FORMATTING INSTRUCTIONS AND TEMPLATES FOR ARTICLES RECOMMENDED BY A PCI

General mandatory guidelines

Data, script, code, and supplementary information availability section (if applicable)

• Data, statistical scripts, command lines and simulation code, and all supplementary information must be made available to readers, in an open repository with a DOI (see the repositories listed by OpenDOAR, eg. Zenodo). A perennial URL can be provided if no DOI is available; please note that GitHub URLs are not perennial. 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 Data, script, code, and supplementary information availability section should list the DOIs and URLs.
• 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, 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 mentionned and to list the corresponding reference(s) in the reference list.

Funding

All sources of funding must be listed in a separate “Funding” section. The absence of funding must be clearly indicated in this section.

Acknowledgments

The last sentence of this section is “Preprint version XXXX of this article has been peer-reviewed and recommended by Peer Community In XXX”. Replace XXX appropriately.

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)]”

Materials and methods

• Details of experimental procedures and quantitative analyses must be made fully available to readers, in the text, as appendices, or as Supplementary Information.
• 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.

References

Please carefully check that all the references cited in the text are in the reference list, and reciprocally.

References should:

• Be complete (with authors, title, year, volume number, page number or article number and clickable DOI at the end) and correct. If any of the preprints listed in your reference list have been published in a journal in the meantime, you may either leave the reference to the preprint or indicate the reference to the journal – in the latter case, please update your reference list accordingly.
• Contain the clickable blue, underlined URL of their DOI (e.g. https://doi.org/10111/100.1023) at the end of the references. A simple way to obtain the URL for the DOI at the end of each reference is to copy/paste your list of references into https://apps.crossref.org/simpleTextQuery. Some DOIs cannot be found in this way, but a Google search with the title of the article generally finds the corresponding DOI.
• Be listed in alphabetical order

You may use the following styles if you wish (not mandatory):

• Zotero/Mendeley style Peer Community Journal.
• EndNote style Peer Community Journal.

Word and Google Docs template instructions

Text update

Please be careful to correctly update all text in these templates (doi, authors’ names, address, title, date, recommender first name and family name …): the text to be replaced by your own text starts with XXX, eg XXXXTitle of the article.

• XXXXthe “cite_as” → replace it by the text we sent you
• XXXXthe_doi_we_sent_you → replace it by the doi we sent you
• XXXXthe surname and name of the recommender → replace it by the names we sent you
• In the acknowledgements replace the last sentence by the sentence we sent you
• Please be careful to choose the badges “Open Code” and “Open Data” only if appropriate (in addition to the “Open Access” and “Open Peer-Review” badges).

Predefined styles for Word

The PCI templates contain styles that you must use if you intend to submit your article to Peer Community Journal.

PCJ styles appear in the style gallery of the home tab of Word: click on the text you want to format (e.g. a section title) and then click on the corresponding predefined PCJ style in the style gallery of the home tab:

• PCJ Text. This style is used to format the text into sections, subsections, sub-subsections, etc.
• PCJ Section. This style is used to format the names of the different sections (i.e. “Introduction”, “Material and methods”, “Results” and “Discussion”). It should also be used to format the names of the final sections (i.e. “Data availability”, “Acknowledgements”, “Conflict of interest disclosure” and “References”).
• PCJ Subsection and PCJ sub-subsection. These styles are used to format the names of the different subsections and sub-subsections, respectively.
• PCJ Table. This style may be used to format the text in tables. Please note: Tables should be centered and adapted to fit into the space delimited by the margins. It may be necessary to create a section in landscape layout. If the table is too large and overlaps the margin, use the Table > AutoFit Windows option of Word. If inserted as images, tables should be positioned “In line with text”. If your original table contained bold or italics font, do not forget to apply again these font types to the tables once formatted with the PCI table style.
• PCJ Table legend. This style is used to format the legends above tables. It also puts the title “Table x.” in bold typeface.
• PCJ note Table. This style is used to format the notes below the table.
• PCJ Figure. This style simply defines the space before and after figures. Figures should be adapted to fit into the space delimited by the margins. It may be necessary to create a section in landscape layout. Figures should be positioned “in line with text”.
• PCJ Caption Figure. This style is used to format the captions below the figure. It also puts “Figure x.” in bold typeface.
• PCJ Reference. This style should be used for the Bibliography section of your article
• PCJ Equation. This style can be used optionally to format isolated equations (i.e. equations not included in the text).

Instructions for LaTeX, org-mode and R templates

• main.tex and sample.bib should be filled.
• in main.tex, fill the recommender’s name and the reviewers’ names, and the “XXXXcite as” section with the information we sent you by Email. Fill the other sections with the appropriate information (PCI, title, authors, affiliations, date of upload, mail of correspondance, recommendation DOI etc.)
• Fill sample.bib with your references. DOI are required. If the citations do not work correctly, make sure that your editor/compiler uses biber correctly, instead of bibtex for example
• Please be careful to choose the badges “Open Code” and “Open Data” only if appropriate (in addition to the “Open Access” and “Open Peer-Review” badges).