CASRAI Dictionary

Tag: biorxiv template

  • bioRxiv Template: LaTeX & Word Formatting Guide

    A bioRxiv manuscript template is a formatting scaffold — in LaTeX or Word — that arranges title page, abstract, figures, and references to match bioRxiv’s posting system, but bioRxiv itself mandates no single template. Authors may submit a plain PDF, a Word file with separate figures, or a LaTeX-derived PDF built from one of several community templates. This guide walks through each formatting field so a manuscript is ready for upload on the first attempt, rather than repeating the general submission-guidelines overview already covered elsewhere on this site.

    bioRxiv is the preprint server for biology, operated by Cold Spring Harbor Laboratory, that posts unpublished research manuscripts after a basic screening step rather than peer review.

    Does bioRxiv Require a Specific Manuscript Template?

    No. bioRxiv’s own guidance states that it “does not require a particular article format/style,” and submission formats can therefore vary considerably between manuscripts. The bioRxiv Submission Guide describes the simplest route as uploading a single PDF containing the full text, figures, and tables.

    This absence of a mandatory template is precisely why community-built templates exist: authors want the discipline of a fixed structure — title page order, figure placement, reference formatting — even though bioRxiv will accept a manuscript without one. The trade-off is that a template also signals to co-authors and affiliates conducting screening that the manuscript is complete and properly ordered.

    Which LaTeX Template Should You Use for bioRxiv?

    For LaTeX users, Overleaf hosts several bioRxiv-tagged templates that compile directly to a submission-ready PDF. Two are widely used within the biology preprint community, and both descend from the same lineage: the HenriquesLab bioRxiv template, itself a modification of the PNAS journal template.

    The quantixed/manuscript-templates repository extends this further: a single manuscript source can generate either a typeset preprint layout (\documentclass[twocolumn]{bioRxiv}) or a line-numbered journal-submission layout (\documentclass[submit]{bioRxiv}) by commenting one line in a merge file, avoiding two parallel documents. It also adds native \orcidlink support so ORCID iDs render correctly on the title page.

    Template Format Platform Notable field-level feature
    arXiv/bioRxiv template LaTeX Overleaf General-purpose preprint layout with figure embedding
    HenriquesLab bioRxiv template LaTeX Overleaf PNAS-derived styling built specifically for bioRxiv
    quantixed/manuscript-templates LaTeX GitHub / Overleaf Switchable preprint vs. journal-submission layout; ORCID support
    chrelli/bioRxiv-word-template Word (.docx) GitHub Styled headings and figure captions for non-LaTeX authors
    finkelsteinlab/BioRxiv-Template Word (.docx) GitHub Reader-friendly layout aimed at readability over journal mimicry

    Whichever LaTeX template is used, the .tex source must still be compiled and converted to PDF before upload — bioRxiv’s submission system does not accept raw .tex files.

    Formatting a bioRxiv Manuscript in Word

    Authors who do not use LaTeX can format directly in Microsoft Word using a template such as the chrelli or finkelsteinlab bioRxiv templates on GitHub, both designed to visually approximate a typeset preprint while remaining fully editable. The practical field order to follow is:

    • Title page: full title, author list, institutional affiliations, ORCID iDs, and the corresponding author’s contact details.
    • Abstract: a single unstructured paragraph summarising rationale, method, and findings.
    • Main text: Introduction, Results, Discussion, and Methods — bioRxiv does not enforce a fixed section order, so discipline-specific conventions (e.g. Methods-first for some biology sub-fields) are acceptable.
    • Figures and tables: either embedded in-line at first citation or supplied as separate files.
    • Author Contributions: a statement of who did what, increasingly expressed using the CRediT contributor role taxonomy.
    • Competing interests and funding: brief declarations, matching journal norms.
    • References and, where applicable, a separate Supplementary Information reference list.

    On the Author Contributions field: CASRAI originated the CRediT contributor role taxonomy in 2014. The standard is now stewarded by NISO as ANSI/NISO Z39.104-2022, and mapping each author to a defined CRediT role gives the statement a machine-readable structure that a free-text sentence lacks.

    What File Formats and Figure Rules Does bioRxiv Require?

    bioRxiv’s accepted formats are narrower than they first appear, and mismatched file types are a common cause of upload failure.

    • Main text: PDF, Microsoft Word, or WordPerfect.
    • Figures and tables submitted separately: GIF, TIFF, EPS, or JPEG.
    • Supplemental files: posted largely as-is, so a wider range of file types is tolerated.
    • LaTeX source: must be compiled to PDF before submission; the system does not ingest .tex directly.

    bioRxiv also offers a print-friendly, in-line-figure PDF generated automatically from the full-text HTML of a posted preprint — a feature introduced in February 2022 specifically so readers are not limited to the author’s originally submitted figure placement.

    Article type matters as much as file type. bioRxiv categorises submissions as New Results, Confirmatory Results, or Contradictory Results; narrative reviews, commentaries, opinion pieces, and step-by-step protocols are not considered appropriate for the server. New manuscripts reporting clinical trial results must go to medRxiv instead of bioRxiv.

    How Does bioRxiv Assign a DOI, and How Should a Preprint Be Cited?

    Every bioRxiv preprint receives a Crossref DOI under the 10.1101/ prefix as soon as it clears screening and posts — no separate application step is required from the author. This DOI remains stable through subsequent revised versions of the same preprint.

    For citation, most style guides treat a bioRxiv preprint as a standard journal-style reference carrying a DOI instead of (or alongside) volume and page numbers; Wikipedia maintains a dedicated {{Biorxiv}} citation template for exactly this purpose. Once a preprint is later published in a peer-reviewed journal, citing conventions typically shift to the journal DOI, with the preprint DOI retained as a historical record of priority.

    Frequently Asked Questions About bioRxiv Submission

    Can anyone submit to bioRxiv?

    Yes. Any author may deposit a manuscript on bioRxiv provided it covers a relevant scientific field, is unpublished at the time of submission, and all co-authors have consented to its deposition. Authors must first register on the submission site before uploading a manuscript.

    How much does it cost to submit to bioRxiv?

    There is no fee to submit an article to bioRxiv. This distinguishes it from many journals’ article-processing charges and from some other preprint servers that levy optional support fees, making template correctness — not payment — the main barrier to a smooth first submission.

    Can you put a paper on bioRxiv after submitting it to a journal?

    Yes. A manuscript can be posted to bioRxiv at any point before a journal formally publishes it, and new revised versions can be posted at any time up to journal publication or assignment of a journal DOI, provided the target journal’s own preprint policy permits it.

    When should you submit to bioRxiv?

    There is no fixed submission window: a manuscript can go to bioRxiv at any stage before journal publication, including alongside or ahead of journal submission. Once a paper has already been formally published by a journal, it can no longer be submitted to bioRxiv.

    What This Means for Authors and Institutions

    The lack of a mandatory bioRxiv template shifts formatting risk onto the author rather than the platform. Choosing a maintained LaTeX template, such as one built to switch between preprint and journal-submission layouts, or a Word template with pre-styled headings, reduces reformatting work twice: once for the preprint and again when the manuscript is later reshaped for a target journal.

    For research offices and library preprint-support teams, standardising on one or two vetted templates — and requiring CRediT-tagged Author Contributions statements — creates consistency across a department’s preprint output without waiting for bioRxiv itself to impose a house style. As preprints increasingly carry citable, versioned DOIs from the moment of posting, formatting discipline at submission time has become part of an institution’s research-integrity record, not just a cosmetic step.

  • 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.