PLOS

Prepare your manuscript for PLOS Computational Biology.

Review the checklist, choose your article type, and turn your draft into a cleaner submission package.

Checked 2026-07-15

Check readiness free Prepare this manuscript

Article types

Research Article

Review

Systematic Review

Clinical Trial

Methods Article

Readiness requirements

Review the key details below, or download the complete checklist with every stored source-backed requirement.

Abstract length

Provide an author-written abstract of no more than 300 words.
The Abstract should be succinct; it must not exceed 300 words.

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This text is subject to editorial change, should be written in the first-person voice, and should be distinct from the scientific abstract.
Authors should always state the organism(s) studied in the Abstract.
Review / Systematic Review: Authors whose systematic review was prospectively registered (e.g., in a registry such as PROSPERO ) should also provide the registry number in their abstract.
While the Abstract is conceptually divided into three sections (Background, Methodology/Principal Findings, and Conclusions/Significance), do not apply these distinct headings to the Abstract within the article file.

Reference style

Articlo formats your supplied references to the journal's stored style and checks that citations match the reference list; source validity is not verified.
Match the label of your figure with the name of the file uploaded at submission (e.g. a figure citation of “Fig 1” must refer to a figure file named “Fig1.tif”).

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In-text citations We recommend that you cite supporting information in the manuscript text, but this is not a requirement.
If you cite supporting information in the text, citations do not need to be in numerical order.
Accession numbers or a citation to the DOI should also be provided when the data set is mentioned within the manuscript.
Do not include any citations.
Do not include citations in abstracts.
Do not provide a shortened DOI or the URL.
For both the code and data you must list the name of the repository or repositories as well as digital object identifiers (DOIs), accession numbers or codes, or other persistent identifiers.
In some cases authors may not be able to obtain accession numbers of DOIs until the manuscript is accepted; in these cases, the authors must provide these numbers at acceptance.
If Mendelian randomization studies replicate previously published work, authors must provide a sound scientific rationale for the submitted work and clearly reference and discuss the existing literature.
In the Materials and Methods section, authors should include a section on statistical analysis that provides a detailed description of the statistical methods: List the name and version of any software package used, alongside any relevant references.
Do not cite the following sources in the reference list: Submitted research should not rely upon retracted research.
Do not cite the following sources in the reference list: Unavailable and unpublished work, including manuscripts that have been submitted but not yet accepted (e.g., “unpublished work,” “data not shown”).
Do not cite the following sources in the reference list: Personal communications (these should be supported by a letter from the relevant authors but not included in the reference list).
Repositories may be subject-specific (e.g., GenBank for sequences and PDB for structures), general, or institutional, as long as DOIs or accession numbers are provided and the data are at least as open as CC BY.

Figure and table rules

Keep every figure and table numbered, captioned, and cited in the manuscript.
Tables require a label (e.g., “Table 1”) and brief descriptive title to be placed above the table.

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Review: A review should aim for 3000-6000 words and two or three figures or other display items.
The file number and name are required in a caption, and we highly recommend including a one-line title as well.
You may also include a legend in your caption, but it is not required.
Cite figures in ascending numeric order at first appearance in the manuscript file.
At a minimum, include the following in your figure captions: A figure label with Arabic numerals, and “Figure” abbreviated to “Fig” (e.g. Fig 1, Fig 2, Fig 3, etc).
Figure Captions and Tables should be inserted immediately after the first paragraph in which they are cited in the article file.
Do not submit captions in a separate file.
Do not submit your tables in separate files.
At a minimum, include the following in your figure captions: A concise, descriptive title.
Place each table in your manuscript file directly after the paragraph in which it is first cited (read order).
Place legends, footnotes, and other text below the table.
Upload a separate file with the corresponding caption.

Funding statement

Add or confirm the author-written Funding statement; Articlo flags it if author input is still needed.
Do not include funding sources in the Acknowledgments or anywhere else in the manuscript file.

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Financial Disclosure Statement This information should describe sources of funding that have supported the work.
The statement should include: URLs to sponsors’ websites.
Funding information should only be entered in the financial disclosure section of the submission system.

Competing interests

Review: Add or confirm the author-written Competing interests statement; Articlo flags it if author input is still needed.

Data availability statement

Add or confirm the author-written Data availability statement; Articlo flags it if author input is still needed.
When submitting a manuscript online, authors must provide a Data Availability Statement describing compliance with both policies.

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Data availability statement The data availability statement must give details of both the data and code that supports the results presented in the article.
Any data that cannot be shared due to ethical or legal restrictions should follow the guidelines set out in the data availability guidelines.
Details of the code location should be given in the data availability statement.
Accession numbers (and version numbers, if appropriate) should be provided in the Data Availability Statement.
If there are ethical or legal restrictions on sharing code, authors should provide the following information within their data availability statement upon submission and should contact the journal editorial office ( ploscompbiol@plos.org): Provide all necessary contact information needed for others to make access requests for the code, including a third party contact.

Ethics statement

Add or confirm the author-written Ethics statement; Articlo flags it if author input is still needed.
If data were anonymized and/or aggregated before access and analysis, informed consent is generally not required.

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Note that Terms of Use contracts do not qualify as informed consent, even if they address the use of personal data for research.
Ethical Oversight We uphold rigorous standards for research ethics and expect authors to report on any ethical approvals required for their study.
Animal research All research involving vertebrates or cephalopods must have approval from the authors' Institutional Animal Care and Use Committee (IACUC) or equivalent ethics committee(s), and must have been conducted according to applicable national and international guidelines.
Manuscripts reporting animal research must state in the Methods section: The full name of the relevant ethics committee that approved the work, and the associated permit number(s).
Manuscripts reporting animal research must state in the Methods section: Where ethical approval is not required, the manuscript should include a clear statement of this and the reason why.
If humane endpoints were not used, the manuscript should report: Whether the institutional animal ethics committee specifically reviewed and approved the anticipated mortality in the study design.
Observational and field studies Methods sections for submissions reporting on any type of field study must include ethics statements that specify: Permits and approvals obtained for the work, including the full name of the authority that approved the study; if none were required, authors should explain why.
Observational and field studies Methods sections for submissions reporting on any type of field study must include ethics statements that specify: Whether the land accessed is privately owned or protected.
Observational and field studies Methods sections for submissions reporting on any type of field study must include ethics statements that specify: Whether any protected species were sampled.
Observational and field studies Methods sections for submissions reporting on any type of field study must include ethics statements that specify: Full details of animal husbandry, experimentation, and care/welfare, where relevant.
In the Ethics Statement, authors should declare any potential risks to individuals or individual privacy, or affirm that in their assessment, the study posed no such risks.
For interventional studies, which impact participants’ experiences or data, the study design must have been prospectively approved by an Ethics Committee, and informed consent is required.
In addition, the following Ethics and Data Protection requirements must be met.
If there are ethical or legal restrictions on sharing code, authors should provide the following information within their data availability statement upon submission and should contact the journal editorial office ( ploscompbiol@plos.org): Explain the restrictions in detail (e.g., code could potentially identify or reveal sensitive patient information).
Additional requirements apply in the following circumstances: If information used could threaten personal privacy or damage the reputation of individuals whose data are used, an Ethics Committee should be consulted and informed consent obtained or specifically addressed.
Additional requirements apply in the following circumstances: If authors accessed any personal identifying information, an Ethics or Data Protection Committee should oversee data anonymization.

Blinded manuscript

Provide details of any blinding, methods of randomization, or inclusion/exclusion criteria (e.g., of subjects included at collection or of data points included in analysis).

Cover letter

Provide the claims and editor-specific context for the cover letter; Articlo creates an editable companion without inventing content.
Include your statement in the Financial Disclosure section of the initial submission form.

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The software must be downloadable anonymously in source code form and licensed under an Open Source Initiative (OSI) compliant license.
Software articles require a cover letter explaining how the above criteria are met.
Personal data from third-party sources For all studies using personal data from internet-based and other third-party sources (e.g., social media, blogs, other internet sources, mobile phone companies), data must be collected and used according to company/website Terms and Conditions, with appropriate permissions.
Do not add it to the author list in the submission system.
The cover letter should address the following questions: Why is this manuscript suitable for publication in PLOS Computational Biology?
The cover letter should address the following questions: Why will your study inspire other members of your field, and how will it drive research forward?
Submit your striking image to the submission system using the file type “Striking Image”.
Methods Article: Methods articles require a cover letter outlining answers to the following questions: Why is the innovation substantial and relevant?
Methods Article: Methods articles require a cover letter outlining answers to the following questions: What is the concrete method being put forth and what is its intended user community?
Methods Article: Methods articles require a cover letter outlining answers to the following questions: How has the method been validated?
Methods Article: Methods articles require a cover letter outlining answers to the following questions: How is the method being made available?
Methods Article: Methods articles should be submitted through our online submission system.
Software articles should be submitted through our online submission system.
Methods Article: Methods articles require a cover letter outlining answers to the following questions: What is the major innovation in the paper, compared with the state of the art of the field?

Author contributions

Add or confirm the author-written Author contributions statement; Articlo flags it if author input is still needed.
Use the CRediT taxonomy to describe each contribution.

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Author contributions Provide at minimum one contribution for each author in the submission system.

Supplementary files

Clinical Trial: Include every cited supplementary file and use matching labels in the manuscript.
Methods Article: Include every cited supplementary file and use matching labels in the manuscript.

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Research Article: Include every cited supplementary file and use matching labels in the manuscript.
Embed or attach the author-supplied supplementary material so Articlo can extract and label it for the package.
They must be deposited as supplemental information file of less than 100 MB (ideally as.7z or.rar).
Format Articles should be concise (less than 3500 words, not including supplementary material) and be organized as follows: Title The title should include the name of the software.
This should be included as part of the supplementary material.
These files must be provided in human-readable formats and should be included as supplementary material.
Details of the supplied test data and how to install and run the software should be detailed in the supplementary material.
Checklists or other documentation should be uploaded as supporting information at submission.
This checklist should be provided as supporting information alongside the submitted manuscript.
Include the full results of any regression analysis performed as a Supporting Information file.
Systematic Review: Systematic reviews and meta-analyses Reports of systematic reviews and meta-analyses must adhere to the PRISMA statement as a guide, and include a completed PRISMA checklist and flow diagram as supporting information.
Review / Systematic Review: Authors must also state in their Materials and Methods section whether a protocol exists for their systematic review, and if so, provide a copy of the protocol as a Supporting Information file.

Title page and author information

Provide the author, affiliation, and correspondence details for the separate title page; Articlo creates the editable companion file.
Each author on the list must have an affiliation.

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Include an email address for each corresponding author listed on the title page of the manuscript.
Title page The title, authors, and affiliations should all be included on a title page as the first page of the manuscript file.
If your corresponding author is affiliated with a participating institution, they must follow the instructions below to demonstrate eligibility.
The corresponding author must provide an ORCID iD at the time of submission by entering it in the user profile in the submission system.
If your corresponding author is not from a participating institution and requires assistance paying publishing fees, please consider applying for a fee waiver at submission.

Article structure and word limits

All file types can be submitted, but files must be smaller than 20 MB in size.
Education articles should aim for 2000 and should not exceed 2500 words.

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The length should be no more than 2500 words.
The writing style should be concise and accessible.
Microsoft Word documents should not be locked or protected.
Layout and spacing Manuscript text should be double-spaced.
Use continuous line numbers (do not restart the numbering on each page).
Do not use MathType, Equation Editor, or the Insert→Equation function for only a portion of an equation.
Equations should not contain a mix of different equation tools.
If you do not use these exclusively, provide the SI value in parentheses after each value.
Use the recommended name by consulting the appropriate genetic nomenclature database (e.g., HUGO for human genes).
Gene prefixes such as those used for oncogenes or cellular localization should be shown in roman typeface (e.g., v-fes, c-MYC).
Obtaining this service is the responsibility of the author and should be done before initial submission.
Manuscript Organization Most manuscripts should be organized as follows.
Titles should be written in sentence case (only the first word of the text, proper nouns, and genus names are capitalized).
Systematic Review / Clinical Trial: For clinical trials, systematic reviews, or meta-analyses, the subtitle should include the study design.
Contributions will be published with the final article, and they should accurately reflect contributions to the work.
Review: Include a brief review of the key literature.
If there are relevant controversies or disagreements in the field, they should be mentioned so that a non-expert reader can delve into these issues further.
PLOS journals require authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception.
Code must be shared openly in an appropriate repository with accompanying documentation and clearly licensed to facilitate reuse by others.
To ensure equitable recognition and avoid any appearance of partiality, do not include editors or peer reviewers—named or unnamed—in the Acknowledgments.
You should avoid citing retracted articles unless you need to discuss retracted work to provide historical context for your submitted research.
Accession numbers All appropriate data sets, images, and information should be deposited in an appropriate public repository.
In all other cases, these numbers must be provided at full submission.
Identifiers should be provided in parentheses after the entity on first use.
All novel structures must have been deposited in a community endorsed database prior to submission (please see our list of recommended repositories ).
Striking images should not contain potentially identifying images of people.
The statement should include: Specific grant numbers.
The statement should include: Initials of authors who received each award.
If related work has been or will be submitted elsewhere or is in press elsewhere, then a copy must be uploaded with the article submitted to PLOS.
Review: When making these suggestions, please provide specific reasons why each person should not review your submission in each “Reason” box.
Novel tools created by the authors in parallel with the benchmark should not be included in the article.
The study must be transparent about how the benchmark was conducted.
Research Article: The article should follow the same general style and format and organization as in a general research article.
The software must already be widely adopted, or have the promise of wide adoption by a broad community of users.
There is no minimal set of hardware platforms or operating systems that the software is required to run on provided they do not limit broad adoption of the software.
This must include instructions for building and installing the software from source, and any dependencies on both proprietary and freely available prerequisites.
For software libraries, instructions for using the API are also required.
Authors should provide links to the location of the software, mailing lists, etc. as part of the article.
For papers written in LaTeX, the LaTeX Guidelines for formatting the paper should be followed.
Approval must be received prior to beginning research.
Provide any relevant regulations under which the study is exempt from the requirement for approval.
Where the study may be confused as pertaining to clinical research, authors should also state the animal model in the title.
Collection Overviews should be concise, with suitable referencing, and provide the appropriate context for the publications in the Collection.
Perspectives are intended to be more prospective than retrospective but require sufficient background to place the points made in context.
Review: A review should not be a mere summary of the field; it should be a critique with new points of view which are supported by existing literature from a variety of authors.
Research submitted to PLOS must comply with internationally-accepted standards for research practice and reporting.
Researchers travelling to another country solely to use laboratory equipment will not normally be required to complete the questionnaire.
Cell lines Manuscripts reporting research using cell lines should include the species and strain, sex of origin, and genetic modification status.
We require adherence to many of the minimum requirements included in the Framework.
For plants, ecotype and cultivar should also be reported where relevant.
More specifically, authors should: Identify research design and independent variables as being between- or within-subjects.
More specifically, authors should: For pre-processed data: If data were transformed, provide a reason for doing so and a description of the transformation performed.
More specifically, authors should: Provide details of how outliers were treated and analysis, both with the full dataset and with the outliers removed.
More specifically, authors should: If relevant, describe how missing/excluded data were handled, including attrition effects.
More specifically, authors should: Define the threshold for significance (alpha).
More specifically, authors should: If appropriate, provide sample sizes, along with a description of how they were determined.
More specifically, authors should: For analyses of variance (ANOVAs), detail any post hoc tests that were performed.
More specifically, authors should: Include details of any corrections applied to account for multiple comparisons.
Include details of the type of t-test conducted (e.g. one sample, within-/between-subjects).
More specifically, authors should: For stepwise multiple regression analyses: Report the alpha level used.
More specifically, authors should: For stepwise multiple regression analyses: Discuss whether the variables were assessed for collinearity and interaction.
More specifically, authors should: For Bayesian analysis explain the choice of prior trial probabilities and how they were selected.
Markov chain Monte Carlo settings should be reported.
Include all estimated regression coefficients, their standard error, p-values, and confidence intervals, as well as measures of goodness of fit.
Effect sizes and confidence intervals should be reported where appropriate.
If percentages are provided, the numerator and denominator should also be given.
Territorial Descriptions Territorial descriptions in submitted manuscripts should follow international treaties and conventions.
Review: When you first submit to the journal, providing you include all the necessary information needed for editorial assessment and review, we will not ask you to make any formatting changes.
LaTeX manuscripts must be submitted as PDFs.
Allergens The systematic allergen nomenclature of the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-committee should be used for manuscripts that include the description or use of allergenic proteins.
For manuscripts describing new allergens, the systematic name of the allergen should be approved by the WHO/IUIS Allergen Nomenclature Sub-Committee prior to manuscript publication.
The current address should be listed in the byline and clearly labeled “current address.” At a minimum, the address must include the author’s current institution, city, and country.
Data reporting All data and related metadata underlying the findings reported in a submitted manuscript should be deposited in an appropriate public repository, unless already provided as part of the submitted article.
Code reporting All author-generated code directly related to the findings reported in a submitted manuscript must be made publicly available without access restriction unless specific legal or ethical restrictions prohibit public sharing of code.
Molecular dynamics data If your study involves molecular dynamics simulations and your data are too large to share easily, please refer to this guide on what should be included with your submission.
Small and macromolecule crystal data Manuscripts reporting new and unpublished three-dimensional structures must include sufficient supporting data and detailed descriptions of the methodologies used to allow the reproduction and validation of the structures.
Small molecule single crystal data Authors reporting X-Ray crystallographic structures of small organic, metal-organic, and inorganic molecules must deposit their data with the Cambridge Crystallographic Data Centre (CCDC), the Inorganic Crystal Structure Database (ICSD), or similar community databases providing a recognized validation functionality.
Macromolecular structures Authors reporting novel macromolecular structures must have deposited their data prior to submission with the Worldwide Protein Data Bank (wwPDB), the Biological Magnetic Resonance Data Bank (BMRB), the Electron Microscopy Data Bank (EMDB), or other community databases providing a recognized validation functionality.
Areas of emphasis include, but are not limited to, macromolecular structure, machine learning providing novel biological insights, dynamics, assembly, folding and interactions.
Areas of emphasis include, but are not limited to: molecular regulation of cellular behavior; multicellular behavior; systems pharmacology; developmental biology; and multi-system regulation.
Areas of emphasis include, but are not limited to: infectious disease modeling; causal inference; simulation-based approaches to understanding disease progression and the impact of interventions.
Areas of emphasis include but are not limited to: emergence of collective behavior in populations; evolutionary game theory; ecological networks; niche modeling; and mechanisms of species interactions and community assembly.
Areas of emphasis include, but are not limited to: microbial ecology and systems biology; viral dynamics; pharmacokinetic/pharmacodynamic models; computational immunology; molecular epidemiology.
Areas of emphasis include, but are not limited to: cognition, learning and memory, behavior, sensory systems, biomechanics and biokinetics, and neural network studies that provide biological insights.
Tools evaluated in the study should be comprehensive, or judiciously selected, among those publicly available in the field and evaluated with regard to their practical relevance for potential users.
The source code must be accompanied by documentation on building and installing the software from source, as well as for using the software, including instructions on how a user can test the software on supplied test data.
The test dataset(s) must enable complete demonstration of the capabilities of the software, and may either be available from a publicly accessible data archive via a provided URI, or may be specifically created and made available with the software.
Non-human primates Manuscripts describing research involving non-human primates must report details of husbandry and animal welfare in accordance with the recommendations of the Weatherall report, The use of non-human primates in research, including: Information about housing, feeding, and environmental enrichment.
Humane endpoints Manuscripts reporting studies in which death of a regulated animal (vertebrate, cephalopod) is a likely outcome or a planned experimental endpoint, must comprehensively report details of study design, rationale for the approach, and methodology, including consideration of humane endpoints.
Antibodies and other reagents Manuscripts reporting research using antibodies and other reagents should identify the commercial supplier or source laboratory, the catalog or clone number and, if known, the batch or lot number.
Authors should state when and where they obtained the cells, giving the date and the name of the researcher, cell line repository (with accession number), or commercial supplier (with catalog or clone number) that provided the cells, as appropriate.
Authors should check established cell lines using the ICLAC Database of Cross-contaminated or Misidentified Cell Lines to confirm that they are not contaminated or misidentified.
Review: Cell line authentication is strongly recommended – e.g., by karyotyping, isozyme analysis, or short tandem repeats (STR) analysis – and may be required during peer review.
For de novo (new) cell lines, including those given to the researchers as a gift, authors must follow PLOS policies for human subjects research and animal research, as appropriate.
Plants and microorganisms Manuscripts reporting research on plants or microorganisms should include the species, strain, source (including location for collected wild specimens), and accession number, if available.
More specifically, authors should: For stepwise multiple regression analyses: Describe the variable selection process by which the final model was developed (e.g., forward-stepwise; best subset).
It should be clear from the text which measures of variance (standard deviation, standard error of the mean, confidence intervals) and central tendency (mean, median) are being presented.
Authors should specifically address the following points: PLOS expects researchers to share software and scripts needed for the work.
Review: Authors are required to deposit the following with the journal upon submission for archival and review purposes.
Authors should specifically address the following points: Provide a README file with a list of included files and/or links to publicly available repositories along with their brief description.
Authors should specifically address the following points: Authors should describe all software used including the specific version(s) used in the work, and how it can be obtained.
Authors should specifically address the following points: Authors should provide the complete set of input files used to initiate the calculations, including input coordinates, topologies and parameter files.
Authors should specifically address the following points: Authors should deposit trajectories in a public repository according to FAIR (Findable, Accessible, Interoperable, Reusable) data principles.
PLOS Computational Biology also requires authors to make any author generated code underlying the findings fully available without restriction, with rare exception.
PLOS Computational Biology staff editors do not consider unsolicited Collection Overviews.
Do not format text in multiple columns.

Reporting guidelines

Include or confirm the reporting guidelines required by the journal. Articlo checks this item and flags anything that still needs author input.

Statistical reporting

More specifically, authors should: Describe all options for statistical procedures.
Test statistics (F/t/r) and associated degrees of freedom should be provided.

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Authors should ensure that results are rigorously reported in accordance with community standards and that statistical methods employed are appropriate for the study design.
In the Materials and Methods section, authors should include a section on statistical analysis that provides a detailed description of the statistical methods: Describe technical details or procedures required to reproduce the analysis.
In the Materials and Methods section, authors should include a section on statistical analysis that provides a detailed description of the statistical methods: Provide a persistent identifier for any code used in the analysis (see our Code Sharing policy ).
More specifically, authors should: For pre-processed data: Justify the selection of statistical tests by describing any analysis confirming that the data meets the assumptions of the analysis performed (e.g., linearity, collinearity, normality of the distribution).

Preprints and prior publication

Include or confirm the preprints and prior publication required by the journal. Articlo checks this item and flags anything that still needs author input.

Submission forms

Include or confirm the submission forms required by the journal. Articlo checks this item and flags anything that still needs author input.

Language and text style

Language Manuscripts must be submitted in English.
Do not use non-standard abbreviations unless they appear at least three times in the text.

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Journal name abbreviations should be those found in the National Center for Biotechnology Information (NCBI) databases.
Keep abbreviations to a minimum.

Authorship and originality

All authors must meet the criteria for authorship as outlined in the authorship policy.
If included, these individuals must qualify for authorship according to our criteria.

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Acknowledgments Those who contributed to the work but do not meet our authorship criteria should be listed in the Acknowledgments with a description of the contribution.
Authors performing research in other countries and communities should ensure the contribution of local collaborators is suitably acknowledged in the authorship list and/or Acknowledgements.
Those who contributed to the work but do not meet the criteria for authorship can be mentioned in the Acknowledgments.
When submitting a manuscript, all authors are asked to indicate that they do not have a related or duplicate manuscript under consideration (or accepted) for publication elsewhere.

Manuscript structure

Authors should mention the techniques used without going into methodological detail and should summarize the most important results.
Introduction The introduction should put the focus of the manuscript into a broader context.

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The Introduction should conclude with a brief statement of the overall aim of the experiments and a comment about whether that aim was achieved.
Results The Results section should provide details of all of the experiments that are required to support the conclusions of the paper.
The section should be written in the past tense.
Discussion The Discussion should spell out the major conclusions of the work along with some explanation or speculation on the significance of these conclusions.
The Discussion should be concise and tightly argued.
Materials and Methods The Materials and Methods should provide enough detail to reproduce the findings.
Submit detailed protocols for newer or less established methods.
Selecting a Section Selecting a section is required for submission and will be used to assign your manuscript to an appropriate Section Editor.
Areas of emphasis include, but are not limited to: novel algorithms; benchmarking methods; identifying biomarkers; and multi-omic integration.
The benchmarked methods must be in an active area of research.
The method must already be widely adopted or have the promise of wide adoption by a broad community of users.
The authors must clearly provide detail, data, and, where necessary, software to ensure readers’ ability to reproduce the methods and results.
Manuscripts reporting animal research must state in the Methods section: Relevant details of steps taken to ameliorate animal suffering.
Full details of humane endpoints use must be reported for a study to be reproducible and for the results to be accurately interpreted.
All data sources must be acknowledged clearly in the Materials and Methods section.
Results must be rigorously and appropriately reported, in keeping with community standards.
If this cannot be made publicly available (e.g. due to licenses), the simulation method should be provided in sufficient detail so the results can, in principle, be reproduced using publicly available software.
Areas of emphasis include, but are not limited to: organ systems and biomechanics, novel multimodal methods applied to biological system data; integrative studies of interacting components; network biology and modeling complex feedback and regulatory systems; systems pharmacology; and computational image analysis.
To ensure the results are reproducible, the training conditions of each tool should be clearly indicated and the input and expected output datasets used in the benchmark must be made freely available in a form that makes them easy to apply and reuse.
A prerequisite for publication is that the results described in the paper must be reproducible when peer reviewers or editors choose to run the software on the deposited dataset using the parameters provided.
The results of running the software on the test data should be reproducible, and any external dependencies (such as external databases that may change) must be documented.
Non-human primates Manuscripts describing research involving non-human primates must report details of husbandry and animal welfare in accordance with the recommendations of the Weatherall report, The use of non-human primates in research, including: Steps taken to minimize suffering, including use of anesthesia and method of sacrifice, if appropriate.
If humane endpoints were not used, the manuscript should report: A scientific justification for the study design, including the reasons why humane endpoints could not be used, and discussion of alternatives that were considered.
For studies in which death of an animal is an outcome or a planned experimental endpoint, authors should include the following information in the Methods section of the manuscript: The specific criteria (i.e. humane endpoints) used to determine when animals should be euthanized.
For studies in which death of an animal is an outcome or a planned experimental endpoint, authors should include the following information in the Methods section of the manuscript: The duration of the experiment.
For studies in which death of an animal is an outcome or a planned experimental endpoint, authors should include the following information in the Methods section of the manuscript: The numbers of animals used, euthanized, and found dead (if any); the cause of death for all animals.
For studies in which death of an animal is an outcome or a planned experimental endpoint, authors should include the following information in the Methods section of the manuscript: How frequently animal health and behavior were monitored.
For studies in which death of an animal is an outcome or a planned experimental endpoint, authors should include the following information in the Methods section of the manuscript: All animal welfare considerations taken, including efforts to minimize suffering and distress, use of analgesics or anaesthetics, or special housing conditions.
Publication charges do not apply to the article types outlined in this section.

Article type and manuscript length

Authors must include the structure reference numbers within the main text and submit as Supplementary Information the official validation reports from these databases.
There is no specific word limit for this section, but details of experiments that are peripheral to the main thrust of the article and that detract from the focus of the article should not be included.

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Authors are also required to include the relevant structure reference numbers within the main text (e.g. the CCDC ID number), as well as the crystallographic information files (.cif format) as Supplementary Information, along with the checkCIF validation reports that can be obtained via the International Union of Crystallography (IUCr).
Education is now an article type comprising Ten Simple Rules, Quick Tips, and any other relevant contribution, and all of these formats should be submitted to the ‘General’ section of the journal.
Review: Review articles should be structured as follows: Title, Authors, Affiliations, Abstract, Introduction, Main Text (broken into subsections as appropriate), Conclusions, Acknowledgments, and References.
Please note that when submitting either a ‘Ten Simple Rules’ or ‘Quick Tips’ piece, the correct article type is ‘ Education ’ and each should be submitted to the General section.

Study reporting guidelines

Diagnostic studies Reports of studies of diagnostic accuracy should conform to the STARD requirements.
Reports of Mendelian randomization studies must include a STROBE-MR checklist completed with page number and relevant text.

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Observational studies in epidemiology For reports of epidemiological studies, authors should conform to the STROBE guidelines.
Authors should take care to maximize the accessibility and reusability of the data by selecting a file format from which data can be efficiently extracted (for example, spreadsheets or flat files should be provided rather than PDFs when providing tabulated data).
Clinical Trial: Clinical trials Clinical trial reports must adhere to the relevant reporting guidelines for their study design, such as CONSORT for randomized controlled trials, TREND for non-randomized trials, and other specialized guidelines as appropriate.
Mendelian randomization studies Manuscripts reporting a Mendelian randomization study must report results of value to the field and should be reported according to STROBE-MR (Strengthening the Reporting of Observational Studies in Epidemiology using Mendelian Randomization) guidelines.

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What your package checks

Abstract: 300 words

Paper: 2,500 words

Title page: separate file

Cover letter: requested

Declarations: Data availability, Funding, Ethics, Author contributions

Format: double spacing

Source transparency

This preparation guide uses published journal-specific author requirements. Journal instructions can change, so authors should complete a final review before submission.

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