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Submission Guidelines

PLOS Computational Biology publishes original research that clearly demonstrates novelty, importance to a particular field, biological significance, and conclusions that are justified by the study.

Our aim is to make the editorial process rigorous and consistent, and to offer the best possible support to our authors throughout this process. Authors are encouraged to decide how best to present their ideas, results, and conclusions. The writing style should be concise and accessible. Editors may make suggestions for how to achieve this, as well as suggestions for cuts or additions that could be made to the article to strengthen the argument.

Submitting a revision? Read our Revision Guidelines.

Style and Format

PLOS Computational Biology will accept initial submissions of manuscripts in a single PDF file including text and figures. If you are submitting a  revised manuscript, you must upload separate files for your text, figures, and supporting information before your submission can be passed back to the editors.

File format

Manuscript files can be in the following formats: DOC, DOCX, RTF, or PDF. Microsoft Word documents should not be locked or protected. 

LaTeX manuscripts must be submitted as PDFs. Read the LaTeX guidelines.

Length

Manuscripts can be any length. There are no restrictions on word count, number of figures, or amount of supporting information.


We encourage you to present and discuss your findings concisely.

Font

Use a standard font size and any standard font, except for the font named “Symbol”. To add symbols to the manuscript, use the Insert → Symbol function in your word processor or paste in the appropriate Unicode character.

Headings

Limit manuscript sections and sub-sections to 3 heading levels. Make sure heading levels are clearly indicated in the manuscript text.

Layout and spacing

Manuscript text should be double-spaced.

Do not format text in multiple columns.

Page and line numbers

Include page numbers and line numbers in the manuscript file. Use continuous line numbers (do not restart the numbering on each page).

Footnotes

Footnotes are not permitted. If your manuscript contains footnotes, move the information into the main text or the reference list, depending on the content.

Language

Manuscripts must be submitted in English. 

You may submit translations of the manuscript or abstract as supporting information. Read the supporting information guidelines.

Abbreviations

Define abbreviations upon first appearance in the text.

Do not use non-standard abbreviations unless they appear at least three times in the text.

Keep abbreviations to a minimum.

Reference style

PLOS uses “Vancouver” style, as outlined in the ICMJE sample references.

See reference formatting examples and additional instructions below.

Equations

We recommend using MathType for display and inline equations, as it will provide the most reliable outcome. If this is not possible, Equation Editor is acceptable.

Avoid using MathType or Equation Editor to insert single variables (e.g., “a² + b² = c²”), Greek or other symbols (e.g., β, Δ, or ′ [prime]), or mathematical operators (e.g., x, ≥, or  ±) in running text. Wherever possible, insert single symbols as normal text with the correct Unicode (hex) values.

Do not use MathType or Equation Editor for only a portion of an equation. Rather, ensure that the entire equation is included. Avoid “hybrid” inline or display equations, in which part is text and part is MathType, or part is MathType and part is Equation Editor.

Nomenclature

 Use correct and established nomenclature wherever possible.

Units of measurement Use SI units. If you do not use these exclusively, provide the SI value in parentheses after each value. Read more about SI units.
Drugs Provide the Recommended International Non-Proprietary Name (rINN).
Species names Write in italics (e.g., Homo sapiens). Write out in full the genus and species, both in the title of the manuscript and at the first mention of an organism in a paper. After first mention, the first letter of the genus name followed by the full species name may be used (e.g., H. sapiens).
Genes, mutations, genotypes, and alleles Write in italics. Use the recommended name by consulting the appropriate genetic nomenclature database (e.g., HUGO for human genes). It is sometimes advisable to indicate the synonyms for the gene the first time it appears in the text. Gene prefixes such as those used for oncogenes or cellular localization should be shown in roman typeface (e.g., v-fes, c-MYC).

Copyediting manuscripts

Prior to submission, authors who believe their manuscripts would benefit from in-depth professional copyediting are encouraged to use language-editing and copyediting services. Obtaining this service is the responsibility of the author and should be done before initial submission. These services can be found on the web using search terms like “scientific editing service” or “manuscript editing service”.

Note that if your manuscript is accepted, PLOS will not perform a detailed copyediting step. Therefore, please carefully review your manuscript, paying special attention to spelling, punctuation, and grammar, as well as scientific content.

Manuscript Organization

Most manuscripts should be organized as follows. Instructions for each element appear below.

  • Title
  • Authors
  • Affiliations
  • Abstract
  • Author Summary
  • Introduction
  • Results
  • Discussion
  • Materials and Methods (also called Methods or Models)
  • Acknowledgments
  • References
  • Supporting information captions

Uniformity in format facilitates the experience of readers and users of the journal. To provide flexibility, however, authors are also able to include the Materials and Methods section before the Results section or before the Discussion section. Please clarify the reasons for including your Materials and Methods section before the Results or Discussion sections in your cover letter when submitting your manuscript files.

Please also note that the Results and Discussion can be combined into one Results/Discussion section.

Other elements

  • Figure captions are inserted immediately after the first paragraph in which the figure is cited. Figure files are uploaded separately.
  • Tables are inserted immediately after the first paragraph in which they are cited.
  • Supporting information files are uploaded separately.

 

  Please refer to our downloadable sample files to ensure that your submission meets our formatting requirements:
 
Viewing Figures and Supporting Information in the compiled submission PDF
The compiled submission PDF includes low-resolution preview images of the figures after the reference list. The function of these previews is to allow you to download the entire submission as quickly as possible. Click the link at the top of each preview page to download a high-resolution version of each figure. Links to download Supporting Information files are also available after the reference list.

Parts of a Submission

Title

Include a full title and a short title for the manuscript.

Title Length Guidelines Examples
Full title 200 characters Specific, descriptive, concise, and comprehensible to readers outside the field

Impact of cigarette smoke exposure on innate immunity: A Caenorhabditis elegans model

Solar drinking water disinfection (SODIS) to reduce childhood diarrhoea in rural Bolivia: A cluster-randomized, controlled trial

Short title 70 characters State the topic of the study

Cigarette smoke exposure and innate immunity

SODIS and childhood diarrhoea

Titles should be written in sentence case (only the first word of the text, proper nouns, and genus names are capitalized). Avoid specialist abbreviations if possible. For clinical trials, systematic reviews, or meta-analyses, the subtitle should include the study design.

Author List

Authorship requirements

All authors must meet the criteria for authorship as outlined in the  authorship policy. Those who contributed to the work but do not meet the criteria for authorship can be mentioned in the Acknowledgments.  Read more about Acknowledgments.

The corresponding author must provide an ORCID iD at the time of submission by entering it in the user profile in the submission system.  Read more about ORCID.

Author names and affiliations

Enter author names on the title page of the manuscript and in the online submission system.

On the title page, write author names in the following order:

  • First name (or initials, if used)
  • Middle name (or initials, if used)
  • Last name (surname, family name)

Each author on the list must have an affiliation. The affiliation includes department, university, or organizational affiliation and its location, including city, state/province (if applicable), and country. Authors have the option to include a current address in addition to the address of their affiliation at the time of the study. 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.

If an author has multiple affiliations, enter all affiliations on the title page only. In the submission system, enter only the preferred or primary affiliation. Author affiliations will be listed in the typeset PDF article in the same order that authors are listed in the submission.

Author names will be published exactly as they appear in the manuscript file. Please double-check the information carefully to make sure it is correct.

Corresponding author

The submitting author is automatically designated as the corresponding author in the submission system. The corresponding author is the primary contact for the journal office and the only author able to view or change the manuscript while it is under editorial consideration.

The corresponding author role may be transferred to another coauthor. However, note that transferring the corresponding author role also transfers access to the manuscript. (To designate a new corresponding author while the manuscript is still under consideration, watch the video tutorial below.)

Only one corresponding author can be designated in the submission system, but this does not restrict the number of corresponding authors that may be listed on the article in the event of publication. Whoever is designated as a corresponding author on the title page of the manuscript file will be listed as such upon publication. Include an email address for each corresponding author listed on the title page of the manuscript.

  How to select a new corresponding author in Editorial Manager

Consortia and group authorship

If a manuscript is submitted on behalf of a consortium or group, include the consortium or group name in the author list, and include the full list of members in the Acknowledgments or in a supporting information file. Read the group authorship policy.

Author Contributions

Provide at minimum one contribution for each author in the submission system. Use the CRediT taxonomy to describe each contribution. Read the policy and the full list of roles.

Contributions will be published with the final article, and they should accurately reflect contributions to the work. The submitting author is responsible for completing this information at submission, and we expect that all authors will have reviewed, discussed, and agreed to their individual contributions ahead of this time.

Cover letter

Upload a cover letter as a separate file in the online system.

The cover letter should address the following questions:

  • Why is this manuscript suitable for publication in PLOS Computational Biology?
  • Why will your study inspire the other members of your field, and how will it drive research forward?

You may recommend a suitable Associate Editor to handle your submission; however, the editors reserve the right to contact an alternative—either from the board or a guest editor.

The cover letter will be available to the editors and to any external peer reviewers, so please send anything confidential directly to the journal office.

Title page

The title, authors, and affiliations should all be included on a title page as the first page of the manuscript file.  

Abstract

The Abstract comes after the title page in the manuscript file. The abstract text is also entered in a separate field in the submission system.  

The Abstract of the paper should be succinct; it must not exceed 300 words. Authors should mention the techniques used without going into methodological detail and should summarize the most important results.

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.

Do not include any citations. Avoid specialist abbreviations.

Author Summary

We ask that all authors of research articles include a 150–200 word non-technical summary of the work as part of the manuscript to immediately follow the abstract. This text is subject to editorial change, should be written in the first-person voice, and should be distinct from the scientific abstract.

Aim to highlight where your work fits within a broader context; present the significance or possible implications of your work simply and objectively; and avoid the use of acronyms and complex terminology wherever possible. The goal is to make your findings accessible to a wide audience that includes both scientists and non-scientists.

Authors may benefit from consulting with a science writer or press officer to ensure they effectively communicate their findings to a general audience.

Introduction

The Introduction should put the focus of the manuscript into a broader context. As you compose the Introduction, think of readers who are not experts in this field. 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. 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. 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. The section may be divided into subsections, each with a concise subheading. The section should be written in the past tense.

PLOS journals require authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. When submitting a manuscript online, authors must provide a Data Availability Statement describing compliance with PLOS's policy. 

Large data sets, including raw data, may be deposited in an appropriate public repository. See our list of recommended repositories.

For smaller data sets and certain data types, authors may provide their data within supporting information files accompanying the manuscript. 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).

For more information on how best to provide data, read our policy on data availability. PLOS does not accept references to “data not shown.”

Discussion

The Discussion should spell out the major conclusions of the work along with some explanation or speculation on the significance of these conclusions. How do the conclusions affect the existing assumptions and models in the field? How can future research build on these observations? What are the key experiments that must be done?

The Discussion should be concise and tightly argued.

The Results and Discussion may be combined into one section, if desired.

Materials and Methods

The Materials and Methods should provide enough detail for reproduction of the findings. Submit detailed protocols for newer or less established methods. Well-established protocols may simply be referenced. 

Details of algorithms and protocol documents for clinical trials, observational studies, and other non-laboratory investigations may be uploaded as supporting information. These are not included in the typeset manuscript, but are downloadable and fully searchable from the HTML version of the article. Read the supporting information guidelines for formatting instructions.

We recommend and encourage you to deposit laboratory protocols in protocols.io, where protocols can be assigned their own persistent digital object identifiers (DOIs).

To include a link to a protocol in your article:

  1. Describe your step-by-step protocol on protocols.io
  2. Select Get DOI to issue your protocol a persistent digital object identifier (DOI) 
  3. Include the DOI link in the Methods section of your manuscript using the following format provided by protocols.io: http://dx.doi.org/10.17504/protocols.io.[PROTOCOL DOI]

At this stage, your protocol is only visible to those with the link. This allows editors and reviewers to consult your protocol when evaluating the manuscript. You can make your protocols public at any time by selecting Publish on the protocols.io site. Any referenced protocol(s) will automatically be made public when your article is published.

Consult our reporting guidelines, and include an ethics statement in the Materials and Methods section when reporting results from human subjects research and animal research.

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 are responsible for ensuring that anyone named in the Acknowledgments agrees to be named.

Do not include funding sources in the Acknowledgments or anywhere else in the manuscript file. Funding information should only be entered in the financial disclosure section of the submission system.

References

Any and all available works can be cited in the reference list. Acceptable sources include:

  • Published or accepted manuscripts
  • Manuscripts on preprint servers, if the manuscript is submitted to a journal and also publicly available as a preprint

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”). Instead, include those data as supplementary material or deposit the data in a publicly available database.
  • Personal communications (these should be supported by a letter from the relevant authors but not included in the reference list)

References are listed at the end of the manuscript and numbered in the order that they appear in the text. In the text, cite the reference number in square brackets (e.g., “We used the techniques developed by our colleagues [19] to analyze the data”). PLOS uses the numbered citation (citation-sequence) method and first six authors, et al.

Do not include citations in abstracts or author summaries. 

Make sure the parts of the manuscript are in the correct order before ordering the citations.

Formatting references

Because all references will be linked electronically as much as possible to the papers they cite, proper formatting of the references is crucial. 

PLOS uses the reference style outlined by the International Committee of Medical Journal Editors (ICMJE), also referred to as the “Vancouver” style. Example formats are listed below. Additional examples are in the ICMJE sample references.

A reference management tool, EndNote, offers a current style file that can assist you with the formatting of your references. If you have problems with any reference management program, please contact the source company's technical support.

Journal name abbreviations should be those found in the National Center for Biotechnology Information (NCBI) databases

Source Format
Published articles

Hou WR, Hou YL, Wu GF, Song Y, Su XL, Sun B, et al. cDNA, genomic sequence cloning and overexpression of ribosomal protein gene L9 (rpL9) of the giant panda (Ailuropoda melanoleuca). Genet Mol Res. 2011;10: 1576-1588.

Devaraju P, Gulati R, Antony PT, Mithun CB, Negi VS. Susceptibility to SLE in South Indian Tamils may be influenced by genetic selection pressure on TLR2 and TLR9 genes. Mol Immunol. 2014 Nov 22. pii: S0161-5890(14)00313-7. doi: 10.1016/j.molimm.2014.11.005


Note: A DOI number for the full-text article is acceptable as an alternative to or in addition to traditional volume and page numbers.
Accepted, unpublished articles Same as published articles, but substitute “Forthcoming” for page numbers or DOI.
Web sites or online articles

Huynen MMTE, Martens P, Hilderlink HBM. The health impacts of globalisation: a conceptual framework. Global Health. 2005;1: 14. Available from: http://www.globalizationandhealth.com/content/1/1/14.

Books

Bates B. Bargaining for life: A social history of tuberculosis. 1st ed. Philadelphia: University of Pennsylvania Press; 1992.

Book chapters Hansen B. New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health; 1991. pp. 21-28.
Deposited articles (preprints, e-prints, or arXiv) Krick T, Shub DA, Verstraete N, Ferreiro DU, Alonso LG, Shub M, et al. Amino acid metabolism conflicts with protein diversity; 1991. Preprint. Available from: arXiv:1403.3301v1. Cited 17 March 2014.
Published media (print or online newspapers and magazine articles) Fountain H. For Already Vulnerable Penguins, Study Finds Climate Change Is Another Danger. The New York Times. 29 Jan 2014. Available from: http://www.nytimes.com/2014/01/30/science/earth/climate-change-taking-toll-on-penguins-study-finds.html. Cited 17 March 2014.
New media (blogs, web sites, or other written works) Allen L. Announcing PLOS Blogs. 2010 Sep 1 [cited 17 March 2014]. In: PLOS Blogs [Internet]. San Francisco: PLOS 2006 - . [about 2 screens]. Available from: http://blogs.plos.org/plos/2010/09/announcing-plos-blogs/.
Masters' theses or doctoral dissertations Wells A. Exploring the development of the independent, electronic, scholarly journal. M.Sc. Thesis, The University of Sheffield. 1999. Available from: http://cumincad.scix.net/cgi-bin/works/Show?2e09
Databases and repositories (Figshare, arXiv) Roberts SB. QPX Genome Browser Feature Tracks; 2013 [cited 2013 Oct 5]. Database: figshare [Internet]. Available from: http://figshare.com/articles/QPX_Genome_Browser_Feature_Tracks/701214.
Multimedia (videos, movies, or TV shows) Hitchcock A, producer and director. Rear Window [Film]; 1954. Los Angeles: MGM.

Supporting Information

Authors can submit essential supporting files and multimedia files along with their manuscripts. All supporting information will be subject to peer review. All file types can be submitted, but files must be smaller than 10 MB in size.

Authors may use almost any description as the item name for a supporting information file as long as it contains an “S” and number. For example, “S1 Appendix” and “S2 Appendix,” “S1 Table” and “S2 Table,” and so forth.  

Supporting information files are published exactly as provided, and are not copyedited.

Supporting information captions

List supporting information captions at the end of the manuscript file. Do not submit captions in a separate file.

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.

Example caption

S1 Text. Title is strongly recommended.
 Legend is optional.

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.

Read the supporting information guidelines for more details about submitting supporting information and multimedia files.

Figures and Tables

Figures

Do not include figures in the main manuscript file. Each figure must be prepared and submitted as an individual file.

Cite figures in ascending numeric order upon first appearance in the manuscript file.

Figure captions

Figure captions must be inserted in the text of the manuscript, immediately following the paragraph in which the figure is first cited (read order). Do not include captions as part of the figure files themselves or submit them in a separate document.

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). 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”).
  • A concise, descriptive title

The caption may also include a legend as needed.

Tables

Cite tables in ascending numeric order upon first appearance in the manuscript file.

Place each table in your manuscript file directly after the paragraph in which it is first cited (read order). Do not submit your tables in separate files.

Tables require a label (e.g., “Table 1”) and brief descriptive title to be placed above the table. Place legends, footnotes, and other text below the table. 

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.

Repositories may be either subject-specific (where these exist) and accept specific types of structured data, or generalist repositories that accept multiple data types. We recommend that authors select repositories appropriate to their field. 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. Authors are encouraged to select repositories that meet accepted criteria as trustworthy digital repositories, such as criteria of the Centre for Research Libraries or Data Seal of Approval. Large, international databases are more likely to persist than small, local ones.

To support data sharing and author compliance of the PLOS data policy, we have integrated our submission process with a select set of data repositories. The list is neither representative nor exhaustive of the suitable repositories available to authors. Current repository integration partners include Dryad and FlowRepository. Please contact data@plos.org to make recommendations for further partnerships.

Instructions for PLOS submissions with data deposited in an integration partner repository:

  • Deposit data in the integrated repository of choice.
  • Once deposition is final and complete, the repository will provide you with a dataset DOI (provisional) and private URL for reviewers to gain access to the data.
  • Enter the given data DOI into the full Data Availability Statement, which is requested in the Additional Information section of the PLOS submission form. Then provide the URL passcode in the Attach Files section.

If you have any questions, please email us.

Accession numbers

All appropriate data sets, images, and information should be deposited in an appropriate public repository. See our list of recommended repositories.

Accession numbers (and version numbers, if appropriate) should be provided in the Data Availability Statement. Accession numbers or a citation to the DOI should also be provided when the data set is mentioned within the manuscript.

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. In all other cases, these numbers must be provided at submission.

Identifiers

As much as possible, please provide accession numbers or identifiers for all entities such as genes, proteins, mutants, diseases, etc., for which there is an entry in a public database, for example:

Identifiers should be provided in parentheses after the entity on first use.

Striking image

You can choose to upload a “Striking Image” that we may use to represent your article online in places like the journal homepage. All striking image files that are submitted are also eligible to be chosen as the monthly Issue Image.

Submission Criteria

  • The image must visually represent the article in a striking and eye-catching way.
  • It can be derived from a figure or supporting information file from the paper, and it may be a cropped portion of an image or the entire image.
  • Alternatively, you may create or source an image which represents the article, as long as it adheres to our CC BY license.
  • High resolution: between 300-600 dpi
  • Single panel
  • Ideally avoid added details like text, scale bars, and arrows.

How to Submit

  1. Submit your striking image to the submission system using the file type “Striking Image”.
  2. Upload a separate file containing the corresponding caption.

If no striking image is uploaded, a member of the journal team will choose an appropriate image, which may be a figure from the submission or a separately sourced CC BY image.

Striking images should not contain potentially identifying images of people.  Read our policy on identifying information.

The PLOS licenses and copyright policy also applies to striking images.

Additional Information Requested at Submission

Funding statement

This section should describe sources of funding that have supported the work. Please include relevant grant numbers and the URL of any funder's web site. Please also include this sentence: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” If this statement is not correct, you must describe the role of any sponsors or funders, and amend the aforementioned sentence as needed.

Competing interests

The corresponding author is asked at submission to declare, on behalf of all authors, whether there are any financial, personal, or professional interests that could be construed to have influenced the work.

Any relevant competing interests of authors must be available to editors and reviewers during the review process and will be stated in published articles.

Related Manuscripts

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. 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. Reviewers will be asked to comment on the overlap between related submissions.

PLOS does support authors who wish to share their work early and receive feedback before formal peer review. Deposition of manuscripts with preprint servers does not impact consideration of the manuscript at any PLOS journal.

Authors choosing bioRxiv may now concurrently submit directly to select PLOS journals through bioRxiv’s direct transfer to journal service.

Read our policies on related manuscripts and preprint servers.

Reviewer and editor suggestions

We ask authors to suggest suitable editors and at least four potential reviewers when submitting their manuscript. Bear in mind any potential competing interests when making these suggestions. It is not appropriate to suggest recent collaborators or other researchers at your institution. See our policy on competing interests for more information. 

Opposed reviewers

Authors may choose to request that an individual is excluded from the review process and not involved in their manuscript. When making these suggestions, please provide specific reasons why each person should not review your submission in each “Reason” box. The editorial team will respect these requests so long as this does not interfere with the objective and thorough assessment of the submission.

Methods Submissions

PLOS Computational Biology publishes articles specifically designated as Methods papers that should describe outstanding methods of exceptional importance that have been shown to provide, or have the promise to provide, new biological insights.

The method must already be widely adopted or have the promise of wide adoption by a broad community of users. Enhancements to existing published methods will only be considered if those enhancements bring exceptional new capabilities. The authors must clearly provide detail, data, and, where necessary, software to ensure readers’ ability to reproduce the methods and results.

Methods articles require a presubmission inquiry. In such an inquiry, the authors are requested to present a concise abstract-like statement on what the manuscript they plan to submit entails and why the authors feel that it fits the Methods section of the journal. They should ensure their presubmission answers the following questions:

  • What is the major innovation in the paper, compared with the state of the art of the field?
  • Why is the innovation substantial and relevant?
  • What is the concrete method being put forth and what is its intended user community?
  • How has the method been validated?
  • How is the method being made available?

For further information, read our recommendations on how to prepare a presubmission inquiry.

Once a positive response to a presubmission inquiry has been obtained, Methods articles should be submitted as a Research Article type. The cover letter should state that the paper is for the Methods section and should include the manuscript number of the presubmission inquiry. The article should follow the same style and format and organization as in a general research article. For papers written in LaTeX, the LaTeX Guidelines for formatting the paper should be followed.

Examples of Methods papers can be found in the Methods Collection.

Software Submissions

PLOS Computational Biology publishes articles describing outstanding open source software of exceptional importance that has been shown to provide new biological insights, either as a part of the software article, or published elsewhere.

The software must already be widely adopted, or have the promise of wide adoption by a broad community of users. Enhancements to existing published open source software will only be considered if those enhancements bring exceptional new capabilities. The software must be downloadable anonymously in source code form and licensed under an Open Source Initiative (OSI) compliant license. The source code must be accompanied with 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.

Software articles require a presubmission inquiry that includes explanations on how the above criteria are met.

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.
Authors and Affiliations  
Abstract Fundamental task(s) which the software accomplishes, examples of biological insights from the use of the software, details of availability, including where to download the most recent source code, the license, any operating system dependencies, and support mailing lists.
Introduction A description of the problem addressed by the software and of its novelty and exceptional nature in addressing that problem.
Design and Implementation Details of the algorithms used by the software, how those algorithms have been instantiated, including dependencies. Details of the supplied test data and how to install and run the software should be detailed in the supplementary material.
Results Examples of biological problems solved using the software, including results obtained with the deposited test data and associated parameters.
Availability and Future Directions Where the software has been deposited. Any future work planned to be carried out by the authors, how others might extend the software.

​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.

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. Similarly, open-source software may depend on proprietary ancillary software, or external closed-source APIs, to run or to build. Such a dependency does not render software ineligible if it is otherwise open-source, but the dependency may be considered when judging the limits to broad adoption.

Authors are required to deposit the following with the journal upon submission for archival and review purposes.

  • Source code, accompanied with the OSI-compliant license.
  • Binaries (optional).
  • Documentation. 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.
  • Test data and instructions. 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. 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.

The archived software and associated test data, parameters and documentation are the copy of record that matches the associated published article. They must be deposited as supplemental information file of less than 100 MB (ideally as .7z or .rar). This ensures that a version of the software is always available to the community.

Recognizing that software is subject to ongoing development we strongly encourage authors to deposit and manage their source code revisions in an established software version control repository (see Wikipedia for a list, and a feature comparison matrix). We further encourage software projects to provide active support and interact with their user communities via public mailing lists. Authors should provide links to the location of the software, mailing lists, etc. as part of the article.

Once a positive response to a presubmission inquiry has been obtained, software articles and software should be submitted as a Research Article type and include a comment that this is a software article and should follow the Submission Guidelines for manuscript, figure, and table file formats. 

For papers written in LaTeX, the LaTeX Guidelines for formatting the paper should be followed.

Other Article Types

If you are submitting content other than a research article, read the guidelines for other article types.

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