peer review before posting. This guide walks first-time authors through each stage, the templates available, and the reasons manuscripts most often get sent back.

    bioRxiv is the life-sciences preprint server operated by the non-profit openRxiv; a preprint is a complete, citable manuscript posted before or during formal peer review, and bioRxiv assigns it a Crossref DOI (prefix 10.1101) as soon as screening is passed. Clinical trial reports and most epidemiology studies must instead go to bioRxiv’s sister server, medRxiv — submitting one of these to bioRxiv is itself a common rejection reason, covered in section four below.

    1. What are bioRxiv’s submission requirements?

    bioRxiv does not enforce a house style, but it does enforce a fixed submission format and a content-eligibility test. The manuscript must be unpublished at the time of deposit, all co-authors must have consented to posting, and the work must fall within a relevant life-sciences subject category.

    Submission route What you upload Conversion
    Single PDF Full text, figures and tables combined None needed — this is the simplest route
    Word + separate figures Word file for text/tables; figures as JPEG, TIFF, EPS or PowerPoint bioRxiv’s automated engine builds the PDF
    LaTeX Manuscript converted to PDF before upload (LaTeX source may accompany it as Supplemental Material) Author-side conversion required

    Large primary datasets belong in a community database such as GenBank or the Protein Data Bank rather than as Supplemental Material, in line with the Fort Lauderdale data-sharing guidelines that bioRxiv references directly in its submission guide.

    2. Setting up your bioRxiv author area

    Every submission starts with a free account on the bioRxiv Manuscript Processing System at submit.biorxiv.org. The bioRxiv author area is where you register, start a new submission, continue a saved draft, proof a converted manuscript, and later submit revisions.

    1. Register with an institutional or personal email address — no institutional affiliation is required to create an account.
    2. Enter the author area and select “Submit a New Manuscript.”
    3. Upload files, enter co-author details for every listed author, and add funder names and grant numbers.
    4. Select an article category: New Results, Confirmatory Results, or Contradictory Results.
    5. Choose a distribution licence — CC BY, CC BY-NC, CC BY-ND, CC BY-NC-ND, CC0, or no reuse.

    Copyright remains with the author throughout. Once a version is posted, it cannot be deleted, but authors can submit a revision at any time before journal acceptance via the same author-area screen.

    3. Choosing a manuscript template

    A bioRxiv template is optional, not mandatory — the platform explicitly states it does not require a particular article format or style, and many authors simply reuse the formatting of their target journal. Two community-maintained options cover most first-time authors.

    • Word template: a community-built .docx template on GitHub styled after published bioRxiv papers, useful if you want a clean starting structure without building one from scratch.
    • bioRxiv LaTeX template: several Overleaf templates are built specifically for bioRxiv preprints and can often be re-purposed for the eventual journal submission, saving reformatting time later in the pipeline.

    Whichever route you choose, convert LaTeX output to PDF before upload — bioRxiv’s system does not compile .tex source directly.

    4. What happens after you submit (timeline and screening)

    Submitted manuscripts go through two screening stages before posting. In-house staff first check completeness and confirm the article type is eligible; volunteer Principal Investigators known as bioRxiv Affiliates then assess whether the work constitutes genuine biological research and whether it poses any public-harm or biosecurity risk.

    This combined process is the answer to a frequent search — bioRxiv submission time — and typically completes within 24-48 hours of upload. Once approved, the PDF posts immediately; conversion to full-text HTML and XML can take a further 1-2 days, so the machine-readable version usually lags the PDF by up to 48 hours.

    Stage Typical duration
    Registration and upload Immediate
    In-house completeness/eligibility check Same day to 24 hours
    Affiliate biosecurity/scope review Within 24-48 hours total
    PDF posting after approval Immediate
    Full-text HTML/XML conversion Up to 48 additional hours

    5. Common rejection reasons and how to avoid them

    bioRxiv’s own screening documentation and content-scope rules point to a consistent set of avoidable rejections for first-time authors.

    • Wrong content type: case reports, narrative reviews, editorials, letters, opinion pieces, hypotheses without new data, and laboratory protocols without accompanying results are all excluded from bioRxiv’s scope.
    • Wrong server: clinical trial results and most epidemiology studies must go to medRxiv, not bioRxiv — this single misrouting error is one of the most common first-submission mistakes.
    • Already published: a manuscript that has already been accepted by a journal cannot be deposited as a new bioRxiv submission.
    • Missing author consent: every listed co-author must have agreed to posting before submission; disputes here stall or block screening.
    • Biosecurity or dual-use concerns: Affiliates specifically screen for material that could pose a health or biosecurity risk, which can delay or prevent posting even for otherwise sound science.
    • Non-scientific or promotional content: bioRxiv is explicitly not a channel for news, product advertisements, or policy statements.

    6. Frequently asked questions

    Can anyone submit to bioRxiv?

    Yes — any author whose manuscript concerns a relevant scientific field, is unpublished, and has the consent of all co-authors can deposit it after free registration. No institutional affiliation is required, and there is no submission fee.

    When should you submit to bioRxiv?

    A manuscript can be submitted at any point before journal publication. Once a journal has formally published the paper, it can no longer be newly deposited as a bioRxiv preprint, though the platform still allows revisions of an existing preprint right up to journal acceptance.

    How long does a bioRxiv submission take?

    Screening typically completes within 24-48 hours of upload, after which the PDF posts immediately. The full-text HTML and XML version follows separately and can take up to 48 further hours to appear.

    How much does it cost to submit to bioRxiv?

    There is no charge for registration or for depositing an article. bioRxiv funds screening and hosting as a non-profit service operated by openRxiv rather than through author-facing fees.

    7. Implications for research offices and institutions

    Research-administration teams increasingly track preprints as part of grant-compliance and output reporting, not just publication records. The U.S. National Institutes of Health has, since Notice NOT-OD-17-050, explicitly permitted investigators to cite preprints — including bioRxiv postings — in grant applications and progress reports, and cOAlition S’s Plan S framework recognises preprints as a valid interim compliance route ahead of a peer-reviewed version.

    Because a bioRxiv DOI is assigned at posting and persists across revisions, institutions can use it as a stable identifier to link the preprint, the eventual journal version, and contributor metadata. Where a project already uses the CRediT contributor role taxonomy to record who did what — CASRAI originated CRediT in 2014, and the taxonomy is now stewarded by NISO as ANSI/NISO Z39.104-2022 — carrying those role assignments into the preprint stage keeps authorship records consistent from first deposit through final publication.

    bioRxiv’s direct-transfer (B2J) programme, which now spans more than 190 partner journals and peer-review services, also removes a second manual re-entry step for research-office staff supporting authors through submission — files and metadata move directly from the bioRxiv author area to the receiving journal without being re-uploaded.

    Building preprinting into standard practice

    For first-time authors, the practical barrier to bioRxiv is low: no fee, no mandatory template, and a screening turnaround measured in hours rather than weeks. The remaining friction is almost entirely about content fit — choosing the right server, the right article category, and confirming every co-author has consented before upload.

    Institutions that build preprint deposit into standard research-administration workflows — alongside DOI tracking, contributor-role records, and funder-mandate checks — turn a one-off submission task into a repeatable, auditable step in the research lifecycle.