What is PCI Genomics​?

PCI Genomics Managing Board​

Gavin Douglas (North Carolina State University, Raleigh, USA)

Jean-François Flot (Univ Libre de Bruxelles, Bruxelles, Belgium)

Danny Ionescu (Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany)

Maxime Tarabichi (Institute of Interdisciplinary Research in Human and Molecular Biology - Jacques E. Dumont, Univ Libre de Bruxelles, Bruxelles, Belgium)

Editorial policy​

Scope​​​

PCI Genomics recommends preprints addressing genomics questions about any organism (or community). We cover all fields of biology, provided that the context of the study and the key question addressed relate 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 The preprint or the preregistration must not be published or under consideration for evaluation elsewhere at the time of its submission to PCI Genomics.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 prior to recommendation. 
• Welcomes studies reproducing previously published work. 
• 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 by authors with relevant 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 many recommenders, which ensures 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.​

Type of articles

There are no formal restrictions on the article types considered at PCI Genomics. In addition to standard research articles, we welcome reviews, comments, opinion papers, genome reports, technical notes, and software notes, among others.

Submission formatting

There are limited formatting requirements for submitting to PCI Genomics. The manuscript must have numbered lines, and contain information on raw data, code, and methods (see next section). There are no specific length requirements.

In addition, these sections are required:

• Acknowledgments,
• Funding
• Conflict of interest disclosure
• Data, script, code, and supplementary information availability
• References

Note that for authors interested in (optionally) publishing their articles in the Peer Community Journal, further format requirements would be needed after recommendation on PCI Genomics.

Repeatability and open science​

PCI wants to promote scientific repeatability and reliability to improve the overall robustness and integrity of our platform. To this aim, we have three mandatory rules and two suggestions for authors:

Mandatory rules:​

​Articles recommended by PCI must provide the readers with: 

• Raw data, made available directly in the text or through an open data 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. ​
• All code/scripts must be made available in the text or through an open data repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI. The scripts or codes must be carefully described such that another researcher can run them. 
• Details on methodology 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.​​​

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 that is relevant.

Recommending Postprints

PCI also recommends “postprints”, which we define as research papers that have already been published in peer-reviewed journals. PCI also considers books to be postprints because, despite not being evaluated by reviewers or editors before being published, they are often treated as such by academics. 

As postprints (other than books, see above) have already undergone peer review before publication, an additional PCI peer review is not required for their recommendation. Each postprint recommendation is written by at least two PCI recommenders. Authors cannot submit their own articles or books to a thematic PCI for postprint recommendation. Instead, a postprint recommendation must be initiated by a recommender who has read the postprint and considers it worthy of recommendation. The recommender must then find at least one other co-recommender for completion of the recommendation process.

When a postprint recommendation is published by a thematic PCI, the word “postprint” is printed below the image illustrating the postprint, to differentiate it from preprint recommendations. 

The recommendation text is published with a DOI, but is not accompanied by a peer review or editorial decision.