[PRE REVIEW]: The Pep Genie: a Django Application for Swift Automation of Peptide Array Data Analysis

[editorialbot]

Submitting author: @thomas-wright-bioinformatics (Thomas Wright)
Repository: https://github.com/thomas-wright-bioinformatics/pep_genie.git
Branch with paper.md (empty if default branch):
Version: v4.3
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3791/52097 is OK
- 10.1039/c0cs00029a is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.yjmcc.2022.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (937.4 files/s, 103069.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            477            365           1148
HTML                            15            450            244            889
JavaScript                       2             64             36            219
Markdown                         2             79              0            145
TeX                              1              4              0             62
CSS                              1             15             15             53
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            39           1090            664           2534
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 941

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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[Kevin-Mattheus-Moerman]

@thomas-wright-bioinformatics thanks for this submission. I am the AEiC and here to help process initial steps. I have just flagged this work with the query-scope label. This is because I need some help from the editorial board to determine if this work is in scope for JOSS. This scope review will take about 2 weeks to complete.

[thomas-wright-bioinformatics]

Hi @Kevin-Mattheus-Moerman,

Thank you for processing my submission. May I ask, what about the project may be out of scope? Thank you again.

[Kevin-Mattheus-Moerman]

@thomas-wright-bioinformatics I have triggered the scope review because the core functionality seems to be captured by around 1148 lines of Python, which is rather small. Furthermore, being a "website application" it may be that this is seen as a "utility tool", rather than pure research software. Hence, I need some help to determine if this work is in scope. Essentially the team, especially those in the bioinformatics space (which is not me), will need to judge if this work is substantial enough and is more than a utility tool in terms of scientific research functionality (For more on this see our: substantial scholarly effort criteria).

Hope this answers your question.

[thomas-wright-bioinformatics]

Hi @Kevin-Mattheus-Moerman ,

Thank you for letting me know.

This may not be relevant to the editorial board's decision, but in case this is information is helpful, I'd like to comment about the criteria of significant scholarly effort.

• The Pep Genie offers a solution to the challenge of peptide array analysis that saves considerable time and effort. This automation also makes array screening accessible to a wider research base who may not have the technical experience necessary.
• Even though The Pep Genie is not a very large project, it is an efficient, tailored and innovative solution to address the opaque format and arduousness of manual analysis, something which hinders application and wider adoption of peptide array technology.
• The data generated by the application is a central part of several projects that are nearing publication in our group. One project in particular is in collaboration between our lab in University of Glasgow and Imperial College London which looks to reach quite high impact. The Pep Genie is currently being used by other groups at University of Glasgow, University of Edinburgh, University of Oslo, and University of Aberdeen. We have a large network of collaborators who are interested in peptide arrays, and by The Pep Genie allowing these collaborators to independently analyse their data, we have more time to begin collaboration with more groups and facilitate progress in their projects.
• Although The Pep Genie is recently released, it will have a significant role in these new projects. I have dedicated a substantial amount of time to develop this application and I would like to be able to gain some recognition for the benefit it has provided and continues to provide in future, particularly in the form of citations, which are unfortunately the currency needed to secure a career in my field. I believe this is in direct alignment with the reason why JOSS was established.

I hope that gives more context for your decision. Thank you very much for your consideration.

[thomas-wright-bioinformatics]

Hi @Kevin-Mattheus-Moermann and editors,

Thank you in advance for your time spent reviewing my submission. In regard to the size of the application, I'd like to mention that the core functionality of 'grid drawing' to obtain grid coordinates by user input makes use of a combination of html and javascript for div positioning and measurement. This information is then passed to the python code in the back end. Because of this, a considerable proportion of the html and javascript code is also part of the functionality, and not just the python files.

Thanks again.

[Kevin-Mattheus-Moerman]

@thomas-wright-bioinformatics apologies for the delays so far. With the holidays (and the start of semester for many) things have been slower than usual. We hope to conclude the scope review within a week.

[thomas-wright-bioinformatics]

Hi @Kevin-Mattheus-Moerman, no worries, thank you for the update!

[Kevin-Mattheus-Moerman]

@thomas-wright-bioinformatics thanks for your patience. The editorial board has concluded the scope review. Unfortunately this work is not deemed in scope as it stands. The main conclusion was that it is out of scope due to its relatively small size. In additional the functionality seems largely confined to visualisation.

Given this work is not deemed in scope we will now proceed to reject this submission.

Note that this conclusion does not mean the work is of a poor quality, or not useful, it merely means that based on size and functionality it is currently out of scope.

We hope you will consider JOSS for any future (re)submission that are of a more substantial nature (in addition we would recommend that any such future submissions should include extensive testing as well).

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.