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PLOS Computational Biology Guidelines for Authors

Contents:

  1. About PLOS Computational Biology
  2. Open Access
  3. Publication Charges
  4. Criteria for Publication
  5. Overview of the Editorial Process
  6. Presubmission Inquiries
  7. Preparation of Research Articles
    1. Organization of the Manuscript
    2. Nomenclature
    3. Accession Numbers
    4. Abbreviations
  8. Software Articles
  9. Materials Required for Manuscript Submission
    1. Cover Letter
    2. Author Status
    3. Financial Disclosure
    4. Competing Interests
    5. Electronic Formats
      1. Manuscript and Tables File
      2. LaTeX files
      3. Tables
      4. Striking Images
      5. Figure Files
      6. Multimedia Files and Supporting Information
    6. Ready to Submit Your Manuscript?
  10. Other Types of Articles
  11. Overview of the Production Process
  12. Blogs, Wikis, Embargoes, and the Media

1. About PLOS Computational Biology

PLOS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery.

Research articles must be declared as belonging to one of the following categories: General, Methods or Software. Software articles form a specific sub-category. More information about Software articles can be found in Section 8.

Research articles should model aspects of biological systems, demonstrate both methodological and scientific novelty, and provide profound new biological insights. Research articles with limited novelty may be more appropriate for PLOS ONE.

Generally, reliability and significance of biological discovery through computation should be validated and enriched by experimental studies. Inclusion of experimental validation is not required for publication, but should be referenced where possible. Inclusion of experimental validation of a modest biological discovery through computation does not render a manuscript suitable for PLOS Computational Biology.

Research articles specifically designated as Methods papers should describe outstanding methods of exceptional importance that have been shown, 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.

For all submissions, authors must clearly provide detail, data, and software to ensure readers' ability to reproduce the models, methods, and results.

Methods articles and Software articles require presubmission inquiries. Presubmission inquiries for general research articles are encouraged, but not essential.

2. Open Access

PLOS applies the Creative Commons Attribution (CC BY) license to all works we publish. Under the CC BY license, authors retain ownership of the copyright for their article, but authors allow anyone to download, reuse, reprint, modify, distribute, and/or copy articles in PLOS journals, so long as the original authors and source are cited. No permission is required from the authors or the publishers.

3. Publication Charges

To provide open access, PLOS journals use a business model in which our expenses—including those of peer review, journal production, and online hosting and archiving—are recovered in part by charging a publication fee to the authors or research sponsors for each article they publish. The fees vary by journal.

PLOS is committed to the widest possible global participation in open access publishing. To determine the appropriate fee, we use a country-based pricing model, which is based on the country that provides 50% or more of the primary funding for the research that is being submitted. Research articles funded by Upper Middle and High Income Countries incur our standard publication fees. Corresponding authors who are affiliated with one of our Institutional Members are eligible for a discount on this fee. Such authors will be informed of the discount applicable after submission of their manuscript.

Fees for Low and Lower Middle Income Countries are calculated according to the PLOS Global Participation Initiative pricing program for manuscripts submitted after 9am Pacific Time on September 4, 2012 (this program is not retroactive).

  • Group One: Countries from this list will not be charged for publishing
  • Group Two: Countries from this list will be charged a flat $500

Our fee waiver policy, whereby PLOS offers to waive or further reduce the payment required of authors who cannot pay the full amount charged for publication, remains in effect. Editors and reviewers have no access to whether authors are able to pay; decisions to publish are only based on editorial criteria.

4. Criteria for Publication

To be considered for publication in PLOS Computational Biology, any given manuscript must satisfy the following criteria:

  • Originality
  • Innovation
  • High importance to researchers in the field
  • Significant biological and/or methodological insight
  • Rigorous methodology
  • Substantial evidence for its conclusions

5. Overview of the Editorial Process

Our aim is to provide all authors with an efficient, courteous, and constructive editorial process. To achieve its required level of quality, PLOS Computational Biology is highly selective in the manuscripts that it publishes; rejection rates are high. To ensure the fairest and most objective decision-making, the editorial process is run as a partnership between the PLOS Computational Biology Editor-in-Chief (EIC), a team of Deputy Editors, and a group of academic experts who serve as Associate Editors (AEs). These individuals are leaders in their fields and represent the full breadth of expertise in computational biology.

Submitted manuscripts are first reviewed by the EIC or one of the Deputy Editors, who may decide to reject the paper or send it on to an AE for further review. The AE is most often a member of the PLOS Computational Biology Editorial Board, but occasionally a guest of the Board is invited to serve in this capacity. The AE evaluates the paper and decides whether it describes a sufficient body of work to support a major advance in a particular field. If so, the paper is sent out for external peer review, at which stage the technical and scientific merits of the work are carefully considered. Once the reviews have been received and considered by the editors, a decision letter to the corresponding author is drafted and sent.

The decision will be within one of the following categories:

  • Reject
  • Major revision
  • Minor revision
  • Accept

Appeals of Decisions

PLOS Computational Biology encourages input from all community members regarding editorial and publishing policy. However, appeals of manuscript decisions should be a) limited to the specific manuscript in question, b) made only by the corresponding author, and c) sent by e-mail to ploscompbiol [at] plos.org. Telephone or other informal appeals will not be considered. Editors involved in considering an appeal will include the Associate Editor, Editor-in-Chief and Deputy Editor; additional editorial board members may also be consulted. The editors will try to handle an appeal expeditiously; however, each appeal is unique and the journal cannot guarantee the turnaround time or the outcome. Appeals of decisions made before review will only be considered in exceptional circumstances.

6. Presubmission Inquiries

When authors are unsure whether their work satisfies the basic requirements for publication in PLOS Computational Biology, we are happy to consider presubmission inquiries. If you would like to submit an informal presubmission inquiry to see if a manuscript is appropriate in principle, please login or register for a new account within our online submission system, and then submit your query by choosing 'Submit Presubmission Inquiry' from the list of article types. Required for all Presubmission Inquiries are contact information for the corresponding author, a cover letter (as a separate file), and an abstract.

Responses to these inquiries are normally provided within one week. Responses may take longer if consultation between members of the editorial board is required. If you are invited to submit your manuscript, we will do our best to provide an expeditious initial assessment of the complete manuscript for suitability and then, if warranted, external peer review.

Methods presubmission inquiries should be succinct but informative. On the basis of the inquiry the editors should be able to answer 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?

Software presubmission inquiries should explain how the proposed Software article meets the following criteria:

  • Article describes outstanding open source software of exceptional importance that has been shown to provide new biological insights.
  • Software must already be widely adopted, or have the promise of wide adoption by a broad community of users.
  • Software must be downloadable anonymously in source code form, with accompanying documentation, and licensed under an Open Source Initiative (OSI) compliant license.

7. Preparation of Research Articles

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.

Although we encourage submissions from around the globe, we require that manuscripts be submitted in English. As a step towards overcoming language barriers, we encourage authors fluent in other languages to provide copies of their full articles or abstracts in other languages. Translations should be submitted as supporting information and listed, together with other supporting information files, at the end of the article text.

Organization of the Manuscript

Articles published in PLOS Computational Biology are organized into the following sections: Title, Authors, Affiliations, Abstract, Author Summary, Introduction, Results, Discussion, Materials and Methods, Acknowledgments, References, Figure Legends, and Tables. 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 also note that the Results and Discussion can be combined into one Results/Discussion section. Although we have no firm length restrictions for the entire manuscript, we urge authors to present and discuss their findings concisely.

Title (150 characters or less)

The title should be specific to the project, yet concise. It should be comprehensible to readers outside your field. Avoid specialist abbreviations, if possible. Titles should be presented in title case, meaning that all words except for prepositions, articles, and conjunctions should be capitalized. Please also provide a brief Short Title (or "running head") of no more than 50 characters.

Example title:
Detection of Specific Sequences among DNA Fragments Separated by Gel Electrophoresis.

Authors and Affiliations

Provide the first names or initials (if used), middle names or initials (if used), surnames, and affiliations—department, university or organization, city, state/province (if applicable), and country—for all authors. One of the authors should be designated as the corresponding author. It is the corresponding author's responsibility to ensure that the author list, and the summary of the author contributions to the study, is accurate and complete. If the article has been submitted on behalf of a consortium, all consortium members and affiliations should be listed after the Acknowledgments.

Abstract

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), please do not apply these distinct headings to the abstract within the article file. Please do not include any citations and 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. Examples are available at:

Systems Analysis of Chaperone Networks in the Malarial Parasite Plasmodium falciparum

Protein–Protein Interaction Hotspots Carved into Sequences

Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis

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. Large datasets, including raw data, should be submitted as supporting files; these are published online alongside the accepted article. The results 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. 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 (also called "Methods" or "Models")

This section should provide enough detail for reproduction of the findings. Protocols for new methods should be included, but well-established protocols may simply be referenced. While we do encourage authors to submit all appendices, detailed protocols, or details of the algorithms for newer or less well-established methods, please do so as Supporting Information files. These are not included in the typeset manuscript, but are downloadable and fully searchable from the HTML version of the article.

Acknowledgments

People who contributed to the work but do not fit the criteria for authors should be listed in the Acknowledgments, along with their contributions. You must also ensure that anyone named in the Acknowledgments agrees to being so named.

Details of the funding sources that have supported the work should be confined to the funding statement provided in the online submission system. Do not include them in the Acknowledgments.

References

Only published or accepted manuscripts should be included in the reference list. Papers that have been submitted but not yet accepted should not be cited. Limited citation of unpublished work should be included in the body of the text only as “unpublished data.” All “personal communications” citations should be supported by a letter from the relevant authors.

Style information:

  • PLOS uses the numbered citation (citation-sequence) method and first five authors, et al.
  • References are listed and numbered in the order that they appear in the text.
  • In the text, citations should be indicated by the reference number in brackets.
  • The parts of the manuscript should be in the correct order before ordering the citations: body, boxes, figure captions, tables, and supporting information captions.
  • Abstracts and author summaries may not contain citations.
  • Journal name abbreviations should be those found in the NCBI databases: http://www.ncbi.nlm.nih.gov/nlmcatalog/journals.

Because all references will be linked electronically as much as possible to the papers they cite, proper formatting of the references is crucial. For convenience, a number of reference software companies supply PLOS style files (e.g., Reference Manager, EndNote).

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

Note: Use of 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 papers
Same as above, but “In press” appears instead of the page numbers.

Electronic Journal Articles
1. Huynen MMTE, Martens P, Hilderlink HBM (2005) The health impacts of globalisation: a conceptual framework. Global Health 1: 14. Available: http://www.globalizationandhealth.com/content/1/1/14. Accessed 25 January 2012.

Books
1. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia: University of Pennsylvania Press. 435 p.

Book Chapters
1. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21-28.

Figure Legends

The aim of the figure legend should be to describe the key messages of the figure, but the figure should also be discussed in the text. An enlarged version of the figure and its full legend will often be viewed in a separate window online, and it should be possible for a reader to understand the figure without switching back and forth between this window and the relevant parts of the text. Each legend should have a concise title of no more than 15 words that can stand alone, without the use of figure part labels. The overall legend itself should be succinct, while still explaining all figure parts, symbols and abbreviations. Avoid lengthy descriptions of methods.

Tables

Tables should be included at the end of the manuscript file and cited sequentially in the text. All tables should have a concise title. Footnotes can be used to explain abbreviations. Citations should be indicated using the same style as outlined above. Tables should not occupy more than one printed page; larger tables can be published as online supporting information. Tables must be cell-based; do not use picture elements, text boxes, tabs, or returns in tables. Please ensure that all tables conform to our Guidelines for Figure and Table Preparation when preparing them.

Nomenclature

The use of standardized nomenclature in all fields of science and medicine is an essential step toward the integration and linking of scientific information reported in published literature. We will enforce the use of correct and established nomenclature wherever possible:

  • We strongly encourage the use of SI units. If you do not use these exclusively, please also provide the SI value in parentheses after each value.
  • Species names should be italicized (e.g., Homo sapiens) and the full genus and species must be written out in full, both in the title of the manuscript and at the first mention of an organism in a paper; after that, the first letter of the genus name, followed by the full species name may be used.
  • Genes, mutations, genotypes, and alleles should be indicated 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: v-fes, c-MYC, etc.
  • The Recommended International Non-Proprietary Name (rINN) of drugs should be provided.

Accession Numbers

All appropriate datasets, images, and information should be deposited in public resources. Please provide the relevant accession numbers (and version numbers, if appropriate). Accession numbers should be provided in parentheses after the entity on first use. Suggested databases include, but are not limited to:

In addition, 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:

Providing accession numbers allows linking to and from established databases and integrates your article with a broader collection of scientific information.

Abbreviations

Please keep abbreviations to a minimum and define them upon first use in the text. Non-standard abbreviations should not be used unless they appear at least three times in the text.

8. Software Articles

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.

Instructions for Authors:

Format: Articles should be concise (less than 3500 words, not including supplementary material) and be organized as follows:

  • Title which includes 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.

  1. Source Code, accompanied with the OSI-compliant license.
  2. Binaries (optional).
  3. 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.
  4. 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 100MB (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 on-going 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 Author Guidelines for manuscript, figure and table file formats. In addition, software articles should further follow the guidelines for software articles. For papers written in LaTeX, the LaTeX Guidelines for formatting the paper should be followed.

9. Materials Required for Manuscript Submission

Cover Letter

It is important that you include a cover letter with your manuscript. Please explain why this manuscript is suitable for publication in PLOS Computational Biology; why will your paper inspire the other members of your field, and how will it drive research forward? You are free to 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—if it is considered more appropriate. Please note that the cover letter will be available to the editors and to external peer reviewers as necessary, so be careful not to reveal anything of a confidential nature.

Author Status

It is the responsibility of the corresponding author to ensure that all authors are aware of and approve the submission of the manuscript, its content, authorship, and order of authorship. Confirmation of this action is required at submission of all manuscripts.

The involvement of any professional medical writer in publication must be declared. We encourage authors to consult the European Medical Writers\' Association Guidelines on the role of medical writers. For all PLOS journals, the corresponding author must submit the manuscript, related files, and all required data and information. From the point of submission through to publication, all communication related to that manuscript will be directed to and received from the corresponding author only.

PLOS Computational Biology bases its criteria for authorship on those outlined in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals, which are summarized below. The contributions of all authors must be described. Contributions that fall short of authorship should be mentioned in the acknowledgments.

"Authorship credit should be based on

  1. substantial contribution to conception and design, or acquisition of data, or analysis and interpretation of data;
  2. drafting the article or revising it critically for important intellectual content; and
  3. final approval of the version to be published
Authors should meet conditions 1, 2, and 3.

When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). These individuals should fully meet the criteria for authorship defined above and editors will ask these individuals to complete journal-specific author and competing interests disclosure forms. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name.

Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. All persons designated as authors should qualify for authorship, and all those who qualify should be listed. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content."

PLOS journals follow the COPE guidelines covering changes in authorship. Please note that if any changes to the list of authors of a manuscript are necessary after the initial submission of a manuscript to a PLOS journal but before its publication, the corresponding author may be asked to provide written confirmation that all authors consent to the change(s). The journal also reserves the right to request written confirmation from all authors (including those added, removed, or moved in the author order). Such written consent may be required before the revised submission is sent to the editors.

Financial Disclosure

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 submitting 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 paper. The information entered here will appear in the published version, so please do not include the same in the manuscript file.

Reviewers are also asked to declare any interests that might interfere with their objective assessment of a manuscript. Any relevant competing interests of authors must be available to editors and reviewers during the review process and will be stated in published articles. Read more about PLOS\'s Competing Interests Policy.

Electronic Formats

Our submission system supports a limited range of formats for text and graphics. The following file formats/types and manuscript information are required before submission. If you are concerned about the suitability of your files, please contact us at ploscompbiol [at] plos.org.

Manuscript and Table Files

Articles can be submitted for review in DOC, DOCX, RTF, or PDF. Any articles that have been prepared in LaTeX will be accepted for review, but only in PDF format. After acceptance, only text files (RTF or DOC) of the revised manuscript and tables can be accepted for use in the production process.

Math Equations and DOCX

If your manuscript is or will be in DOCX and contains equations, you must follow the instructions below to make sure that your equations are editable when the file enters production.

If you have not yet composed your article, you can ensure that the equations in your DOCX file remain editable in DOC by enabling “Compatibility Mode” before you begin. To do this, open a new document and save as Word 97-2003 (*.doc). Several features of Word 2007/10 will now be inactive, including the built-in equation editing tool. You can insert equations in one of the two ways listed below.

If you have already composed your article as DOCX and used its built-in equation editing tool, your equations will become images when the file is saved down to DOC. To resolve this problem, re-key your equations in one of the two following ways.

  1. Use MathType to create the equation. MathType is the recommended method for creating equations.
  2. Go to Insert > Object > Microsoft Equation 3.0 and create the equation.

If, when saving your final document, you see a message saying “Equations will be converted to images,” your equations are no longer editable and PLOS will not be able to accept your file.

LaTeX

Articles prepared in LaTeX may be submitted in PDF format for use during the review process. After acceptance, however, .tex files and formatting information will be required as a zipped file. Please consult our LaTeX Guidelines for a list of what will be required.

Tables

Tables must conform to our Guidelines for Figure and Table Preparation and placed at the end of the article DOC or RTF file. Accepted LaTeX submissions only should have table files—which must also conform to these guidelines—uploaded individually into the online submission system.

Striking Images

Authors are encouraged to upload a "striking image" that may be used to represent their paper online in places like the journal homepage or in search results. Striking images should ideally be high resolution, eye-catching, single panel images, and should ideally avoid containing added details such as text, scale bars, and arrows. If no striking image is uploaded, a figure from the paper will be designated as the striking image.

Please keep in mind that PLOS applies the Creative Commons Attribution (CC BY) license to striking images. As such, do not submit any figures or photos that have been previously copyrighted unless you have express written permission from the copyright holder to publish under the CC BY license. Note that all published materials in PLOS Computational Biology are freely available online, and any third party is permitted to read, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution.

For license inquiries, e-mail license [at] plos.org.

Figure Files

For the article to be accepted for publication, the author will need to supply high-resolution versions of the figures in TIF or EPS format only. When preparing your figures, please ensure that the files conform to our Guidelines for Figure and Table Preparation. Please do not upload panels for a single figure separately (for example, Figure 1A, Figure 1B-1D, Figure 1E); each figure file should be a single montage of all panels. Queries can be sent to figures [at] plos.org.

If you are uploading your files in EPS format, please use the "create outlines" option under the type menu in Illustrator so that all text and fonts appear as intended in print. If you need additional help with figure preparation, please contact figures [at] plos.org.

PLOS does not accept vector EPS figures generated using LaTeX. We only accept LaTeX generated figures in TIFF format. Export your LaTeX files as PDFs, and then open them in GIMP or Photoshop and save as TIFF. In general, Figures must be generated in a standalone graphics application such as Adobe Illustrator, InkScape, PyMol, MatLab, SAS, etc. Please see our Figure Guidelines for more information.

PLOS applies the Creative Commons Attribution (CC BY) license to all figures we publish, which allows them to be freely used, distributed, and built upon as long as proper attribution is given. Please do not submit any figures that have been previously copyrighted unless you have express written permission from the copyright holder to publish under the CC BY license.

Multimedia Files and Supporting Information

We encourage authors to submit essential supporting files and multimedia files along with their manuscripts. All supporting material will be subject to peer review, and should be smaller than 10 MB in size because of the difficulties that some users will experience in loading or downloading files of a greater size.

Supporting files should fall into one of the following categories: Dataset, Figure, Table, Text, Protocol, Audio, or Video. All supporting information should be referred to in the manuscript with a leading capital S (e.g., Figure S4 for the fourth supporting information figure). The numbered title and caption for each supporting information file should be included in the main article file, after the titles and captions for the main figures.

Supporting files will not be included in the typeset PDF, but will be referenced in the text and hosted online.

Supporting files may be submitted in a variety of formats, but should be publication-ready, as these files are not copyedited. Carefully consider whether your supporting information needs to be searchable and/or editable, and choose the most suitable format accordingly. See the Supporting Information Guidelines for more details about our requirements for supporting information and multimedia files.

Ready to Submit Your Manuscript?

We have provided a Submission Checklist to help you prepare your materials for submission and to make the online submission process as straightforward as possible. Please take the time to look through the list before submitting your article.

Please login or register at our online submission system to begin the submission process. Files can be uploaded individually or together in a single ZIP file, and are automatically combined into a single PDF file, which must be approved by the author at the end of the submission process. This merged PDF is for internal and external peer review only. Original source files will be used to prepare accepted articles for publication.

10. Other Types of Articles

PLOS Computational Biology publishes a range of articles other than research articles, methods articles and software articles. Contributions to the front section of the journal are subject to peer review. No publication charges apply. Prospective contributors are encouraged to review contributions in the respective sections of the journal before considering a submission.

Editorials — Editorials are written by PLOS Computational Biology editors. Guest editorials are invited by or at the discretion of the Editor-in-Chief. Editorials typically introduce new and changed features to the journal, discuss issues of professional development, and highlight developments in the field relevant to the readership.

Education articles — The goal of the Education section of PLOS Computational Biology is to provide both practical and background information on important computational methods and approaches used to investigate interesting biological problems. Contributions to the Education section can take several forms, including historical reviews and practical tutorials. Education articles should aim for 2000 and should not exceed 2500 words. The articles are generally invited, but unsolicited submissions will be considered and proceed at the discretion of the Education Editor.

Reviews — Reviews reflect rapidly advancing or topical areas in computational biology research that are of broad interest to the entire biology community and have not been covered significantly by other journals. A review should aim for 3000-6000 words and no more than 100 references and two or three figures or other display items. 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. Reviews are received both by invitation and as unsolicited submissions.

Perspectives — Perspectives in PLOS Computational Biology typically reflect an author's viewpoint on a particular development in science and how, based on current knowledge of the field and the progress in it, this development evidences or can lead to change in how science is conducted or interpreted. Perspectives are intended to be more prospective than retrospective but require sufficient background to place the points made in context. Perspectives are intended to invite debate and further comment as appropriate. The length is ideally around 2000 and limited to 2500 words. Suggestions for topics may be forwarded to ploscompbiol [at] plos.org and are usually handled by the Editor-in-Chief.

Topic Pages — Topic Pages are intended to increase the coverage of computational biology in Wikipedia. The Topic Page becomes a published copy of record of a dynamic version of the article as found in Wikipedia. Further information about Topic Pages can be found in the series editorial. Suggestions for ideas should be emailed to ploscompbiol [at] plos.org

Messages from ISCB — As an official journal of the International Society for Computational Biology (ISCB), PLOS Computational Biology publishes in this section short informational articles invited by the ISCB Editor as well as announcements from the Society.

11. Overview of the Production Process

Before formal acceptance of the article for publication, the manuscript and all related files will be checked by PLOS staff to ensure that they comply with all essential formatting and manuscript preparation requirements. Please note that manuscripts are not subject to detailed copyediting. Therefore, please carefully review your manuscript, paying special attention to spelling, punctuation, and grammar, as well as scientific content. Authors who believe their manuscripts would benefit from in-depth professional copyediting are encouraged to use language-editing and copyediting services, such as the ones offered below (in alphabetical order):

PLOS neither endorses nor takes responsibility for contracting with any of these individuals/companies, but we do recognize the value of the services they provide.

When an article has been accepted for publication, the manuscript files are transferred into our production system and will be published in PDF and HTML formats, with an XML download option. Articles are published online on a weekly schedule and archived in PubMed Central/PubMed within 5 to 10 days of publication.

12. Blogs, Wikis, Embargoes, and the Media

Authors are of course at liberty to present their findings at medical or scientific conferences ahead of publication. We recommend, however, that authors not contact the media or respond to such contact unless an article has been accepted for publication and an embargo date has been established. Respect for press embargoes will help to ensure that your work is reported accurately in the popular media. If a journalist has covered a piece of work ahead of publication, this will not affect consideration of the work for publication. See also our embargo guidelines for journalists.