[REVIEW]: Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides

[editorialbot]

Submitting author: @oleksulkowski (Aleksander Sułkowski)
Repository: https://github.com/oleksulkowski/Syn-CpG-Spacer
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @fboehm
Reviewers: @babinyurii, @KatyBrown
Archive: 10.5281/zenodo.10781374

Status

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Markdown: [![status](https://joss.theoj.org/papers/1edc7b46400b5b662030a231288cef97/status.svg)](https://joss.theoj.org/papers/1edc7b46400b5b662030a231288cef97)

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Checklists

📝 Checklist for @babinyurii

📝 Checklist for @KatyBrown

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (199.8 files/s, 179853.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1           1802              2           6393
Python                           2            175             77           1320
JavaScript                       2            175              0           1230
TeX                              1             10              0            162
SVG                              1              0              0            139
Markdown                         2             42              0             88
YAML                             3              8              4             46
JSON                             1              0              0             32
-------------------------------------------------------------------------------
SUM:                            13           2212             83           9410
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 697

[editorialbot]

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

OK DOIs

- 10.1146/annurev-virology-091919-104213 is OK
- 10.1186/1756-0500-5-50 is OK
- 10.18129/B9.bioc.SynMut is OK
- 10.1371/journal.ppat.1000079 is OK
- 10.1042/BST20200695 is OK
- 10.1128/spectrum.02529-23 is OK
- 10.1371/journal.ppat.1011357 is OK
- 10.7554/eLife.12735 is OK
- 10.1038/s41564-022-01223-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[babinyurii]

Review checklist for @babinyurii

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/oleksulkowski/Syn-CpG-Spacer?

• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?

• Contribution and authorship: Has the submitting author (@oleksulkowski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.

• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[KatyBrown]

Hi, sorry to be slow, I should be able to look at this on Friday.

[fboehm]

Hi, sorry to be slow, I should be able to look at this on Friday.

No problem, @KatyBrown . Please let us know if you encounter any difficulties as you work through the review.

[fboehm]

@babinyurii - thank you for the thorough review. It looks like you have left unchecked a couple of the review checklist items. Are there associated tasks or edits needed from teh authors before you can check these last items? Or did you just now have time yet to assess them?

[babinyurii]

Hi, @fboehm !
I've left unchecked Functionality documentation. I think docstring are needed in the index.py at least describing the classes and other objects.

Should I address other issues here which are not covered by these checkboxes? I've got some.

[KatyBrown]

Review checklist for @KatyBrown

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/oleksulkowski/Syn-CpG-Spacer?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@oleksulkowski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[fboehm]

Hi, @fboehm ! I've left unchecked Functionality documentation. I think docstring are needed in the index.py at least describing the classes and other objects.

Should I address other issues here which are not covered by these checkboxes? I've got some.

Thank you @babinyurii - yes, please do offer suggestions that may improve the product. Please feel free to open new issues on the software repo's github page to describe the issues and offer suggestions.

[KatyBrown]

Hi, @fboehm ! I've left unchecked Functionality documentation. I think docstring are needed in the index.py at least describing the classes and other objects.

I agree with this and similarly comments would be useful in the JS wrapper in index.js

[KatyBrown]

I'm not sure if this is outside of my scope as a reviewer, but I think it would be preferable to read the code in index.py - either directly or into a string - and then process this within index.js, if that's possible, rather than pasting it across. It seems risky to have to remember to paste the code and it brings the Python code which is actually running outside of the CI testing.

[oleksulkowski]

Hi @KatyBrown, thank you for your feedback. The code in index.py is transferred to index.js when panel convert index.py --to pyodide-worker --out docs/app --title Syn-CpG-Spacer --pwa is run. If you want, I can emphasise that this command must always be run after changes are made to index.py in the "Development" section on the repository page.

@babinyurii could you please share the other issues? I will start working on your suggestions then.

[KatyBrown]

Hi @KatyBrown, thank you for your feedback. The code in index.py is transferred to index.js when panel convert index.py --to pyodide-worker --out docs/app --title Syn-CpG-Spacer --pwa is run. If you want, I can emphasise that this command must always be run after changes are made to index.py in the "Development" section on the repository page.

@oleksulkowski apologies, I missed that - in that case I think it’s fine as it is.

[KatyBrown]

I’d just like a last quick look through tomorrow - I’ll comment when I’m done.

[KatyBrown]

@fboehm OK, my review is complete now. Apart from extending the in-code documentation as @babinyurii discussed above, I think it looks good and meets all the requirements. It will be a useful tool and is well written and documented.

[fboehm]

Thank you, @KatyBrown! @babinyurii - did you have a chance to open issues in the software repository? If so, can you link to the issues in this thread? Thanks again!

[babinyurii]

Here are the links to the issues:
oleksulkowski/Syn-CpG-Spacer#1

oleksulkowski/Syn-CpG-Spacer#4

oleksulkowski/Syn-CpG-Spacer#5

[fboehm]

@oleksulkowski - do you have questions about the issues and how to resolve them? Please feel free to link here to your proposed resolutions for the issues. And please let me know if you have any questions.

Thanks :)

[oleksulkowski]

Hi, @babinyurii @KatyBrown, I have applied changes based on your suggestions - could you please check the issue pages and referenced commits?

I added the docstrings in commit oleksulkowski/Syn-CpG-Spacer@dc58e2a

[babinyurii]

Hi, @oleksulkowski ! Everything is ok. I've closed the issues.

[fboehm]

@oleksulkowski - are you using the proper citation for Bokeh? I found this: https://docs.bokeh.org/en/1.0.4/docs/citation.html#:~:text=To%20cite%20Bokeh%20in%20publications,.bokeh.pydata.org.

It looks my link here is to an older version, maybe, of Bokeh? It seems like the citation in your pdf should include which version you use, too.

[fboehm]

@oleksulkowski - I can't quickly find another way to cite Progressive Web Apps, so, unless you know of one, we can leave it as is... although, if it has a version number, or a date on which you downloaded it or used it, you might want to add that to the citation.

[oleksulkowski]

I changed the Bokeh reference to include the version we used now. Regarding the PWA reference, the date accessed is there in the paper.bib file (urldate) but I think that the JOSS compiler doesn't show it on the pdf.

[fboehm]

I changed the Bokeh reference to include the version we used now. Regarding the PWA reference, the date accessed is there in the paper.bib file (urldate) but I think that the JOSS compiler doesn't show it on the pdf.

Excellent, @oleksulkowski !

[fboehm]

@editorialbot check references

[fboehm]

@editorialbot generate pdf

[fboehm]

@editorialbot commands

[editorialbot]

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

OK DOIs

- 10.1146/annurev-virology-091919-104213 is OK
- 10.1186/1756-0500-5-50 is OK
- 10.18129/B9.bioc.SynMut is OK
- 10.1371/journal.ppat.1000079 is OK
- 10.3389/fimmu.2019.01250 is OK
- 10.1042/BST20200695 is OK
- 10.1128/spectrum.02529-23 is OK
- 10.1371/journal.ppat.1011357 is OK
- 10.7554/eLife.12735 is OK
- 10.1038/s41564-022-01223-8 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.5281/zenodo.8378122 is OK
- 10.5281/zenodo.10563859 is OK

MISSING DOIs

- No DOI given, and none found for title: Bokeh: Python library for interactive visualizatio...
- No DOI given, and none found for title: Progressive web apps

INVALID DOIs

- None

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[editorialbot]

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

[fboehm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1146/annurev-virology-091919-104213 is OK
- 10.1186/1756-0500-5-50 is OK
- 10.18129/B9.bioc.SynMut is OK
- 10.1371/journal.ppat.1000079 is OK
- 10.3389/fimmu.2019.01250 is OK
- 10.1042/BST20200695 is OK
- 10.1128/spectrum.02529-23 is OK
- 10.1371/journal.ppat.1011357 is OK
- 10.7554/eLife.12735 is OK
- 10.1038/s41564-022-01223-8 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.5281/zenodo.8378122 is OK
- 10.5281/zenodo.10563859 is OK

MISSING DOIs

- No DOI given, and none found for title: Bokeh: Python library for interactive visualizatio...
- No DOI given, and none found for title: Progressive web apps

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5192, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@oleksulkowski as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Everything seems in order, I only have the below point that requires your attention:

• Most of your text in the paper features British English, except for optimizing and utilizing, you may consider editing these to be consistent.

[oleksulkowski]

Thanks @Kevin-Mattheus-Moerman, it's fixed now.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@oleksulkowski Everything seems to be in order so we will now proceed to process this work for acceptance.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Sulkowski
  given-names: Aleksander
  orcid: "https://orcid.org/0000-0002-0624-428X"
- family-names: Bouton
  given-names: Clément
  orcid: "https://orcid.org/0000-0001-9607-6533"
- family-names: Swanson
  given-names: Chad
  orcid: "https://orcid.org/0000-0002-6650-3634"
contact:
- family-names: Sulkowski
  given-names: Aleksander
  orcid: "https://orcid.org/0000-0002-0624-428X"
doi: 10.5281/zenodo.10781374
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sulkowski
    given-names: Aleksander
    orcid: "https://orcid.org/0000-0002-0624-428X"
  - family-names: Bouton
    given-names: Clément
    orcid: "https://orcid.org/0000-0001-9607-6533"
  - family-names: Swanson
    given-names: Chad
    orcid: "https://orcid.org/0000-0002-6650-3634"
  date-published: 2024-04-03
  doi: 10.21105/joss.06332
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6332
  title: "Syn-CpG-Spacer: A Panel web app for synonymous recoding of
    viral genomes with CpG dinucleotides"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06332"
  volume: 9
title: "Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral
  genomes with CpG dinucleotides"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06332 joss-papers#5202
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06332
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@oleksulkowski congratulations on this publication !!

@fboehm Thank you for editing this one!

And a special thanks to the reviewers: @babinyurii, @KatyBrown !!! 🥳

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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