1. Introduction to PCI and PCI Genomics

2. Editorial policy​

2.1 Scope​​​

The scope of this PCI encompasses all aspects of genomics (structural genomics, functional genomics, epigenomics, evolutionary genomics, population genomics, proteomics, bioinformatics) dealing with every type of organism (viruses, bacteria, fungi, plants, animals,...) as well as metagenomes.

PCI Genomics recommends preprints addressing genomics questions about all types of organisms. We cover all fields of biology, provided that the context of the study and the key question addressed relates to genomics. The preprint or the preregistration must not be published or under consideration for evaluation elsewhere at the time of its submission to PCI Genomics.

​PCI Genomics recommends only preprints of high scientific quality that are methodologically and ethically sound. To this end, PCI Genomics: 
- Requires data, computer codes and mathematical and statistical analysis scripts to be made available to reviewers and recommenders at the time of submission and to readers after recommendation. 
- Welcomes reproductions of studies. 
- Welcomes preprint submissions based on preregistrations (whether or not reviewed) 
- Welcomes preprints reporting negative results, provided that the questions addressed and the methodology are sound. 
- Does not accept submissions of preprints presenting financial conflicts of interest. Other conflicts of interest must be minimal and declared. 
- Ensures that, as far as possible, the recommenders and referees have no conflict of interest with the content or authors of the study being evaluated. 

PCI Genomics does not guarantee the evaluation or recommendation of all submitted preprints. Only preprints considered interesting by at least one competent recommender (equivalent to an associate editor in a classical journal) will be peer-reviewed. The interest of the preprint, as determined by the recommender, can relate to its context, the scientific question addressed, the methodology, or the results. PCI Genomics has a large number of recommenders, ensuring a considerable diversity of interests. The recommendations published by PCI Genomics are designed to draw the attention of the research community to the qualities of the article, including the subjective reasons for the recommender’s interest in it.

2.2 Type of articles

The articles recommended may be of different types: reviews, comments, opinion papers, research articles, data papers, technical notes, computer notes, etc. Preregistrations should be submitted to PCI Registered Reports.​

2.3 Repeatability of science and open science​

PCI wants to promote scientific repeatability and reliability to improve the overall robustness and integrity of our scientific conclusions. To this aim, PCI has set up three mandatory rules and makes two suggestions to authors:

Mandatory rules:​

Articles recommended by PCI must provide the readers with: 

-Raw data, made available directly in the text or through an open repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI. Data must be reusable, and the metadata and accompanying text must, therefore, carefully describe the data. ​

-Details on the quantitative analyses (e.g. data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and details concerning simulations (scripts, codes) in the text or through a correctly versioned deposit in an open repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI or another permanent identifier (such as a SWHID of Software heritage). Note that Git URLs are not permanent. Information on how to issue a DOI for a GitHub repository is given at https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content. The scripts or codes must be carefully described such that another researcher can run them. 

-Details on experimental procedures must be given in the text.​

Suggestions to authors:

​​​​-PCI encourages authors to submit preprints based on preregistrations: Authors may post their research questions and analysis plan to an independent registry before observing the research outcomes, and, thus, before writing and submitting their article. This provides a way of clarifying their hypotheses, avoiding confusing “postdictions” and predictions, and carefully planning appropriate statistical treatment of the data (e.g. see 10.1073/pnas.1708274114).​​​

-Preregistrations should be submitted to PCI Registered Reports

-PCI welcomes submissions proposing replication studies. All submissions are assessed according to the same criteria, provided that the article is considered interesting by the recommender handling it and the research question is judged to be scientifically valid.​​​

2.4 Ethics​

Peer Community In is a member of and subscribes to the principles of the Committee on Publication Ethics (COPE). In addition:

• Financial conflicts of interest are forbidden, see the PCI code of conduct.
• Authors should declare any potential non-financial conflict of interest.

2.5 Use of artificial intelligence for article writing and software code generation

-Authorship and artificial intelligence
Artificial intelligence cannot be considered an author of an article submitted to PCI because  "All people listed as authors of the MS meet the authorship criteria, i.e. they contributed substantially to study planning, data collection or the interpretation of results and wrote or critically revised the MS and approved its final submitted version and agree to be accountable for all aspects of the work (ICMJE 2017)."

-Citing artificial intelligence
Scientists use sophisticated tools such as artificial intelligence to write text or software code. This is similar to using language proofreading services. Authors are invited to disclose such use in the acknowledgments of the article so that it is public information.

-Artificial intelligence and intellectual property
Plagiarism issues may arise when using artificial intelligence because they may generate texts identical to texts found in existing sources. Authors must ensure that no part of the manuscript has been published except for passages that are properly cited.

3. Submission guidelines

3.1 Requirements

3.1.1 Deposition of the MS and supplementary information

• Authors should first post their article on a preprint server, such as bioRxiv or arXiv (see details). When the article has appeared on this server, authors can submit their article to PCI Genomics.
• Raw data, statistical scripts in R, bioinformatic pipeline scripts, scripts and codes used for simulation or for statistical analyses and all other supplementary information must made available to reviewers and recommenders at the time of submission and to readers after recommendation. After recommendation, they must be available in the text or through a correctly versioned deposit in an open repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI or another permanent identifier (such as a SWHID of Software heritage). Note that Git URLs are not permanent. Information on how to issue a DOI for a GitHub repository is given at https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content. Raw data, scripts or codes must be carefully described such that another researcher can reuse them.

3.1.2 Ethics

 Original or acceptable secondary publication

• No part of the manuscript (MS) has been published, except for passages that are properly cited.
• In the MS, original data are clearly distinguished from published data. All information extracted from other publications is provided with citations.

Authorship

• All people listed as authors of the MS meet the authorship criteria, i.e. they contributed substantially to study planning, data collection or the interpretation of results and wrote or critically revised the MS and approved its final submitted version and agree to be accountable for all aspects of the work (ICMJE 2017).

• All people listed as authors of the MS are aware of their authorship and have agreed to be listed.
• No person who meets the authorship criteria has been omitted.

Ethical experimentation and interpretation

• If the study reported in the MS involved human participants, it should meet the ethical principles of the Declaration of Helsinki (WMA 2013).
• If appropriate, the study reported in the MS should meet the Consensus Author Guidelines on Animal Ethics and Welfare for Veterinary Journals concerning the humane treatment of animals and should be approved by an ethical review committee.
• In fields of research requiring approval from an ethics committee or institutional review board, the authors should generally ensure that all the necessary approvals have been obtained before submission.
• The authors should include a statement in the manuscript that informed consent was obtained, for experimentation with human subjects.
• The authors should do their best to avoid errors in experimental design, data presentation, interpretation, etc. However, should they nevertheless ​discover any serious error in the MS (before or after recommendation), they will alert PCI Genomics
• None of the data presented in the MS has been fabricated or distorted, and no valid data have been excluded. The images shown in the figures have not been manipulated to make a false impression on readers.
• The study results have been interpreted objectively. Any findings that run contrary to the authors’ point of view are discussed in the MS.
• The article does not, to the best of the authors’ knowledge, contain anything that is libellous, illegal, infringes anyone’s copyright or other rights, or poses a threat to public safety.

Acknowledgements

• All sources of funding for the study reported in the MS are stated.
• All people who are not listed as authors but contributed considerably to the study reported in the MS or assisted in its writing (e.g. author’s editors, translators, medical writers) are mentioned in the Acknowledgements.
• All people named in the Acknowledgements have agreed to be mentioned. They are not, however, responsible for the final version of the
• Consent has been obtained from the authors of any unpublished data cited in the MS.
• The owners of the copyright to any previously published figures or tables have agreed to their inclusion in the MS.

Conflict of interest

• Financial conflicts of interest are forbidden, see the PCI code of conduct.
• Authors should declare any potential non-financial conflict of interest.

Reference Sources

https://www.ease.org.uk/wp-content/uploads/2018/11/doi.10.20316.ESE_.2018.44.e1.pdf

https://www.wma.net/wp-content/uploads/2016/11/DoH-Oct2013-JAMA.pdf

http://www.icmje.org/recommendations/

https://ethics.iit.edu/ecodes/node/5487

3.1.3 Nomenclatural acts

3.2 Formatting guidelines

3.2.1 Word limits and formatting requirements

To make sure that your manuscript contains all the required features and sections, we encourage you to use our Word and Latex submission templates.

Although PCI Genomics imposes no word limits or specific formatting requirements on submissions, authors are requested to respect the following guidelines to ​facilitate peer review:

• Lines must be numbered
• Tables and figures must be located in the main text, not at the end of the manuscript.
• All the abbreviations used in the article should be defined, except those obvious to non-specialists.
• As PCI Genomics does not copy-edit articles, authors should pay careful attention to typographical and other errors. A recommended article should be as close to perfect as possible in form, because it is a finished article.
• The text should be cohesive, logically organized, and, thus, easy to follow.
• The presence of all tables and figures, additional materials, the accessibility of the data, scripts and codes and the accuracy of the references must be checked.

Manuscripts should be as concise as possible, but as long as necessary, to ensure that the description of the rationale and methods is clear and comprehensive, and that all methods are reproducible. Authors should ensure that they follow established formatting conventions for articles in their discipline. Authors who intend to publish their article in a journal afterwards should also take note of any sectional or overall word limits or other formatting requirements applying to the journal targeted.

3.2.2 Manuscript structure and organization

Submissions should usually include the following sections (reviews, commentaries and opinions may have a different organization):

Title

• The title should be unambiguous, understandable to specialists in other fields, and reflect the content of the article

Authors

• Indicate the full name and affiliation of each author. Provide e-mail addresses, at least for the corresponding author, and for the first authors if different.
• Authors are invited to indicate their ORCID.
• PCI Genomics welcomes anonymous submissions (see section 3.3). 

Abstract

• Should be concise and present the main findings of the study.
• Structured abstracts (e.g., Background, Methods, Results, Discussion) can be used.

Introduction

• The introduction should clearly explain the reasons for the study.
• The introduction should build on relevant recent and past research performed in the field.
• The research question/hypothesis/prediction should be clearly presented.

Materials and methods

• Details of experimental procedures and quantitative analyses must be made fully available to readers, in the text or through deposition in an open repository, such as Zenodo, Dryad or institutional repositories with a DOI.
• For specimen-based studies, complete repository information should be provided and institutional abbreviations should be listed in a dedicated subsection (if applicable). Specimens on which conclusions are based must be deposited in an accessible and permanent repository.

Results

• Data must be available to readers, in the article or through deposition in an open repository, such as Zenodo, Dryad or institutional repositories, with a DOI.
• The authors’ data and ideas should be clearly distinguished from those of other people and from the authors’ earlier publications. Citations should be provided whenever relevant.

Discussion

• The research questions should be answered and the main results should be compared with published data, as objectively as possible.
• Conclusions must be clearly stated and supported by the data.
• Interpretations are possible, but must be clearly identified as such.

Tables and figures

• Figures and tables should be easily understandable without reference to the main body of the article.
• Captions of tables and figures must be informative but concise.

Acknowledgements

Funding

• All sources of funding must be listed in a separate funding section.

Conflict of interest disclosure

• Authors should declare any potential non-financial conflict of interest (financial conflicts of interest are forbidden, see the PCI code of conduct).
• In the absence of competing interests, the authors should nevertheless add the following sentence to the “Conflict of interest disclosure” section: “The authors declare that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article. [IF APPROPRIATE: The authors declare the following non-financial conflict of interest: XXX (if some of the authors are recommenders of a PCI, indicate it here)]”

Data, scripts, code, and supplementary information availability (if applicable)

• Data, statistical scripts, command lines and simulation code must made available to reviewers and recommenders at the time of submission and to readers after recommendation. After recommendation, they must be available to readers, either in the text
•  or through a correctly versioned deposit in an open repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI or another permanent identifier (such as a SWHID of Software heritage). Note that Git URLs are not permanent. Information on how to issue a DOI for a GitHub repository is given at https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content. Data, scripts or codes must be carefully described such that another researcher can reuse them.
• If data are not directly accessible, the reason should be given in the "Data, scripts, code, and supplementary information availability" section
• Wherever possible, data, scripts, codes and supplementary information should be provided in machine-readable formats. Avoid PDFs other than for textual or figure supplementary information.
• Readme files explaining data, scripts, and code are required to make data, scripts, and code understandable and reusable by the reader.
• If the data, script, code and supplementary information availability section contains one or several dois (or urls), it is necessary to cite the corresponding reference(s) in the text when data, scripts, code or supplementary information are mentioned and to list the corresponding reference(s) in the reference list.

References

• Authors are free to use their preferred reference style, as long as usual bibliographic information is provided (e.g., Authors, Year, Title, Editor/Journal, Volume, Pages/DOI) and style is consistent.
• If available, the DOI of each reference must be provided.
• Author-year or numerical citation schemes can be used.
• All references cited in the text must be included in the reference section and listed either in alphabetical order (author-year format) or by order of appearance (numerical format).
• In accordance with the 10^th point of the Declaration on Research Assessment (DORA) signed by Peer Community In, authors are encouraged to cite the original research reporting new data and discoveries as the primary source of information, rather than the review articles discussing them (see more here).

3.3 Submitting a preprint

To submit an article, authors should first post it on a preprint server, such as bioRxiv or arXiv. Once the article has appeared on this server, the authors should click on the “Submit preprint” button on our website home page, for access to a very simple submission process.

During the submission process, authors will be asked to suggest between 5 and 10 recommenders who could handle the evaluation of their preprint. Recommenders are very similar to journal editors. They are responsible for finding reviewers, collecting reviews, and making editorial decisions based on reviews. They may eventually recommend the article after one or several rounds of review.

Note that PCI Genomics is under no obligation to consider the submitted preprint. Only submitted preprints selected by a recommender enter the evaluation process. Although we cannot guarantee that the preprint will be reviewed, all possible efforts will be made to make this possible.

If, for some reason, authors have difficulty with the submission process, they can contact us at contact@genomics.peercommunityin.org.

For more details on the step-by-step procedure, authors can consult the how to? section  

3.4 Submitting a preprint anonymously

4. The evaluation and recommendation process

4.1 Overview

1. Once the Managing Board has validated your submission, the recommenders you suggest receive an alert, drawing their attention to your preprint.
2. We cannot guarantee that your preprint will be reviewed, but all possible efforts will be made to make this possible. If no recommender – including all recommenders in your field of expertise – has initiated the evaluation of your preprint after 20 days, you will be notified by e-mail. If this happens, we suggest that you cancel your submission.
3. Alternatively, a recommender finding your preprint particularly interesting can decide to initiate the evaluation process. In this case, you will be notified by e-mail. The recommender will invite reviewers, so as to obtain at least two high-quality reviews. Note that the recommender and reviewers must declare that they have no conflict of interest of any kind with the content or the authors of your preprint – see the code of conduct.
4. One or several classic cycles of reviews/decision/authors’ response follow, eventually leading to the recommendation or rejection of the article. At each round of review, the recommender may decide to reject or recommend your article. Alternatively, the recommender may ask you to revise your article, generating another round of reviews. The recommender signs all decisions, whereas reviewers may choose to remain anonymous or to sign their reviews. The median time to the first decision is 45 days.
5. If the recommender eventually decides to reject your article, the reviews and decision will be sent to you, but will not be published or publicly released by PCI Genomics. They will be safely stored in our database, to which only the Managing Board has access.
6. Alternatively, if the recommender decides to recommend your article, PCI Genomics publishes a “recommendation” of your article. This recommendation is a short article, written and signed by the recommender, similar to a News & Views piece, describing the context of your study and explaining why the recommender found your article particularly interesting. PCI Genomics will also publish all the editorial correspondence (reviews, recommender's decisions, authors’ replies).
7. Once PCI Genomics has published the recommendation text, your article becomes a valid reference that can be used by scientists and cited in scientific publications. You no longer need to publish your article in ‘traditional’ journals, although you remain free to do so if you wish.

4.2 Transparent review

PCI Genomics publishes all reviews of recommended manuscripts, with reviewers choosing whether to sign their reviews or remain anonymous. All reviews and recommender decision letters are published on the PCI Genomics platform at the point of acceptance. Reviews of rejected submissions are sent to the authors, but are not published. Reviewers and recommenders are expected to adhere to the PCI code of conduct, avoiding abusive or discriminatory language in their comments. Reviews that are considered to violate the code of conduct may be edited by recommenders or the Managing Board, returned to the reviewer for editing, or discarded.

4.3 Handling of manuscripts by recommenders

4.4 Appeals process

Authors of rejected manuscripts can appeal against a PCI Genomics decision within 30 days of receiving it, by contacting us at contact@genomics.peercommunityin.org. Appeals will be considered by the specialist recommender(s) that handled the manuscript and the PCI Genomics Managing Board. Decisions following appeal are final.

4.5 Self-assessment questionnaires

Reviewers are encouraged to answer the following questions to help recommenders make well-informed and efficient decisions. Consequently, it is recommended that authors engage in a self-assessment of their manuscript by using the following questionnaire. For more details, see the guide for reviewers in the Help menu.

Self-assessment questionnaire regarding the article:

• Title and abstract
  • Does the title clearly reflect the content of the article?
  • Does the abstract present the main findings of the study?

• Introduction
  • Are the research questions/hypotheses/predictions clearly presented?
  • Does the introduction build on relevant research in the field?

• Materials and methods
  • Are the methods and analyses sufficiently detailed to allow replication by other researchers?
  • Are the methods and statistical analyses appropriate and well described?

• Results
  • In the case of negative results, is there a statistical power analysis (or an adequate Bayesian analysis or equivalence testing)?
  • Are the results described and interpreted correctly?

• Discussion
  • Have the authors appropriately emphasized the strengths and limitations of their study/theory/methods/argument?
  • Are the conclusions adequately supported by the results (without overstating the implications of the findings)?

During the evaluation process, there is a possibility that your data, scripts, and code (if applicable) will undergo a review by the reviewers or the recommender. Should your data and scripts be reviewed, they will be retrieved from their repository, the scripts will be executed, and the outcomes verified.

We recommend proactively addressing common pitfalls and self-assessing against the questions listed below prior to submission. A negative response to any of these queries necessitates prompt rectification to achieve a "yes" status, thereby facilitating a smoother evaluation process. 

Self-assessment questionnaire regarding data, scripts, and code:

• Can the data and script be accessed via the links provided in the submission form or directly within the manuscript?
• Is a readme file present?
• Are metadata for the data and annotations for the scripts available?
• Are the readme and data files comprehensible?
• Do the scripts function as intended with the data?
• Do the results generated match those presented in the manuscript? 

• Frequent errors that hinder affirmative responses include:
  • Absence of scripts' verification since conducting the analyses (prior to drafting the manuscript).
  • Scripts referencing files with names that do not match the available files.
  • Scripts using absolute paths to files rather than relative paths.
  • Scripts authored in languages other than English.
  • Readme files lacking adequate details regarding the scripts' purpose.
  • Absence of program installation instructions in the readme file.
  • Insufficient or inadequate script annotations.
  • Omission of comments on the duration of lengthy script executions.
  • Non-preconfigured installations of necessary packages or libraries within the scripts.

5. Fate of PCI-recommended preprints: PCI-friendly journals and the Peer Community Journal

The goal of PCI is to evaluate and recommend preprints, converting them into valid, citable final articles. The theoretical outcome is for PCI-recommended preprints to remain on preprint servers.

However, for various reasons, the authors of PCI-recommended preprints may prefer:

-To submit their preprint to a PCI-friendly journal (accepts the article with no further peer-review, or provides the authors with a response in usually less than 5 days, or uses the PCI evaluation if appropriate)
-To submit their preprint to the Peer Community journal (published as is, free of charge)
-To submit their preprint to another journal

In the case of PCI submissions being recommended and eligible for multiple journals, the authors will make the final decision as to where the manuscript should be published. The journal chosen may be any PCI-friendly journal, other journals, or no journal if the authors prefer the article to be hosted solely on their preferred preprint server. In all cases, the reviews and decision letters for recommended submissions will be published on the PCI platform.

5.1 PCI-friendly journals

5.1.1 Journals committed to accepting PCI-recommended articles without further peer review

• These journals endorse the PCI review criteria and agree to accept, without further peer review, any manuscript obtaining a positive final recommendation from PCI while also meeting any additional procedural requirements that do not require further scientific evaluation by these journals. Such additional requirements could include falling within a defined disciplinary scope. 
• Note that subjective judgments about the importance, novelty or timeliness of a research question are not relevant to the judgment of research quality at PCI and are not assessed as an additional requirement by these journals.
• These journals accept PCI-recommended articles for publication even if the reviews performed by PCI are anonymous. 
• Similarly, these journals will not relitigate any scientific elements of the study that PCI has already approved.
• These journals agree to display clearly, on the homepage of the article, a note indicating that the evaluation process was carried out by PCI of the following type: 

Editor's note: This article has been reviewed and recommended by Peer Community in Evolutionary Biology: Mathieu Joron (2020) Studying genetic antagonisms as drivers of genome evolution. Peer Community in Evolutionary Biology, 100108. https://doi.org/10.24072/pci.evolbiol.100108 

5.1.2 Journals providing authors with a fast response

• These journals do not automatically accept PCI-recommended articles, but have agreed to the following commitment: once the article is submitted by the authors, the journal agrees to provide the authors with one of the following three responses, within a specified short turnaround time (e.g. 5 days):

1. Acceptance with minor modifications with no further peer-review, 
2. Need for further peer-review before decision,
3. Not interested.

• In case of acceptance, these journals agree to display clearly on the homepage of the article a note indicating that the evaluation process was carried out entirely or partly by PCI, of the following type: 

Editors' note: A previous version of this article was reviewed and recommended by Peer Community in Evolutionary Biology: Mathieu Joron (2020) Studying genetic antagonisms as drivers of genome evolution. Peer Community in Evolutionary Biology, 100108. https://doi.org/10.24072/pci.evolbiol.

5.1.3 Journals committed to using PCI evaluations if appropriate

• These journals do not automatically accept PCI-recommended articles but have agreed to the following commitment: The journal will consider submissions of articles recommended by a PCI and they may use PCI reviews and recommendations for their own review processes, if appropriate.
• In case of acceptance, these journals agree to display clearly on the homepage of the article a note indicating that the evaluation process was carried out entirely or partly by PCI, of the following type: 

Editors' note: A previous version of this article was reviewed and recommended by Peer Community in Evolutionary Biology: Mathieu Joron (2020) Studying genetic antagonisms as drivers of genome evolution. Peer Community in Evolutionary Biology, 100108. https://doi.org/10.24072/pci.evolbiol.100108

5.2 The Peer Community Journal

Once an article is recommended by a PCI, the authors can opt to publish their article in the Peer Community journal.

This Peer Community journal is

• Unique = a single journal for all PCIs
• Free = diamond open access (free for authors and for readers).
• Exclusive = Publishes only preprints recommended by PCI 
• Unconditional = can publish all PCI recommended articles without further modification 
• Opt-in = only if the authors wish to publish in it
• Immediate = no delay between submission and publication 

This journal, created and funded by the PCI organization, is hosted by a not-for-profit publisher.

The Peer Community journal does not provide copyediting or typesetting services.

The Peer Community journal is currently being evaluated by an international scientific database for indexing.