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Aperta User Guide for Authors

   Important information about PLOS Biology submissions

PLOS Biology is no longer accepting new submissions in Aperta™. Please submit new manuscripts in Editorial Manager

Read more about submitting to PLOS Biology.

About this Guide

This guide contains step-by-step instructions for submitting a manuscript in the Aperta™ submission system. Sign in to Aperta.

Before you begin

Quick links

Signing In

You must have a PLOS account to access Aperta. You only need one account to access all of your manuscripts in Aperta, whether you are an author, reviewer, or Editorial Board member.

If you have previously used a PLOS account to comment on published articles on the PLOS journal websites or to sign up for eTOC alerts, you will use the same credentials to access Aperta. You may also have a PLOS account if you have served as an Editorial Board Member.

Go to the Aperta homepage and click Sign in with PLOS.

Enter your credentials on the PLOS sign-in screen to access the system. If you need to recover your password, click the Forgot your password link to have reset instructions emailed to you. 

Please do not create more than one account for yourself. To change your email address, affiliation, or other details, sign in to to your account and edit the information. 

If you are having trouble accessing your account, try resetting your password. For further assistance, email the journal.

Your Aperta Profile

Your Profile in Aperta displays your account information. To access your Profile, click on your name in the upper right-hand corner of your screen and select Profile in the dropdown menu.

The Profile includes a button to connect or create an ORCID iD. This opens a popup window where you can enter your ORCID information or register for a new ORCID iD.

PLOS requires that all corresponding authors provide an ORCID iD when submitting a manuscript, and we encourage everyone participating in the peer review process to have one. Learn more about ORCID at PLOS. For more information about how to set up your ORCID iD in Aperta, watch this short video

Creating Your Initial Submission

To create an initial submission, start on the Your Manuscripts page. Click the green Create New Submission button to begin the submission process.

Your first task is to enter basic information and upload your manuscript file. Green check marks indicate you have filled in each field. 

The following information is required:

  • Title
  • Select the journal from the dropdown menu
  • Select the article type
  • Upload your manuscript document
Which file types can I submit to Aperta?

Aperta supports submissions in DOC, DOCX, and PDF formats. For submissions written in LaTeX, please submit your manuscript in PDF and follow our LaTeX guidelines.

After completing the information on the create submission screen, you will be brought to a new page and the next step of the submission process. The text of your manuscript file will load on the left side of the screen (this may take a few seconds). On your right are a few submission cards where you will provide additional information and files. 

You can adjust the width of the manuscript or the cards by clicking and dragging the divider between the two sides. If you experience any issues with the manuscript view, click the Downloads button to access and check the original file.

Click a card title to expand the contents and enter the requested information. When you are done, complete the task by clicking I am done with this task at the top of the card. This will add a green check mark next to the card name.

If you need to make changes to the card before sending your submission to the journal, click the Make changes button.

Is my work saved automatically?
Once you start your initial submission, Aperta will automatically save your work as you go. If you exit the system, your uploaded manuscript and the information entered in the submission cards will be saved. You can return to the submission at any time from the Your Manuscripts page.

How do I edit my manuscript file?
If you need to replace your existing manuscript file, you can upload a new version on the Upload Manuscript card that appears with the other cards on the Manuscript Page.

How do I edit my title?
To edit your manuscript title after you have started your submission, edit the title in your manuscript file outside of the system, and then upload the new version of the file. The edit the title card to match.

For the initial submission, you will need to complete the following cards. Once all submission cards are complete, you will be able to submit your manuscript to the journal office.  

Important
You must mark each card complete even if you have no information to add. For example, if you are not uploading any figures or supporting information, you will still need to click the button to indicate you are done with the task.

When you have completed all of the cards, a green Submit button will appear at the top of the card list. Click Submit to complete the submission of your manuscript to the journal office for evaluation.

You will receive an automated confirmation email when your manuscript is submitted. If you do not receive an email, please double-check that all cards have been completed and that you have clicked Submit.

Title and Abstract

Open the Title and Abstract card to verify that your title exactly matches the title in your manuscript file. Use the text box to make any changes. If you need to change the title in your manuscript file, upload a new version of the file and then update the text box accordingly.

You will also need to enter your abstract on the Title and Abstract card. The abstract should exactly match the abstract in your manuscript file. If you need to make changes to your abstract, upload a new version of your manuscript file and then update the abstract text box accordingly.

 

Figures

For detailed instructions about preparing your figure files for submission, please consult the figure guidelines. You may also use a tool called PACE to prepare and review your figures for submission.

If you are submitting a manuscript in Word format, upload figures separately to the Figures card. Do not embed them as images in the manuscript.

If you are submitting a PDF for initial assessment, you can embed your figures directly in the manuscript or upload them to the Figures card. If you are uploading figures to the card, the system will not generate a preview of the figure files in the manuscript body. However, you can download a PDF copy of the submission, which includes the figures appended at the end.

If you are invited to send us a full submission, you will need to add all figures to the Figures card. Follow the detailed instructions below to upload your figures to the card.

Figure submission checklist

  • Cite each figure.
    Cite figures in ascending numeric order after its first appearance in the text of your manuscript. 
  • Insert each figure caption.
    Place captions in the manuscript text immediately following the paragraph where the figure is first cited. Read more about figure captions.
  • Match figure name in four places.
    Match the in-text citations, the figure caption in the manuscript, the figure file name, and the label on the figures card. For example, an uploaded figure file named “Fig1.tif” would be labeled “Fig 1” on the Figures card, be cited as “Fig 1” in the manuscript, and be named “Fig 1” in the caption.
  • Upload figures separately from the manuscript file.
    If you previously embedded images in the manuscript, remove those now.

Add each new figure by clicking the Add New Figures button or by dragging and dropping your files. If the file is successfully uploaded, you will see a preview of the image on the card.

Figure labels (e.g., Fig 1) are generated from file names and will automatically insert your figures in the corresponding place in the body of the manuscript.

You can also add multiple figure files at once, but double-check your file names before uploading to make sure the system can register the correct order.

  • Edit an uploaded figure: Click the pencil icon.
  • Delete a figure: Click the trash icon.

  • Re-order figures: Click the pencil icon, and change the figure number. The figure will automatically slide into its new position on the card. 

  • Replace an uploaded figure: Click the replace link next to the file name.

Problems with figure placement?
If you have submitted in Word format and your figure is not appearing in the right place in the manuscript body, make sure that you also update the in-text citation (e.g., Fig 1) in the manuscript, and update the file name to match.

Problems uploading your figures?
If your figures are not uploading, email the files and a description of the problem to the journal office: plosbiology@plos.org.

Tables

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

Equations

Use MathType for display and inline equations, as it will provide the most reliable outcome. Please do not embed equations as images. Read the Submission Guidelines for further information about formatting equations.

Supporting Information

To provide supporting information files with your submission, (1) upload the files to the Supporting Information card and (2) include a caption for each item at the end of your manuscript. 

Upload files

Click Add Files on the Supporting Information card to begin uploading files. You can also drag and drop your files to the card. 

After you upload, an error message will prompt you to enter a number label and category for each file. 

  • Number label: Number your files beginning with S1 and then increase sequentially (e.g., S1, S2, S3, etc.). If you have files in multiple categories, start at S1 within each category (e.g., if you upload a text file and a table, both files will be numbered S1 because they are in different categories). 
  • Category: Choose from table, data, text, figure, or other (please specify).

By default, all supporting information files will be published with the manuscript if it is accepted. For any uploaded file that is not meant to be published (such as an ethical approval document), you need to uncheck the “For publication” box. 

Once you have entered the relevant details for the file, click Save

When you are finished uploading files, mark the card task as done.

Insert captions

Insert the captions for your supporting information files at the end of your manuscript, after the reference list. Captions should include the following information:

  • Number label (required)
  • Category (required)
  • Title (strongly recommended)
  • Legend (optional)
Example caption

S1 Text. This is the title. This is the legend. 

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. Place in-text citations within parentheses and include the “S” prefix, number label, and category. For example: (S1 Text)

Read the full supporting information guidelines for detailed information about preparing your files and which file types are accepted.

Striking Images

Use the Supporting Information card to nominate a striking image: 

  • Upload your image file

  • Enter XX for the number label.  
  • Select Other as the file category and enter Striking Image when prompted
  • Uncheck the publication box

Additional Information

The Additional Information card contains quick questions about your submission for the journal to reference:

Dual publication Read our policy on dual publication​.
Related submissions Read our policy on related submissions.
Previous interactions with PLOS Indicate any previous interactions here by checking the appropriate box. If you have received any prior correspondence regarding this submission, please enter the name of the staff editor who handled your inquiry, along with the reference code for the correspondence. If a previous version was submitted via Aperta or Editorial Manager, please include the manuscript tracking number.
PLOS Collections If you are submitting to a PLOS Collection, enter the title here and also include it in your cover letter. Read more about PLOS Collections.
Short title Read our guidelines for titles.

License agreement
 
When you submit your work to PLOS, you must be prepared to adhere to our content license on behalf of all co-authors. 

PLOS applies the Creative Commons Attribution (CC BY) license to works we publish. Under this license, authors agree to make articles legally available for reuse, without permission or fees, for virtually any purpose. Anyone may copy, distribute, or reuse these articles, as long as the author and original source are properly cited. Read the full licenses and copyright policy.

Submissions Selected for Peer Review

If your manuscript is selected for peer review, you will receive an email requesting additional information for the peer review process. Follow the link in your email or click the manuscript title in Your Manuscripts to view your submission. Your additional tasks will appear in the card list along with the information you have already entered.

Can I edit information I entered during the initial submission?
To change information you have previously entered, click  Make changes to this task, add or update the information, and then mark the card complete.

For the peer review process, you will need to complete the following cards. Once all cards have been completed, a green Submit button will appear at the top of the card list. Click the button to complete your submission and send it to the journal office. 

Important
Your Financial Disclosure,  Competing Interests, Data Availability, and Ethics Statements will be published as written if the manuscript is accepted. Make sure the information is clear, complete, and correct.

Author and Coauthor Information

All authors who meet ICMJE authorship criteria must be listed as authors. Read the authorship requirements in our authorship policy, and find manuscript requirements in the submission guidelines.

Add each author by clicking Add a New Author. You can add an individual author or a group author. Make sure the authors are listed in the correct publication order.

Information required for each individual author

Full name Match each full name given in the Authors card with the full name given in the manuscript.
Affiliation Enter only the preferred or primary affiliation for each author on the card. If an author has multiple affiliations, enter the full list of affiliations on the manuscript title page.

Author initials

Enter initials for each author on the Authors card. Ensure that the initials match the author’s name in full, as written on the title page of the manuscript, and that each set of author initials is unique. The initials should use the format of first name initial, middle initial(s) if applicable, and surname initial. In order to distinguish between authors that have the same initials, use middle initials or the second letter of the last name.

Email address Provide an active email address where the author can be contacted. When you submit the manuscript, an email will be sent to the author at this address to confirm authorship.
Author contributions Provide at minimum one contribution for each author. PLOS uses the CRediT Taxonomy to describe author contributions. Read the policy and full list of roles.

U.S. Government affiliation status

Provide if applicable.
Important: PLOS requires an ORCID iD for all corresponding authors. To register for a new ORCID iD or connect an existing ORCID iD to your Aperta account, click the ORCID button on the Authors card and follow the steps in the pop-up window. You can also connect or create an ORCID iD from your Aperta Profile in the upper right-hand corner of the screen. Watch this short video for detailed instructions on how to set up your ORCID iD.  Read more about ORCID at PLOS.

Reordering the author list

To change the order after adding an author, hover over the author’s name on the card and click and drag it to the desired position.

Entering group authors

To add a group author, (e.g., for a Consortium) click Add a New Author and choose the group author option. Then enter the requested information for the group. Remember to also include the name on the manuscript title page.

If the manuscript is accepted for publication, the name will display as shown on the Authors card. If the full member list is too long to add to the Acknowledgments, add a supporting information file with the list to the Supporting Information card and check For publication.

Corresponding author

The submitting author is automatically designated the corresponding author in Aperta upon submission. You can only designate one corresponding author on the submission during editorial consideration. 

Note: We do 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.

Each author entry has a tick box that allows you to designate a corresponding author on the published manuscript. Checking this box will not change the corresponding author during editorial consideration.

Important
If you need to change the corresponding author during editorial consideration, email the journal.

Responding to Journal Requests

After receiving your submission with the additional information requested for the peer review process, the journal will conduct internal technical checks and may request changes or missing information. You will receive an email notifying you of any changes that you will need to make. 

To view the request, follow the link in your email or click the manuscript title on the Your Manuscripts page. The changes that you need to make will be detailed on a Changes for Author card.

You will make all required changes on the original submission cards. To edit a card or to upload a new version of your manuscript, you will need to click the Make changes to this task button on the appropriate card, enter your changes, and then complete the task by clicking I am done with this task.

When you are ready to resubmit, click I am done with this task on the Changes for Author card. Then click the Submit button at the top of the card list.

LaTeX Submissions

If you are submitting a manuscript in LaTeX, upload a review version in PDF. You can choose whether to provide your LaTeX source file along with the PDF version for the initial submission. If your manuscript receives a revise decision, you will be asked to provide the LaTeX source file during the revision process.

Follow our  LaTeX guidelines and use our LaTeX template​ to prepare your submission.

Submitting Other Article Types

If you are submitting to the magazine section, choose the article type from the dropdown menu when you create your new submission.

Submitting Revisions

If you are asked to revise your manuscript after peer review, upload the revised version of your manuscript file to the Upload Manuscript card. 

Use the Response to Reviewers card to upload a marked-up copy of your revised manuscript file showing the changes you have made since the previous submission. Then type or upload a point-by-point response to the reviewers’ comments. You can also access the current decision and any prior decision letters on this card.

To complete the revision process:

  • Make changes to other submission cards (if required). If you need to make changes to any information on the submission cards, edit the relevant details and then click the button on each card to mark it as completed. 
  • Include an Author Summary in your manuscript file. The Author Summary is a non-technical summary of your work. Include the Author Summary in your manuscript file after the Abstract and before the Introduction. Read more about the Author Summary.
  • Upload a Blurb. The Blurb is a brief statement about your work. Upload the Blurb as a separate file on the Supporting Information card. Check the box on the card to exclude it from publication. Read more about the Blurb.
  • Click Submit at the top of the card list to send the revised submission back to the journal office. 

Manuscript Versioning

You can compare two versions of a DOC or DOCX manuscript file by using the Versions tool in the navigation bar. You can also compare information entered on the submission cards.

Note that the versioning tool cannot be used to compare PDF to DOC/DOCX submissions. Also, if the previous manuscript was submitted as a PDF, figures and supporting information files will not be comparable on the Figures and Supporting Information cards. To view and compare these items, click the Downloads button to access the previous PDF.

Now Viewing refers to the current version of the manuscript or submission card

  • Compare With refers to the older version of the manuscript or submission card that you are comparing against the current version

The versions window will highlight all deleted text in red highlights and all new text in green. Click X to return to the current submission.

Which version is which?
Version numbering starts at R0.0 and is triggered when you submit your initial submission.
 
R0.0 Initial submission
R0.1 Manuscript submitted with additional information for the peer review process
R0.2, R0.3, R0.4, etc. When a full submission goes through the technical check process, the version number increases incrementally depending on how many times the submission is returned to the author to make any changes in preparation for peer review.
R1.0 Manuscript revised and resubmitted after receiving its first revise decision
R1.1, R1.2, etc. When a revised submission goes through the technical check process, the version number increases incrementally depending on how many times the revised submission is returned to the author to make any changes.

Withdrawing a Manuscript

Only the submitting author can withdraw a manuscript. To withdraw a manuscript, open the Manuscript Page and click the More button in the navigation bar in the upper right-hand corner of the screen. Then click Withdraw Manuscript. Please provide a reason for withdrawing.

Important 
The withdraw action is permanent and not for minor changes after submission. By withdrawing the manuscript, you stop the consideration process at the journal. The manuscript will be marked as withdrawn in Your Manuscripts.