[REVIEW]: gesel: a JavaScript package for client-side gene set enrichment

[editorialbot]

Submitting author: @LTLA (Aaron Lun)
Repository: https://github.com/LTLA/gesel.js
Branch with paper.md (empty if default branch): submission
Version: 0.3.3
Editor: @arfon
Reviewers: @majensen, @bede
Archive: 10.5281/zenodo.10032294

Status

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Markdown: [![status](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400/status.svg)](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@majensen & @bede, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @majensen

📝 Checklist for @bede

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1933.7 files/s, 134711.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      31            279            372           1349
Markdown                         2             75              0            323
TeX                              1             13              0            129
YAML                             3             20              1             93
JSON                             2              0              0             63
-------------------------------------------------------------------------------
SUM:                            39            387            373           1957
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1186/1471-2105-14-128 is OK
- 10.1093/bioinformatics/btr260 is OK
- 10.1038/75556 is OK
- 10.1101/2022.03.02.482701 is OK
- 10.1093/bioinformatics/btaa591 is OK
- 10.1073/pnas.0506580102 is OK
- 10.1093/nar/gks461 is OK
- 10.1186/gb-2010-11-2-r14 is OK
- 10.1101/060012 is OK
- 10.1093/nar/gkm323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 2541

[arfon]

@majensen, @bede – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5777 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[LTLA]

Thanks to all for getting involved in this. We've added some more functionality to gesel in the meantime (including a fun little visualization of all gene sets on a t-SNE), but we'll give everyone a chance to read the current manuscript first.

[arfon]

Friendly reminder @majensen & @bede to get started on your reviews soon please.

[majensen]

@editorialbot generate pdf

[majensen]

@editorialbot create checklist

[majensen]

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[majensen]

Review checklist for @majensen

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/LTLA/gesel.js?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@LTLA) 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?

[editorialbot]

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

[majensen]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1186/1471-2105-14-128 is OK
- 10.1093/bioinformatics/btr260 is OK
- 10.1038/75556 is OK
- 10.1101/2022.03.02.482701 is OK
- 10.1093/bioinformatics/btaa591 is OK
- 10.1073/pnas.0506580102 is OK
- 10.1093/nar/gks461 is OK
- 10.1186/gb-2010-11-2-r14 is OK
- 10.1101/060012 is OK
- 10.1093/nar/gkm323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[bede]

Review checklist for @bede

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/LTLA/gesel.js?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@LTLA) 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?

[bede]

Hi @LTLA, I didn't find any community guidelines. Would you either point me to them or add them? Thank you.

[LTLA]

Hi @bede, done: https://github.com/LTLA/gesel.js/blob/master/CONTRIBUTING.md

[bede]

Excellent, thank you!

[majensen]

@LTLA - looks like the rendered paper is missing the Subramaniam 2005 ref and the Lun & Manchera 2023 (or is it 2022?). Can you have a look?

[majensen]

(Is that ref this guy: https://pubmed.ncbi.nlm.nih.gov/15980550/ ?)

[LTLA]

@majensen not sure what you mean. The latest rendering has both references on the last page:

I took the liberty of updating Lun and Kancherla reference, given that #5603 has been accepted (yay).

[Kevin-Mattheus-Moerman]

@LTLA I am the EiC in this track and here to help with final steps. I have checked this review, your repository, the paper, and the archive link. Most seems in order, I only have the below points which require your attention:

• In your affiliations, please spell out USA as United States of America
• The reference for Visualizing data using t-SNE does not have a DOI. I also was not able to find one manually so leaving out a DOI is fine. However I did find this link: https://jmlr.org/papers/v9/vandermaaten08a.html, which shows that the number field in the bib file entry is wrong (currently 11, should be 86), and that the page numbers are missing. Furthermore, perhaps the URL link can be added. In short, could you consider updating your bib file for this reference to have the following:

@article{van2008visualizing,
  author  = {Laurens van der Maaten and Geoffrey Hinton},
  title   = {Visualizing Data using t-SNE},
  journal = {Journal of Machine Learning Research},
  year    = {2008},
  volume  = {9},
  number  = {86},
  pages   = {2579--2605},
  url     = {http://jmlr.org/papers/v9/vandermaaten08a.html}
}

[LTLA]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@LTLA looks like you made the requested changes. Can you confirm you are happy to proceed to processing this for final acceptance?

[LTLA]

Yep, happy to proceed.

[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: Lun
  given-names: Aaron T. L.
  orcid: "https://orcid.org/0000-0002-3564-4813"
- family-names: Kancherla
  given-names: Jayaram
  orcid: "https://orcid.org/0000-0001-5855-5031"
doi: 10.5281/zenodo.10032294
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lun
    given-names: Aaron T. L.
    orcid: "https://orcid.org/0000-0002-3564-4813"
  - family-names: Kancherla
    given-names: Jayaram
    orcid: "https://orcid.org/0000-0001-5855-5031"
  date-published: 2023-10-24
  doi: 10.21105/joss.05777
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5777
  title: "gesel: a JavaScript package for client-side gene set
    enrichment"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05777"
  volume: 8
title: "gesel: a JavaScript package for client-side gene set enrichment"

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.05777 joss-papers#4721
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05777
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...

[bede]

Congratulations 🎉

[LTLA]

Thanks all!

[Kevin-Mattheus-Moerman]

@LTLA congratulations on this JOSS publication!

Thanks @arfon for editing, and a special thanks to the reviewers: @majensen, @bede

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.05777/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05777/status.svg
   :target: https://doi.org/10.21105/joss.05777

This is how it will look in your documentation:

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[LTLA]

@Kevin-Mattheus-Moerman Don't know whether this is the most appropriate place to mention this, but I notice that my name doesn't show up properly on the JOSS website (note the lack of capitalization on the L):

Clicking on the link on my name takes me here:

This seems to have some implications for indexers, e.g., Google scholar reports:

I'm guessing it's my two initials that's causing the system to throw a fit. The same problem with the links is observed for my two other papers on JOSS:

• https://joss.theoj.org/papers/10.21105/joss.04742
• https://joss.theoj.org/papers/10.21105/joss.05603

[majensen]

@openjournals/dev : is the below in your domain?

@Kevin-Mattheus-Moerman Don't know whether this is the most appropriate place to mention this, but I notice that my name doesn't show up properly on the JOSS website (note the lack of capitalization on the L):

Clicking on the link on my name takes me here:

This seems to have some implications for indexers, e.g., Google scholar reports:

I'm guessing it's my two initials that's causing the system to throw a fit. The same problem with the links is observed for my two other papers on JOSS:

• https://joss.theoj.org/papers/10.21105/joss.04742

• https://joss.theoj.org/papers/10.21105/joss.05603

[arfon]

@LTLA – for your name to appear properly, I think we'll need you to follow this guide to update your paper.md to be more explicit about the structure of your name: https://joss.readthedocs.io/en/latest/submitting.html#article-metadata

The error clicking the link on the JOSS site is an unrelated bug.

[LTLA]

Thanks @arfon, just updated paper.md with my full name ("Aaron Tin Long Lun"). Hopefully the heuristics will be smart enough to do the initialization of the multiple middle names properly this time; otherwise, suggestions are welcome.

[LTLA]

@arfon do I need to run an @editorialbot command here to propagate the fix?

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4924

[arfon]

@LTLA – does this look better to you now?

[LTLA]

Thanks @arfon, looks good. Should I proceed to update the other two affected papers?

[arfon]

Thanks @arfon, looks good. Should I proceed to update the other two affected papers?

Please do. And if you could directly mention me on those reviews that would be very helpful. Thanks!