For authors

• to find guidelines for authors

• to prepare a preprint

• to submit a preprint

• to submit a preregistration of a study

• to modify a submission before it has been validated by the managing board

• to cancel a submission

• to suggest (additional) recommenders

• to reply to the reviewers’ and recommenders’ comments and submit a new version of the preprint

For recommenders

• to find guidelines for PCI recommenders

• to recommend a published article (postprint)

• to handle the evaluation of a preprint

• to declare a co-recommender

• to invite reviewers

• to send a reminder to reviewers

• to cancel a request for a review

• to send a review due message to reviewers

• to change the due date of a review

• to check the e-mails you have already sent to an invited reviewer

• to view the reviews

• to view author's reply

• to communicate your decision or write a recommendation

• to request an additional round of reviews from the reviewers  

• to initiate a postprint recommendationTo initiate a postprint recommendation

For reviewers

• to find guidelines for PCI reviewers

• to read a preprint before deciding whether or not to agree to review it

• to accept or decline an invitation to review a paper

• to read a preprint after agreeing to review it

• to write, edit or upload your review

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For authors

To find guidelines for authors

Go to the guide for authors.

To prepare a preprint

No specific format is required but we advise you to use the PCI template. Make sure data, scripts and codes are available to the reader (in case the article is based on data, scripts and codes). For an anonymous submission, remove all nominative information from the manuscript and supplementary files (including the properties of the files).

When your preprint is ready, post it on a preprint server, such as bioRxiv¹ or arXiv. For an anonymous submission, post your article and supplementary files on a server (e.g. Github, Googledoc, Drop Box, etc.) allowing to share the files via an anonymous URL link.

When the article has appeared on this server, you can submit it to PCI Math Comp Biol (see next paragraph).

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To submit a preprint

To submit a preprint, when the article has appeared on the preprint server,

1) Go to PCI Math Comp Biol and log in
2) Click on the green 'SUBMIT A PREPRINT' button
3) Complete the form (title, authors, DOI, abstract, keywords, thematic fields)
4) Suggest recommenders by clicking on the blue 'SUGGEST RECOMMENDERS' button. Each time you suggest a new recommender, you can add others, or remove a suggested recommender by clicking on the orange ‘REMOVE’ button
5) Complete your submission by clicking on the green 'COMPLETE YOUR SUBMISSION' button. This will result in your submission being sent to the managing board for validation.

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To submit a preregistration of a study

Submit to Peer Community In Registered Reports.

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To modify a submission before it has been validated by the managing board

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> YOUR SUBMITTED PREPRINTS' in the top menu
3) To add or remove suggested recommenders: click on the black 'ADD/REMOVE' button in the middle of the line referring to the preprint in question, and add or remove suggested recommenders. Click on the green 'COMPLETE YOUR SUBMISSION' button when you have finished
4) To modify the title, authors, DOI, abstract, keywords, or disciplines: click on the blue 'VIEW/EDIT' button at the right end of the line referring to the preprint in question, and then click on the 'EDIT ARTICLE' button below the PCI Math Comp Biol logo. Click on the blue 'SAVE' button when you have completed your modifications  

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To cancel a submission

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> YOUR SUBMITTED PREPRINTS' in the top menu
3) Click on the blue 'VIEW/EDIT' button at the right end of the line referring to the preprint in question.
4) Click on the orange 'I WISH TO CANCEL MY SUBMISSION’ button

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To suggest (additional) recommenders

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> YOUR SUBMITTED PREPRINTS' in the top menu
3) Click on the black 'ADD/REMOVE' button in the middle of the line referring to the preprint in question and add or remove suggested recommenders
4) Click on the green 'COMPLETE YOUR SUBMISSION' button when you have finished

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To reply to the reviewers’ and recommenders’ comments and submit a new version of the preprint

1) Deposit the new version of your preprint on the preprint server (e.g. bioRxiv¹ / OSF) of your choice
2) Go to PCI Math Comp Biol and log in
3) Go to 'FOR CONTRIBUTORS —> YOUR SUBMITTED PREPRINTS' in the top menu.
4) Click on the blue ‘VIEW/EDIT' button at the right end of the line referring to the preprint in question.
5) Click on the black ‘EDIT YOUR ARTICLE DATA’ button (mandatory step). You can then edit the title, authors, DOI, abstract, keywords, or disciplines. Do not forget to save your modifications by clicking on the green button.
6) Click on the blue ‘EDIT YOUR REPLY TO THE RECOMMENDER’ button (mandatory step). You could then write or paste your text, upload your reply as a PDF file, and upload a document with the modifications marked in TrackChange mode. If you are submitting the final formated version ready to be recommended, you should only add a sentence indicating that you posted the final version on the preprint server. Do not forget to save your modifications by clicking on the green button.
 7) Click on the green ‘SEND RESUBMISSION’ button. This will result in your submission being sent to the recommender.

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For recommenders​​

​To find guidelines for PCI recommenders

Go to the guide for recommenders.

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To recommend a published article (postprint)

1) Go to PCI Math Comp Biol and log in
2) Click on the blue 'RECOMMEND A POSTPRINT' button. You will be asked to declare that you have no conflict of interest with the authors or the content of the article
3) Complete the form (title, authors, source, DOI, abstract, keywords, disciplines) and click on the blue 'CONTINUE...' button
4) To choose your co-recommenders (co-authors of your recommendation), select one or more co-recommenders from the list of PCI Math Comp Biol recommenders and click on the blue 'ADD' button. Click on 'Done' when finished
5) To write your recommendation, click on the VIEW/EDIT buttona and then on the black 'WRITE/EDIT YOUR RECOMMENDATION' button and complete the form (recommendation title, recommendation). -You can save a draft version of your recommendation by clicking on the blue 'SAVE' button (you can then continue to write or modify your recommendation, moving on to step 5 when it is ready to send)
6) When you have completed your recommendation, click again on the VIEW/EDIT button and then on the green 'SAVE AND SUBMIT YOUR RECOMMENDATION' button. This will result in the recommendation being sent to the managing board for validation. Your co-recommenders will receive your recommendation.

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To handle the evaluation of a preprint

1) Go to PCI Math Comp Biol and log in
2) If you wish to act as the recommender handling the evaluation of a preprint but have not been invited to do so, go to 'FOR RECOMMENDERS—> PREPRINTS IN NEED OF A RECOMMENDER' in the top menu to see the list of preprints still requiring a recommender, and then go to step 3.
3) If you have been invited to act as the recommender handling the evaluation of a preprint, go to 'FOR RECOMMENDERS —> REQUESTS TO HANDLE A PREPRINT' in the top menu.
4) Click on the blue 'VIEW' button at the right end of the line referring to the preprint in question to obtain information about the preprint.
5) Indicate whether you agree or decline the invitation to act as the recommender handling the evaluation of the preprint by clicking on the green or orange buttons. If you click on the green button, you will be asked, notably, to declare that you have no conflict of interest with authors or the content of the article.
6) You will then be invited to find reviewers (you can postpone the invitation of reviewers by clicking on the blue 'DONE' button, but you will then need to follow the instructions 'to invite reviewers' at a later stage).
-To invite a reviewer not included in the PCI Math Comp Biol database: click on the black ‘INVITE A REVIEWER FROM OUTSIDE PCI Math Comp Biol DATABASE’ button and complete the form (first name, last name and e-mail address of the reviewer). You can change the subject and/or the message if you wish. You should then click on the blue 'SEND E-MAIL' button at the end of the form.
-To invite a reviewer listed in the database of PCI Math Comp Biol: click on the green ‘INVITE A REVIEWER FROM PCI Math Comp Biol DATABASE’ button. A search engine and a filter based on thematic fields may be used. Select a reviewer by clicking on the black ‘ADD’ button at the right end of the corresponding line. You can modify the subject and/or the message of the e-mail before sending it to the reviewer concerned. Then, click on the blue 'SEND E-MAIL' button at the end of the form. 
7) When you have sent invitations to all your chosen reviewers, click on the blue 'DONE' button.

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To declare a co-recommender

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu
3) Click on the black 'ADD' button located below the "Co-recommenders" column
4) Scroll the list of recommenders and select the recommender you would like to declare as a co-recommender and click on the blue 'ADD' button
5) Click on the black 'Done' button when you are finished

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To invite reviewers

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu
3) Click on the green 'INVITE A REVIEWER' button in the line corresponding to the preprint considered. To invite a reviewer, click on the black ‘INVITE A REVIEWER’ button. Fill the form with the first name, last name, and email address of the reviewer and then, click on the blue 'SEND E-MAIL' button at the end of the form.
4) When you have sent invitations to all your chosen reviewers, click on the blue 'DONE' button.

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To send a reminder of invitation to reviewers

Reminders of invitation are sent automatically by the website to the referees (4 and 8 days after the first invitation) in case they have not accepted or declined the invitation yet.

You can modify the content and the timing of these reminders in the following way:

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) On the line of the corresponding preprint, click on the black 'ACTIONS' button located just to the left of the name of the reviewer and select 'VIEW E-MAILS'.
4) Click on the blue 'EDIT' button of the corresponding scheduled pending e-mail. You can then edit the content and the sending time of this pending reminder. Once you have made your changes, click on the blue 'SUBMIT' button at the bottom of the page.

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To cancel a request for a review

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) On the line of the corresponding preprint, click on the black 'ACTIONS' button located just to the left of the name of the reviewer concerned and select 'PREPARE A CANCELLATION'. You can then edit the content of this cancellation message.
4) Click on the blue 'SEND EMAIL' button at the bottom of the page.

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To send a review due message to reviewers

Reminders are sent automatically by the website to the referees (17, 21 and 26 days after they accept to review the preprint) in case they have not uploaded their review yet.

You can modify the content and the timing of these reminders in the following way:

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) On the line of the corresponding preprint, click on the black 'ACTIONS' button located just to the left of the name of the reviewer and select 'VIEW E-MAILS'.
4) Click on the blue 'EDIT' button of the corresponding scheduled pending e-mail. You can then edit the content and the sending time of this pending reminder. Once you have made your changes, click on the blue 'SUBMIT' button at the bottom of the page.

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​​​​To change the due date of a review

You can modify the Due date of a review in the following way:

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) On the line of the corresponding preprint, click on the black 'ACTIONS' button to the left of the reviewer's name and select 'CHANGE DATE OF THE REVIEW DUE'.
4) Select the updated deadline and click on the green 'CHANGE DUE DATE'.

This change will automatically reschedule the reminder email sent to the reviewers.

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To check the e-mails you have already sent to an invited reviewer

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) Click on the 'VIEW/EDIT' button located at the end of the line of the corresponding preprint.
4) Click on the yellow 'VIEW E-MAILS' button located on the top right of the screen.

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To view the reviews

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING' in the top menu.
3) On the line of the corresponding preprint, click on the black 'ACTIONS' button located just to the left of the name of the reviewer and select 'SEE REVIEW'.
OR 
3) Click on the blue VIEW/EDIT button at the end of the line of the preprint

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To view author's reply

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> PREPRINTS YOU ARE HANDLING'  in the top menu.
3) Click on the black 'VIEW/EDIT' button at the right end of the corresponding line.
4) You can view the author's reply or, if they uploaded it, you must click on the blue link 'Download author’s reply’

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To communicate your decision or write a recommendation

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR RECOMMENDERS —> 'PREPRINTS YOU ARE HANDLING' in the top menu.
3) Click on the black 'VIEW/EDIT' button at the right end of the corresponding line.
4) Click on the black 'WRITE, EDIT OR UPLOAD YOUR DECISION/ RECOMMENDATION’ button.
5) Indicate your decision by selecting 'I RECOMMEND THIS PREPRINT', 'THIS PREPRINT MERITS REVISION' or 'I REJECT THIS PREPRINT'.
6) Choose a decision or recommendation title (this is of particular importance only for decisions to recommend the preprint concerned) and write or copy/paste your decision or recommendation text.
You do not need to copy-paste the comments of the reviewers in your decision (as the reviews are automatically attached to your decision).
If you are ready to recommend, you do not need to submit an "Acceptation" decision. You should directly post your recommendation.
You can save a draft version of your decision or recommendation text by clicking on the blue 'SAVE' button (you will then have to go through steps 0 to 5 to complete your decision or recommendation). 
7) To submit your decision or recommendation, click on the green 'SAVE AND COMPLETE' button. This will result in your decision or recommendation being sent to the managing board for validation.

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To request an additional round of reviews from the reviewers

Follow the steps described in the rubric 'To invite reviewers’.

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To initiate a postprint recommendation

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For reviewers

To find guidelines for PCI reviewers

Go to the guide for reviewers.

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To read a preprint before deciding whether or not to agree to review it

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> INVITATIONS TO REVIEW A PREPRINT' in the top menu.
3) You can read the preprint by clicking on the blue hyperlink to the digital object identifier (DOI) in the line corresponding to the preprint considered.

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To accept or decline an invitation to review a paper

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> INVITATIONS TO REVIEW A PREPRINT' in the top menu.
3) Click on the black 'ACCEPT OR DECLINE' button at the right end of the line corresponding to the preprint in question.
4) At the bottom of the page, click on either the green ‘YES, I WOULD LIKE TO REVIEW THIS PREPRINT’ button, or the orange ‘NO THANKS, I’D RATHER NOT’ button.

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To read a preprint after agreeing to review it

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> 'YOUR REVIEWS' in the top menu.
3) You can read the preprint by clicking on the blue hyperlink to the digital object identifier (DOI) in the line corresponding to the preprint considered.

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To write, edit or upload your review

1) Go to PCI Math Comp Biol and log in
2) Go to 'FOR CONTRIBUTORS —> YOUR ONGOING AND PAST REVIEWS' in the top menu.
3) Click on the black 'VIEW/EDIT' button at the right end corresponding to the preprint concerned.
4) Click on the black 'WRITE, EDIT OR UPLOAD YOUR REVIEW' button at the bottom right.
5) You can now write, modify or upload your review.

• You can save a draft version of your review by clicking on the blue 'SAVE' button (you will then have to go through steps 0 to 4 to complete your review).
• When you have written or uploaded your review, click on the green 'SAVE & SUBMIT YOUR REVIEW' button. Your review is not considered to be complete until you have clicked on this button.

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Footnotes:

1. Note that bioRxiv currently displays a sentence stating that "This article is a preprint and has not been certified by peer review". If your preprint is recommended by PCI, this sentence will unfortunately not be removed. Choose carefully the open repository in which you deposit your article (arXiv, OSF-preprints, zenodo, hal, university repositories, etc.).