What is Peer Community in Mathematical and Computational Biology?
Peer Community in Mathematical and Computational Biology (PCI Math Comp Biol) has been launched in March 2020. It is a community of recommenders devoted to reviewing, improving and recommending high-level scientific articles previously posted on open archives in mathematical and computational sciences applied to all fields of biology. As a result, the recommenders make these unpublished articles complete, reliable and citable articles, without the need for publication in ‘traditional’ journals. Evaluation and recommendation by PCI Math Comp Biol are free of charge. When a recommender decides to recommend an article, he/she writes a recommendation text that is published along with all the editorial correspondence (reviews, recommender's decisions, authors’ replies) by PCI Math Comp Biol. The article itself is not published by PCI Math Comp Biol; it remains in the preprint server where it has been posted by the authors. PCI Math Comp Biol recommenders can also recommend, but to a lesser extent, postprints.
PCI Math Comp Biol is a community of the parent project Peer Community In, an original idea of Denis Bourguet, Benoit Facon and Thomas Guillemaud.
PCI Math Comp Biol is not designed to be a free peer-reviewing service for authors aiming to improve their articles before submission to a journal. It is, of course, possible, for authors to then submit their recommended article to a traditional journal, but this is not the goal of PCI Math Comp Biol.
PCI Math Comp Biol is stimulating: it recommends remarkable articles.
PCI Math Comp Biol is free: there are no fees associated with the evaluation process, and no charge for access to the comments and recommendations. The website is freely accessible.
PCI Math Comp Biol is transparent: Reviews and recommendations (for unpublished articles) and recommendations (for published articles) are freely available for consultation. Recommendations are signed by the recommenders. Reviews may also be signed if the reviewers agree to do so.
PCI Math Comp Biol is not exclusive: An article may be recommended by different Peer Communities in X (a feature of particular interest for articles relating to multidisciplinary studies) and may even be published in a traditional journal (although this is not the goal of PCI Math Comp Biol).
Acknowledging that advances in quantitative biology frequently require joint efforts from researchers with varied skills, PCI Math Comp Biol offers a venue for scientific work at the interface of biology, mathematics and computational science. PCI Math Comp Biol welcomes the submission of articles exposing innovative models and/or methods with deep mathematical or computational content and contributing substantially to the advancement of the natural and biological sciences. Implementation of methods and their application to data are encouraged but not compulsory. Articles are expected to be sufficiently well written to be superficially understood by any reader working at the interface of biology and mathematics or computational science. In addition, the objective of the work, the basic principles of the model/method, the relation to previous work and the potential applications of the results should be accessible to a broad audience.
Not in the scope of PCI Math Comp Biol are in particular
articles treating mathematical/computational problems only remotely inspired from biology and
articles with elementary mathematical content or applying classic bio-informatic tools.
PCI Math Comp Biol recommends only preprints of high scientific quality that are methodologically and ethically sound. To this end, PCI Math Comp Biol:
- 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 preregistration submissions and 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 reviewers and referees have no conflict of interest with the content or authors of the study being evaluated.
PCI Math Comp Biol 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 Math Comp Biol has a large number of recommenders, ensuring a considerable diversity of interests. The recommendations published by PCI Math Comp Biol 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.
Why submit your preprint to PCI Math Comp Biol?
Which manuscripts can be recommended?
PCI Math Comp Biol will evaluate preprints, and to a lesser extent articles published in journals, dealing with all fields of Mathematical and Computational Sciences applied to all fields of biology, including and not limited to Neurobiology, Evolutionary Biology, Cell Biology, Molecular Biology, Ecology, Epidemiology, Immunology, Genetics and population Genetics, Genomics and Transcriptomics, Structural Biology, Physiology, Development, Biophysics, Medical Sciences and Agricultural Sciences.
The articles recommended may have diverse formats: reviews, comments, opinion papers, research articles, data papers, technical notes, computer notes, movies, etc. No editing, formatting or proofing of the recommended papers is required. We only ask the authors of recommended articles to add a cover page to their article and a sentence at the beginning of the abstract stating that their article has been recommended by PCI Math Comp Biol.
PCI Math Comp Biol welcomes anonymous submissions (see details).
Peer Community In promotes the repeatability of science
PCI wants to promote scientific repeatability to improve the overall robustness and integrity of our scientific conclusions. To this aim, PCI has set up 3 mandatory rules and made 2 suggestions to authors:
Articles recommended by PCI must provide the readers:
-Raw data by making them available either in the text or through an open data repository such as Zenodo, Dryad or some other institutional repositories (see Directory of Open Access Repositories). Data must be reusable, thus metadata and accompanying text must 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, as appendices, or through an open data repository, such as Zenodo, Dryad or some other institutional repositories (see Directory of Open Access Repositories). The scripts or codes must be carefully described such that another researcher can run them.
-Details on experimental procedures. These details must be given in the text or as appendices at the end of the article.
-Open source implementations. If a new tool is presented in the preprint, it should be made publicly available. Even better, the source code should be shared with the community via platforms such as GitLab or BitBucket.
Suggestions to authors:
-PCI encourages authors to use 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 for them to clarify their hypotheses, avoid confusing “postdictions” and predictions, and carefully plan appropriate statistical treatment of the data (eg see 10.1073/pnas.1708274114).
-PCI also welcomes submissions of preregistrations. Authors can submit their preregistrations to a PCI before beginning their study, and thus before acquiring the data. Preregistrations are then evaluated by recommenders based on independent reviews, in exactly the same way as preprint articles. Preregistrations can thus be rejected or undergo revisions, improving the quality and robustness of the experimental design. When a preregistration is accepted, the subsequent article submitted to the corresponding PCI would be recommended provided the study has been conducted as described in the preregistration (or with any modifications clearly justified). In this way, an article cannot be rejected due to the outcome of the study only. Details on preregistration submissions can be found for example here.
Managing board of PCI Math Comp Biol
Caroline Colijn (Vancouver, Simon Fraser University, Canada & London, Imperial College, UK) Christophe Dessimoz (Lausanne, University of Lausanne, Switzerland) Barbara Holland (Hobart, University of Tasmania, Australia) Hirohisa Kishino (Tokyo, University of Tokyo, Japan) Anita Layton (Durham, University of Durham, UK) Wolfram Liebermeister (Jouy-en-Josas, INRAE, France) Christian Robert (Paris, Ceremade, Université Paris-Dauphine, France) Celine Scornavacca (Montpellier, ISEM, France) Donate Weghorn (Barcelona, CRG, Spain)
Recommenders manage the evaluation of preprints (and, to a lesser extent, published articles), which they may choose to recommend. Recommenders have a role similar to that of a journal editor (finding reviewers, collecting reviews, and taking an editorial decision based on reviews), and they may eventually recommend the article after several rounds of reviews. If they decide to recommend an article, they write a “recommendation” that has its own DOI and is published in the PCI Math Comp Biol electronic journal.
PCI Math Comp Biol recommenders can recommend up to five articles per year. They are expected to comply with the code of conduct of PCI Math Comp Biol, are eligible for selection as a member of the Managing Board for a period of two years, and they can propose the nomination of new recommenders to the Managing Board.
The current list of recommenders can be found here.
New recommenders are nominated by current recommenders, with the approval of the Managing Board. If you are interested in becoming a recommender, please contact a current recommender in your field.