Publication on MEE: complete checklist

[Giappo]

These are the rules for an initial submission on MEE (from here):

Quick Checklist for initial submission

To simplify the process for authors we differentiate between initial and revised submissions. Initial submissions can be submitted in any file type providing they adhere to the following requirements:

• [x] Single column, double line spaced
• [x] Within the word count (6000-7000 words for Standard Articles, 3000 words for Applications)
• [x] Continuous line and page numbering throughout
• [x] Clearly defined manuscript structure as standard: Author details, Abstract (must be numbered according to Manuscript Specifications), Keywords, Introduction, Materials and Methods, Results, Discussion, Figures and Tables with captions
• [x] Figures and Tables can be embedded within the text where referenced to facilitate reviewing
• [x] Statement of where you intend to archive your data

If you are asked to submit a revision you must comply with the full manuscript specifications below.

Article types (mutually exclusive)

• [x] Research article: should have a maximum of 6000-7000 words (including tables/figure captions and references) and describe new methods and how they may be used. We place emphasis on methods that are applicable as broadly as possible. Papers describing methods that apply to one species or system are unlikely to meet these criteria, unless authors are able to show that their methods can be generalised. Structure: see Manuscript specifications below.

• [ ] Application: Short (up to 3000 words) descriptions of new software that are intended to describe and promote the software as well as act as a citeable resource for developers. Application papers are made free to access for all readers upon publication in order to encourage uptake of the methodologies they describe. Uploading a package to a site such as CRANor sourceforge in advance is not considered prior publication and will not hinder your submission to MEE. View our previously published Applications here.

Manuscript specifications

Submissions should be divided into the following sections:

• [x] Title Page

It should include:

• [x] A concise and informative title. Do not include the authorities for taxonomic names.

• [x] A list of all authors' names with names and addresses of Institutions.

• [x] The name, address and e-mail address of the correspondence author.

• [x] A running headline of not more than 45 characters.

• [x] Abstract

• [x] The Abstract must not exceed 350 words and should list the main results and conclusions, using simple, factual, numbered statements:

• [x] Point 1: set the context for and purpose of the work;

• [x] Point 2: indicate the approach and methods;

• [x] Point 3: outline the main results;

• [x] Point 4: identify the conclusions and the wider implications.

• [x] Key-words

• [x] A list in alphabetical order not exceeding eight words or short phrases. The most important key-words should appear in the title and the abstract as well as the key-word list. More advice on selecting good keywords can be found here.

• [x] Introduction

This should state the reason for doing the work, the nature of the hypothesis or hypotheses under consideration, and should outline the essential background.

• [x] Materials and Methods (we called it "Description", as in Babette's paper)

Include sufficient details for the work to be repeated. Where specific equipment and materials are named, the manufacturer’s details (name, city and country) should be given so that readers can trace specifications by contacting the manufacturer. Where commercially available software has been used, details of the supplier should be given in brackets or the reference given in full in the reference list. Do not describe or refer to commonplace statistical tests in this section but allude to them briefly in Results.

• [x] Results (this is included in section "Usage")

State the results and draw attention in the text to important details shown in tables and figures.

• [x] Discussion

This should point out the significance of the results in relation to the reasons for doing the work, and place them in the context of other work.

• [x] Acknowledgements (optional)

A brief statement acknowledging collaborators and research assistants who do not meet the criteria for authorship described above, or acknowledging funding sources, providing relevant permit numbers (including institutional animal use permits), or giving recognition to nature reserves or other organizations that made the work possible.

• [x] Authors’ contributions

All submissions with more than one author must include an Authors’ contributions statement. All persons listed as authors on a paper are expected to meet ALL of the following criteria for authorship:

substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data, or drafting the article or revising it critically for important intellectual content; final approval of the version to be published; agreement to be accountable for the aspects of the work that they conducted and ensuring that questions related to the accuracy or integrity of any part of their work are appropriately investigated and resolved. Acquisition of funding, provision of facilities, or supervising the research group of authors without additional contribution are not usually sufficient justifications for authorship. The statement should include an explanation of the contribution of each author. We suggest the following format for the Authors’ contributions statement:

AB and CD conceived the ideas and designed methodology; CD and EF collected the data; EF and GH analysed the data; AB and CD led the writing of the manuscript. All authors contributed critically to the drafts and gave final approval for publication.

• [x] Data Availability

To enable readers to locate archived data from papers, we require that authors list the database and the respective accession numbers or DOIs for all data from the manuscript that has been made publicly available. For example, “Data available from the Dryad Digital Repository http://dx.doi.org/10.5061/dryad.41qh7 (Kiere & Drummond 2016).” When a DOI is available for the data, the full data citation should also be given in the reference list. See below. Please see our editorial policies page for further information

• [x] References

In text citations should follow the author-date method whereby the author's last name and the year of publication for the source should appear in the text, for example, (Jones, 1998). The complete reference list should appear alphabetically by name at the end of the paper. Please note that a DOI should be provided for all references where available.

[Giappo]

Word count: 3952 + ~500 (captions/figures etc)

[Giappo]

:heavy_check_mark: Article type: I think it is unrealistic to cut 1000+ words. So I suggest we go for Research Article.

[Giappo]

References: The guidelines explicitly state that "a DOI should be provided for all references where available." In our bibliography DOIs are not reported. I tried to add one but the compiler does not add it to the pdf. I also saw that babette's paper by @richelbilderbeek actually features them. Can you tell me how you did it? In case, I can look for and add all the DOIs we need.

[Giappo]

:heavy_check_mark: Data Availability: The application form states: "As a condition for publication, our Data archiving policy requires that all data supporting the results in a paper should be archived in an appropriate public archive. For theoretical papers the underlying model code must be archived. Please indicate your intention to archive by selecting one of the options below:" Since our work is theoretical our "data" is actually the code. In section 6 "pirouette resources" we explicitly refer to the public github repo. So this should be ok.

[richelbilderbeek]

The guidelines explicitly state that "a DOI should be provided for all references where available." I also saw that babette's paper by @richelbilderbeek actually features them. Can you tell me how you did it? In case, I can look for and add all the DOIs we need.

I uploaded a zipped babette release at Zenodo. I remember that this went very smooth!

[Giappo]

The guidelines explicitly state that "a DOI should be provided for all references where available." I also saw that babette's paper by @richelbilderbeek actually features them. Can you tell me how you did it? In case, I can look for and add all the DOIs we need.

I uploaded a zipped babette release at Zenodo. I remember that this went very smooth!

Sorry Richèl, I am not sure I get what you mean by that. Do you mind to send me the latex source code of babette plus the bibliography? I can just build the references for pirouette article in the same way you did it there...

[richelbilderbeek]

The babette article source can be found at the babette_article GitHub (of course :smile:).

At releases you'll see:

I did that by creating a new release for the article. Creating a new release:

Click here:

Then click here:

I hope that helps :+1:

[Giappo]

Ok, @richelbilderbeek, I think I understood where is the problem. The DOI for babette is not hard to find, even without Zenodo. It's here, on the first line: https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.13032 My problem is that I would like to add a DOI to every reference in the bibliography, which is something you already did for babette (see bibliography in the link). The question is: did you add yourself all the DOIs or did the journal add them it for you? Because in the .bib file in the babette_article repo I cannot find any. I've seen this Zenodo thing, and it doesn't look like it can help in doing this. Am I wrong?

[richelbilderbeek]

The question is: did you add yourself all the DOIs or did the journal add them it for you?

The journal added these for me, I only sent them the DOI of the (released version's zip file of the) article.

I think that means less work for you than you thought :+1:

[Giappo]

Great! :rainbow:

So now I am just waiting for Rampal to revise the cover letter and I think we can proceed with the submission.

[richelbilderbeek]

It's submitted and we are working on the response letter of this day. Well done! Closing this Issue!