Publishing has never been this easy

We've worked hard on, and continue to refine, a set of tools and instructions that make the submission process an enjoyable experience.

Preparing your submission

1
PeerJ does not accept formal pre-submission inquiries and submissions should not be accompanied by a cover letter (there are fields in our submission form which replace the need for a cover letter).
2
Include line numbers, an approx. 2.5cm margin on all edges, and 12 point Times font for readability. This makes your review pdf easy to read, and your editor and reviewers very happy!
3
Files typically expected:

- Manuscript text
- Any figures
- Any tables
- Any raw data or code
- Any supplemental information files

4
Your reviewers must have your raw data or code to review. Please submit:
  • As a link to a repository where the data is accessible.
  • Uploaded as a supplemental file.
Generally however, there are very few circumstances in which we can accept a manuscript without raw data. It is not required if your submission does not deal with raw data or code.
Some examples of invalid reasons for not submitting raw data or code:
  • The data is owned by a third-party who have not given permission to publish it within this article.
    Please add a note to PeerJ staff to not publish the raw data alongside your article.
  • The raw data is too large.
    Please upload the raw data to an online repository (e.g. Figshare, Dryad etc).
5
TeX/LaTeX users should submit a single PDF document including line numbers to be used for peer review as the "Manuscript" file, and also upload the original source files in the "Primary files" section (select "LaTeX Source Files" from the drop down menu to set the file type).
We do not require the use of any specific LaTeX style file; PeerJ's styles will be applied to the document during production.
PeerJ recommends the use of Overleaf - a free online service that provides a user friendly interface for the preparation of LaTeX manuscripts. Users of Overleaf can use a standard PeerJ template and can initiate their submission to PeerJ or PeerJ Preprints with a single click. Note: the use of Overleaf for a PeerJ submission is NOT a requirement, but it might just make your life easier!

6
There are two ways you can submit:

Single file

Upload a manuscript with figures and tables embedded.
  • Upload your manuscript as a single file (pdf, docx, doc, odt) with figures and tables embedded.
  • Embed low-resolution figures and tables (no tables as images) within the text or at the end of the manuscript (one page each).
  • Each figure and its legend must reside on the same page.
  • You can embed compressed images to reduce the file size, but they must be sufficiently legible for review.
  • On resubmission (after the first decision) you must upload original hi-resolution figures and tables as separate files. Keep embedded figures or tables as before, DO NOT remove them from the manuscript text other than to update. The low-res embedded versions are for review only, while the hi-res will be used in production.
  • Upload supplemental files separately.

Multiple files

Upload a text-only manuscript with separate hi-res figure and table files.
  • Upload your manuscript, figure and table files separately.
  • Legends are entered manually for every figure and table.
  • Many authors prefer to submit everything when the article is fresh in their minds.
  • Reduces the risk of having misplaced files when you get to the point of final production.
  • Upload supplemental files separately.

Submitting

First start your submission, then complete the submission screens:
Use the checklist on every screen:
1Read the directions and enter your article info.
2Use the checklist to make sure everything is done.
When all the checks are good, save and continue.
Using the checklists will reduce the chances that your manuscript is returned for changes, which means a faster time to publish.

Basic Manuscript Organization

1
The Author Cover Page listing all authors and affiliations must be the first page of the manuscript document you submit (view example). To include:
  • Article title
  • Authors
    • First names (or first initials in combination with full middle names)
    • Middle names (or initials, if used)
    • Last names (surname, family name)
  • Affiliations (indicate multiple affiliations, or current addresses where appropriate)
    • Department, university, or organizational affiliation
    • Location: city, state/province (if applicable)
    • Country
  • Corresponding Author
    • First and Last name
    • Email address

OR

  • If the article was authored by a consortium, list full names and full affiliations in the intended order for publication in the acknowledgements.
2
A standard front page is added to your reviewing manuscript when it is generated by the system. Please make sure that the author order and details on this standard front page (entered by you in our online submission forms) exactly match that in your Author Cover Page described above.
3
Contributors who do not qualify under ICMJE authorship guidelines should not be listed as authors. They should be included in the Acknowledgements and should agree to being acknowledged.

Standard Sections

PeerJ covers a wide range of fields and although we can accommodate a variety of ‘standard sections’, we recommend that the following Standard Sections, in this order, are used wherever possible. Note: Short manuscripts may not require all sub-sections.
Author Cover Page (see above)
Abstract
  • No more than approx. 500 words (or 3,000 characters).
  • Headings in structured abstracts should be bold and followed by a period. Each heading should begin a new paragraph. For example:
    Background. The background section text goes here. Next line for new section.
    Methods. The methods section text goes here.
    Results. The results section text goes here.
    Discussion. The discussion section text goes here.
Introduction
Materials & Methods
Results
Discussion
Conclusions
Acknowledgements
  • Should not be used to acknowledge funders – that information will appear in a separate Funding Statement on the published paper.
  • As a matter of courtesy, we suggest you inform anyone whom you acknowledge.
References

Reference Format

Formatting Tip

We want authors spending their time doing science, not formatting.

We include reference formatting as a guide to make it easier for editors, reviewers, and preprint readers, but will not strictly enforce the specific formatting rules as long as the full citation is clear.

Styles will be normalized by us if your manuscript is accepted.

PeerJ uses the "Name. Year" style with an alphabetized reference list.
In-text citations
  • For three or fewer authors, list all author names (e.g. Smith, Jones & Johnson, 2004). For four or more authors, abbreviate with ‘first author’ et al. (e.g. Smith et al., 2005).
  • Multiple references to the same item should be separated with a semicolon (;) and ordered chronologically.
  • References by the same author in the same year should be differentiated by letters (Smith, 2001a; Smith, 2001b).
  • Cite articles that have been accepted for publication as 'in press', include in the reference list, and provide a copy in the Supplemental Information.
  • Cite unpublished work, work in preparation, or work under review as 'unpublished data' using the author's initials and surname in the text only; do not include in the reference section
  • References to personal communications should be avoided but, if absolutely necessary, should be referred to as "pers. comm.", include the relevant individual's name, and the relevant year.
The Reference Section
  • Each journal reference should be listed using this format: the full list of Authors with initials. Publication year. Full title of the article. Full title of the Journal, volume: page extents. DOI (when it's available). Example journal reference: Smith JL, Jones P, Wang X. 2004. Investigating ecological destruction in the Amazon. Journal of the Amazon Rainforest 112:368-374. DOI: 10.1234/amazon.15886.
  • References to 'gray literature' such as patents, technical reports from government agencies or scientific research groups, working papers from research groups or committees, white papers, and preprints should be described as thoroughly as possible. Include any author names, titles of the page or the paper, publication date, names of publisher where possible, URL, accessed by dates, and identification numbers such as patent numbers, series numbers as applicable.
    Examples:
    • Boettiger C. 2013. knitcitations: citations for knitr markdown files. Available at https://github.com/cboettig/knitcitations (accessed 10 July 2012)
    • Dorch B. 2012. On the Citation Advantage of linking to data. hprints. Available at http://hprints.org/hprints-00714715 (accessed 5 July 2012)
  • Example book reference: James FY. 2010. Understanding corn and wheat. Oxford: Oxford University Press.
  • Example book excerpt: Smith PG. 2011. Behavior in ants. In: Jones HY, ed. Insect behavior in the Andes. Berlin: Springer Verlag, 101–200.
  • Example thesis: Blair HJ. 1989. Structural modifications of the fern genus Lecanopteris (Polypodiaceae). D. Phil. Thesis, Cambridge University.
  • Example webpage: Johnson S. 2010. Italian Plants. Available at http://www.italianplants.com (accessed 22 March 2011).
  • Example abstract: Thomas D, Scharfenecker U, Schiltmeyer B. 2006. Low potential for drug-drug interaction of lacosamide [abstract no. 2.235]. Epilepsia 47 (Suppl. 4): 200
  • The References Section should be sorted by Author, Year, Title. All citations in the text must appear in the reference list, and all references listed must be cited in the manuscript text. Any references that are relevant, but are not cited in the text, must be placed in a "Further Reading" section.
  • Zotero users can also download the Zotero PeerJ style.
  • EndNote users can download the EndNote PeerJ style. If you have used EndNote, you can change the references using the following steps:
    1. Open EndNote
    2. Open library (the citation file)
    3. Set style to "PeerJ"
    4. Go to Edit --> Output Styles --> Edit "PeerJ"
    5. Under Bibliography --> Author Lists, set "Abbreviated author list" to "List all author names".
Mendeley
  • Before submitting, Mendeley users on Microsoft Word need to change their field codes (used by the software) into plain text by performing the following:
    • If using Windows
      Ctrl-A (Selects all the text in the manuscript)
      Ctrl-Shift-F9 (Changes the fields codes)
    • If using OSX
      Command-A (Selects all the text in the manuscript)
      Command-6 (Changes the fields codes)

File Types

Manuscript
    Check your manuscript with the Manuscript checks
  • For manuscript text, PeerJ accepts .DOC (MS Word), .DOCX (MS Word), .TeX, .ODT (OpenDocument) and .RTF formats. A 'single file' PDF document may also be supplied for initial submissions.
  • For MS Word submissions .DOCX is preferred as it usually produces higher quality reviewing PDFs and avoids problems with reference lists.
  • Text must be formatted with the "Normal" template (and/or ‘Heading 1,2,3 etc" for Sections).
  • Use of ‘unusual’ document templates, for example "Normal (Web)", may affect the quality of the review PDF.
  • Do not 'full width' justify your document, instead justify all text to the left-hand margin.

Accepted and preferred file formats
Manuscripts DOCX (preferred), DOC, ODT; PDF for LaTeX users

Figures
    Check your figures with the Figure and Table checks
  • Please include the figure numbers in the figure filenames (e.g. "Figure 1" or "Figure 2").
  • A button will display next to each file you upload. Please use this button to verify details for every file. This may be as simple as selecting the type of file you have uploaded (manuscript, figure, table etc) or you may be required to enter a title and legend.
    • The Title is the ‘one sentence’ title of a figure. Don't include "Figure 1", we add that for you.
    • The Legend is the ‘several sentence’ description.
  • Figure and Table numbering is determined by the system based on the ordering in which it appears on the file upload screen. You can re-order them using drag and drop.
  • Figures can be submitted as EPS and PDF (for vector images), or PNG (for lossless images) for initial review. If figures are provided as PDF for initial review, high quality EPS or PNG files must be submitted at revision for use in final publication.
  • Unnecessary white space should be eliminated around each figure & figure part.
  • Uniform fonts and font sizes should be used for labels (letter sizing should be readable at ‘actual sized’ reproduction - we suggest a vertical height of 2 mm).
  • The panels of each multi-part figure should be arranged however the figure is intended to be published and saved in a single file. Each part should be labeled with an uppercase letter for each figure part (e.g. Fig. 3C) and a single number for the whole figure group.
  • Minimum image size: 900 by 900 pixels.
  • These requirements ensure appropriate on-screen reproduction at an acceptable size. However, there will also be an opportunity to provide high-resolution versions of your images at revision.

Accepted and preferred file formats
Figures Use the original file format and image size whenever possible.
Vector images
(e.g. charts, diagrams):
  • PDF (preferred)
  • EPS
  • PNG
Raster/bitmap images
(e.g. drawings, screenshots):
  • PNG (preferred)
  • JPEG (photographs only)
  • PDF
  • EPS
Ideally at least 3000px wide.
Must be over 900px.

Tables
    Check your tables with the Figure and Table checks
    … can be submitted as .DOC (MS Word), .DOCX (MS Word), .ODT (Open Doc). PDFs may be provided for initial review, text-based source files must be provided at revision for use in final publication.
  • For clarity, the name of your uploaded files should include "Table 1" "Table 2" etc.
  • A button will display next to each file you upload. Please use this button to verify details for every file. This may be as simple as selecting the type of file you have uploaded (manuscript, figure, table etc) or you may be required to enter a title and legend.
    • The Title is the ‘one sentence’ title of a table. Don't include "Table 1", we add that for you.
    • The Legend is the ‘several sentence’ description.
  • Cite tables in text as "Table 1." "Table 2."
  • Include units in column and row headings, in parentheses.
  • Tables must fit in a single 21.6 x 28 cm page with 2.5 cm margins.
  • Place footnotes below the table; these may be used to explain abbreviations.
  • Note that our system allows multiple files to be uploaded at once.

Accepted and preferred file formats
Tables DOCX (preferred), DOC, ODT; PDF for LaTeX users

    Figure/table referencing

  • You must have appropriate permissions and attribute credit when reproducing copyrighted material included in your figures or tables. If any photographs, maps or images are taken from copyrighted material, we will need a copy of the permissions to publish under CC BY uploaded as a Supplemental File for our records and the source credit reference needs to be included in the figure legend.

    Referencing examples:

    Photo credit: San Diego Zoo Global.
    Photo credit: Ali Smith.
    Image credit: the MESH archive at http://ondemand.nssl.noaa.gov
    3D model credit: Ishmael Kreill
    Map data © 2016 Google


  • Please upload a signed photography/video permission letter for any copyrighted content created by non-named-authors.
    Download photo/video permission letter (.doc)



  • To publish figures including identifiable human subjects, you must have appropriate written consent from the human subject and permission from the image-owner or photographer to publish the image in PeerJ under CC BY. If the human subject is a minor and could not legally consent, the consent must have been given by the parent or guardian. Both the consent and permission to publish should both be uploaded as a Supplemental File for our records and the photo credit reference needs to be included in the figure legend.

    Example:

    I [name] give [photographer / researcher name] permission to use my image for research and for publication.



TeX / LaTeX users
... since our system cannot convert .tex files, we ask that you upload a PDF that you have generated yourself as the manuscript. Then upload the source tex files as "Latex source files" in the Primary file category.
Data and Materials
  • All authors are responsible for making materials, code, raw data and associated protocols relevant to the submission available without delay.
  • Please ensure that all relevant datasets, code, images and information are available in one of the following possible ways and provide a link to the appropriate location: uploaded as Supplemental Files, deposited in a public repository, or hosted in a publicly accessible database. There are very few circumstances in which we can accept a manuscript without raw data (see point 4 in 'Preparing your submission').
Supplemental Information (SI)
... SI files are published as links alongside the article, which point to downloadable files. These files do not form an integral part of the manuscript and may include supplemental information or important data which are too large for inclusion in the main manuscript. As they are provided as ‘original’ files, readers will need to be able to open them using their own resources. Therefore to ensure widest compatibility you should utilize common file types and avoid proprietary formats.
  • All files should be named as a “Supplemental [Item] S[number]”. Please include a brief descriptive title and legend in the metadata when uploading the file.
  • In total, all Supplemental Files should not exceed 50 MB (if more space is needed, please contact us). Individual files should not exceed 30 MB.
  • Note that our system allows multiple files to be uploaded at once.
  • If it's necessary to cite Supplemental Information files in the text, use the following style: Fig. S1, Table S1, Data S1, Video S1, Article S1, Audio S1.
  • If the Supplemental Files are only intended for review purposes and cannot be published, please upload the files as review-only info from the drop down menu in the Supplemental Files section.

For maximum compatibility, we suggest that you submit Supplemental Information using the following formats:
Supplemental Figures Submit as JPG (use maximum quality settings), EPS (for vector images), or PNG (for lossless images).
Supplemental Tables Submit as PDF, DOC, Excel, RTF or TeX / LaTeX files.
Supplemental Articles Submit as PDF.
Supplemental Videos Submit as AVI, MOV, and MP4 files. For widest compatibility, we suggest authors provide video files as 128 kbit/s AAC audio and 480p H.264 video in an MPEG-4 (mp4) format. Regardless of format submitted, authors should double check that their videos open and play in recent versions of both QuickTime and Windows Media Player.
Supplemental Audio Submit as WAV or MP3 files. Please include a legend. Ensure that the files open and play in common audio players such as iTunes or Windows Media Player.
Large Supplemental Data sets Submit in a compressed format (e.g. zip or tar.gz).

Style Considerations

Units, Symbols, Mathematics, Abbreviations
  • Where possible and appropriate, use the International System of Units.
  • Use discipline specific (non-SI) units only where they are widely adopted within the field.
  • Symbols should be used in lieu of abbreviations for mathematical expressions & defined at first use.
  • Spell out the numbers 1-9 unless used with units.
Manuscript Text
  • Submissions which will result in a final typeset manuscript greater than 45 pages may incur an additional service charge to cover production costs. If you have a manuscript of this extent then please email editor@peerj.com to discuss.
  • Articles must be written in clear, unambiguous English for an international audience.
  • The established norms of academic writing within your field should be followed.
  • Either English or American spelling is acceptable provided it is consistently used throughout.
  • Nomenclature: Biological & medical nomenclature should adhere to recognized guidelines set forth by international committee regulations or authoritative bodies for specific fields, as applicable.
Figures
  • Image Manipulation: Figures should only be (minimally) processed or manipulated in order to add labels, arrows, or to change contrast or brightness if applied to the entire image as well as the controls. They should not be adjusted in any way that could lead to misinterpretation of the information in the original image. Unprocessed figure files and data must be retained for editorial review upon request. The descriptions of changes, hardware and software used to take images and make adjustments must also be provided. Inappropriate figure manipulation is grounds for article retraction and/or reporting to institutional oversight boards.
  • "Figure" refers to all images such as graphs, charts, line drawings and photographs. When citing figures in the text, the abbreviation "Fig." should be used. If the citation is the beginning of the sentence, use the full word "Figure" instead.
  • All figures must be cited in the main text.
  • Ideally legends should not be included in your image files. However legends in images are accepted for initial review, when the legend is placed below the image. For revisions, legends in images are not accepted. Single file submissions should include legends in the manuscript text alongside the figure. Multi-file submissions require legends to be entered manually using the 'Details needed’ button, and should not be included in the manuscript text.
  • Figure legends should be self contained and clearly describe the figure and its contents.
  • The graphical area of a figure should include information about scales, abbreviations, limits, etc.
  • When submitting photographs as figures please indicate the identity of the photographer. If the photographer is not one of the co-authors, please upload a supplemental document with permission from the photographer allowing you to publish the image under a CC BY license.
  • If you use a map as a figure please cite the source of the map. Wherever possible, use map services which allow unrestricted re-use. If you must use Google Earth or Google Maps then in order to accurately attribute a map from Google, we need to know the third-party data providers cited with the map: find out how.
  • When creating figures and images consider the accessibility of your chosen color schemes to those with non-normal color vision. Wherever possible avoid using color alone to distinguish between parts of images. When color is used, we suggest that you consult the following resources to ensure maximum accessibility: J*FLY, Mapbox and ColorBrewer.
Linnean Binomials
  • Authors are encouraged to provide taxonomic authors of Linnean binomials when first used in the text, particularly for taxa that are the focus of the paper in question. Where several taxa are named, citation of taxonomic authors in Tables is regarded as an adequate substitute for citation in the body of the text. Authors of zoological names should consist of initials plus full surnames, whereas authors of botanical names should be abbreviated following Brummitt & Powell's (1992) 'Authors of plant names'. In either case, binomials carrying more than three authors should be abbreviated to 'et al.' subsequent to the name of the third author.
https://peerj.com/about/author-instructions/
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