Login or Register to make a submission.

As part of the submission process, authors are required to check off their submission's compliance with all of the following items, and submissions may be returned to authors that do not adhere to these guidelines.

  • The submission has not been previously published, nor is it before another journal for consideration (or an explanation has been provided in Comments to the Editor).
  • The submission file is in OpenOffice, Microsoft Word, or RTF document file format.
  • Where available, URLs for the references have been provided.
  • The manuscript topic is within the journal focus and scope.
  • Original Papers (up to 14 pages; this is approx. 10000 words).
    Original papers that describe new research developments in agricultural and environmental studies. Actual biological data, as opposed to purely simulated data, must be used.

    Discovery Notes (up to 4 pages, this is approx. 3000 words)
    Discovery notes report biologically interesting discoveries. The results presented should present new discoveries, bringing insight to a relevant biological, agricultural or environmental problem, and not be the simple extension of current knowledge. The results are expected to proceed from the specialized use of tools, methods, and databases. The inclusion of experimental results is considered very positively.

    Application Notes (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure)
    Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). Software or data must be freely available to non-commercial users. Availability and Implementation must be clearly stated in the article. Authors must also ensure that the software is available for a full TWO YEARS following publication. Web services must not require mandatory registration by the user. Additional Supplementary data can be published online-only by the journal. This supplementary material should be referred to in the abstract of the Application Note. If describing software, the software should run under nearly all conditions on a wide range of machines. Web servers should not be browser specific. Application Notes must not describe trivial utilities, nor involve significant investment of time for the user to install. The name of the application should be included in the title.

    Reviews (3-8 pages)
    Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance submit a draft or abstract/summary no longer than a page.

    Letters to the Editor
    JAE publishes "letters to the editors" on the broad range of topics covered by the journal, including political, technical and scientific analyses of issues related to agriculture and environment. The letters can also include the discussion of papers published by the journal.

    Conference Papers
    JAE considers proposals for publishing conference proceeding papers, as supplementary issues or as special sections of the journal. Please be sure to include the following information in your proposal:
    What is the theme of the conference and submitted papers?
    What numbers of papers are expected to be submitted and published?
    What peer review process will be put in place by the conference organisers to recommend papers for publication in the journal?
    How many delegates are expected to attend the conference?
    Assurance that the papers proposed for publication have not and will not be published elsewhere prior to publication in JAE, or afterwards without the permission of the journal's publisher.
  • The text adheres to the stylistic and bibliographic requirements outlined in the Author Guidelines.
  • The manuscript is prepared in accordance with the template

We recommend to get ORCID and link it with DataCite Profiles before submitting a paper. Also please indicate ORCID on your profile within the journal, this will allow to track your publications and citations. How to get ORCID?


Papers must be clearly and concisely written in English and within the recommended length. In the interests of speed, manuscripts are not extensively copyedited and authors are requested to check their texts carefully before submitting them so that proofs will require only correction of typographical errors.

How to prepare text and figures

For guidelines on the types of documents that can be uploaded to the online submission system, please clickhere. Please use Word's "Save As" option to save your document as .doc or .docx file type. As publication is an olnine publication, please prepare your figures at web quality (72dpi); these versions of the figures can be saved in .jpg, .gif, .tif or .eps format. 

Sections of the manuscript

Please subdivide manuscripts into the following sequence of sections, according to the type of paper:

  • Original papers: Title page, Structured Abstract, Introduction, System and methods, Algorithm, Implementation, Discussion, References.

  • Reviews: May be in a format best suited to subject matter, but should include Title page, Structured Abstract, Text, References. For clarity the main body of text should be sub-divided into sections.

  • Applications notes: Title page, Short Structured Abstract, Text.

  • Discovery notes: The description of the analysis can be up to four pages long including one or two figures. Please include an abstract. Sequences must be freely available in the database and the results of the analyses should not have been published elsewhere.

Title page

The title should be short, specific and informative, avoiding if possible version number and the words: tool, package, application, software (and similar). If novel software is being described, the name of the software should be included in the title. The surname and initials of each author should be followed by his/her department, Institution, city with postal code and country. Any changes of address may be added to the footnotes. The author to whom offprint requests are to be sent should be indicated by an asterisk and the footnote 'To whom correspondence should be addressed'. Please provide a running head of not more than 50 characters.

Structured Abstract (see recent issues of journal for examples)

Original papers

Abstracts are structured with a standard layout such that the text is divided into sub-sections under the following five headings: Motivation, Results, Availability and Implementation, Contact and Supplementary Information. In cases where authors feel the headings inappropriate, some flexibility is allowed. The abstracts should be succinct and contain only material relevant to the headings. A maximum of 150 words is recommended. If internet hyperlinks are available for any part of the abstract, then this should be given in the form of 'clickable text', i.e.{{http://www...}}.

  • Motivation: This section should specifically state the scientific question within the context of the field of study.

  • Results: This section should summarize the scientific advance or novel results of the study, and its impact on computational biology.

  • Availability and Implementation: This section should state software availability if the paper focuses mainly on software development or on the implementation of an algorithm. Examples are: 'Freely available on the web at http://www.example_url.org.' Website implemented in Perl, MySQL and Apache, with all major browsers supported'; or 'Source code and binaries freely available for download at URL, implemented in C++ and supported on linux and MS Windows'. The complete address (URL) should be given. If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users. Authors must also ensure that the software is available for a full TWO YEARS following publication. The editors of encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples.

  • Contact: Full email address to be given, preferably an institution email address.

  • Supplementary information: Links to additional figures/data available on a web site, pr reference to online-only supplementary data available at the journal's web site.

Applications Notes

Abstracts for Applications Notes are much shorter than those for an Original Paper. They are structured with four headings: Summary, Availability and Implementation, Contact and Supplementary Information.

  • Summary: This section should summarize the purpose/novel features of the program in one or two sentences.

  • Availability and Implementation: See above for advice and examples for this section.

  • Contact: Full E-mail address to be supplied, preferably an institution address.

  • Supplementary information: Links to additional figures/data available on a web site, or reference to online-only Supplementary data available at the journal's web site.


These should be included at the beginning of the text right below the title. Please ensure you acknowledge all sources of funding, see funding section below.

Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear after the 'Acknowledgements' section.

Funding information

The following rules should be followed:

The sentence should begin: "This work was supported by" The full official funding agency name should be given, i.e. "National Institutes of Health", not "NIH" (full RIN-approved list of UK funding agencies) Grant numbers should be given in brackets as follows: "[grant number xxxx]". Multiple grant numbers should be separated by a comma as follows: "[grant numbers xxxx, yyyy]". Agencies should be separated by a semi-colon (plus "and" before the last funding agency). Where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number 'to [author initials]'.

An example is given here: This work was supported in part by the research grants: NIH 2 R01GM069430, NSFC81573253, NIHR03DE024198, NIH R01GM081488, NIH P60AR064172, NIH UL1TR001417, and NSF DMS‐1462990.


These should conform to standard scientific reporting style. Previous work in the field should be mentioned. Sufficient information should be given so that an application can be re-implemented. A test data set and results must be provided (where appropriate).

Authors are responsible for the accuracy of the References. Published articles and those in press (state the journal which has accepted them) may be included. In the text, a reference should be cited by author and date and enclosed by round brackets; not more than two authors may be cited per reference; if there are more than two authors use et al. References must NOT be numbered. At the end of the manuscript, the citations should be given in alphabetical order, with the author's surname followed by the initial. References should include in the following order: author, year, paper title, journal title, volume number, inclusive page numbers, doi. The name of the journal should be abbreviated according to the World List of Scientific Periodicals. Book references should also include the editors and the name and address of the publisher. References should therefore be listed as follows:

Personal communications (J.Smith, personal communication) should be authorized by those involved in writing, and unpublished data should be cited as (unpublished data). Both should be used as sparingly as possible and only when the unpublished data referred to is peripheral rather than central to the discussion. Personal communications, unpublished results, manuscripts submitted or in preparation, statistical packages, computer programs and web sites should be cited in the text only, NOT included in the References section. References to manuscripts accepted for publication but not yet published should be included in the reference list as 'in press'.

Examples are given here:

Journal article:

Absoud M., Cummins C., Lim M., Wassmer E., Shaw N. (2011). Prevalence and Predictors of Vitamin D Insufficiency in Children: A Great Britain Population Based Study. PLoS ONE, 6(7), e22179. doi: 10.1371/journal.pone.0022179


Hochberg, Y. & Tamhane, A. (1987). Multiple comparison procedures. New York: Wiley.

If the original source is in a foreign language title that is not in Roman script should be transliterated and the translation should be given in square brackets:

Ivanova, А.R., Nagimova, I.А., & Semenova К.А. (2016). Osobennosti upravlenija realizaciej investicionnyh proektov neftjanoj otrasli v sisteme jekonomicheskoj bezopasnosti predprijatija [The features of management the realisation investment projects electricity companies in the economic security system]. Meždunarodnyj naučno-issledovatel’skij žurnal, № 10 (52) Part 1, 25-29. http://dx.doi.org/10.18454/IRJ.2016.52.152


Tables should be embedded within the main document file and be numbered consecutively. Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables should be indicated in italic but should not include extensive experimental detail.


All figures should be embedded within the text inside the main document file and referred to in the text as Figure 1 etc. All figures should be formatted to fit into, or be reduced to, a single (86 mm) or double (178 mm) column width. Figure legends should appear adjacent to the relevant figure.

  • Web screen dumps: The editors prefer tables or figures instead of web screen dumps. All figures should have a white background to increase the contrast between the illustration and the background, so that the figure is easy to read.

  • Line illustrations: These must be of sufficient quality for publication as submitted, i.e. clear, sharp, clean and of even density. Figures will NOT be redrawn or relabelled. Any lettering or text should be in proportion with the rest of the figure.

  • Photographs: These must be of sufficient quality with respect to detail, contrast, and fineness of grain to withstand the unavoidable loss of contrast inherent in the printing process.


TEX-based manuscripts should be produced using the LATEX article style format only. The document style options used must indicate two-column text with 86 mm column widths.

English Language Editing

Language editing, if your first language is not English, to ensure that the academic content of your paper is fully understood by journal editors and reviewers is optional. Language editing does not guarantee that your manuscript will be accepted for publication.  

Copyright Notice

In order for JAE to publish and disseminate research articles, we need publishing rights. This is determined by a publishing agreement between the author and JAE. This agreement deals with the transfer or license of the copyright to JAE.

For subscription articles:

Authors transfer copyright to the publisher as part of a journal publishing agreement, but have the right to:

  • Retain patent, trademark and other intellectual property rights (including raw research data).

  • Proper attribution and credit for the published work.

For open access articles:

Authors sign an exclusive license agreement, where authors have copyright but license exclusive rights in their article to the publisher**. In this case authors have the right to:

  • Share their article in the same ways permitted to third parties under the relevant user license (together with Personal Use rights), the end user license, and a DOI link to the version of record on JAE website.

  • Retain patent, trademark and other intellectual property rights (including raw research data).

  • Proper attribution and credit for the published work.

The names and email addresses entered in this journal site will be used exclusively for the stated purposes of this journal and will not be made available for any other purpose or to any other party.