[REVIEW]: Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data

[whedon]

Submitting author: @kescobo (Bonham, Kevin)
Repository: https://github.com/EcoJulia/Microbiome.jl
Version: v0.8.2
Editor: @will-rowe
Reviewer: @adRn-s, @aguang
Archive: 10.5281/zenodo.5682344

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Review checklist for @adRn-s

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@kescobo) 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

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 and who the target audience is?
• 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?

Review checklist for @aguang

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@kescobo) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @adRn-s, @aguang it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 963

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (654.1 files/s, 130989.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              2              2           4026
Julia                           10            282             53           1178
Markdown                        10            296              0            953
TeX                              1             17              0            182
YAML                             7              4             10            154
TOML                             4              4              0             46
-------------------------------------------------------------------------------
SUM:                            36            605             65           6539
-------------------------------------------------------------------------------


Statistical information for the repository 'ae19e4e1828a385fdaef2501' was
gathered on 2021/11/02.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.3390/nu13082833 is OK
- 10.3390/microorganisms9081608 is OK
- 10.3389/fmicb.2021.670336 is OK
- 10.1186/s13059-017-1359-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/joss.03349 is OK
- 10.7554/eLife.65088 is OK
- 10.5281/zenodo.5566503 is OK

MISSING DOIs

- 10.1186/s13059-017-1359-z may be a valid DOI for title: Experimental design and quantitative analysis of microbial community multiomics

INVALID DOIs

- None

[whedon]

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

[kescobo]

Co-authors: @annelle-abatoni @anikaluo @vanjakle

[aguang]

I have finished my review and think the package and paper are a nice contribution to the EcoJulia ecosystem. The documentation is overall solid, I've made a few suggestions to the documentation based on my attempts to run some of the functions on my own data, but those are only suggestions rather than necessary revisions. Nice job, I look forward to trying this package out more extensively soon.

[adRn-s]

It has been an honor for me to be a reviewer for this software. I have made some suggestions in their respective repositories, and all have positively been taken into account. The core functionality of both packages is in perfect condition. I look forward to seeing these software libraries grow into the whole framework functionality that EcoJulia has to offer.

I would like to take the opportunity to urge that more diversity metrics (alpha and beta) be incorporated. Then, this could include measures of computational efficiency that the Julia language provides as a modern basis. This way, benchmark comparisons to other software suits could be made. Of course, these are not requirements to approve the publication of your scientific article.

For my part, as a JOSS reviewer, I suggest to the editors that they accept this work as is.

Congratulations to all the authors, keep up with the good work!

[kescobo]

Thanks @adRn-s and @aguang for the thoughtful reviews and suggestions! I am working on a number of the suggested changes here.

I would like to take the opportunity to urge that more diversity metrics (alpha and beta) be incorporated. Then, this could include measures of computational efficiency that the Julia language provides as a modern basis.

There's been some discussion in the #ecology stream on zulip about incorporating Diversity.jl, which may end up being an even better solution. I think either pulling Diveristy.jl in as a dependency or just making sure CommunityProfiles play nicely, and maybe adding some examples to the doc. I've opened EcoJulia/Microbiome.jl#117 to keep track, and see also EcoJulia/EcoBase.jl#22

[kescobo]

@will-rowe Can you chime in with next steps here?

@adRn-s you didn't check off the "performance" or "state of the field" items in your review - were there specific comments you had on that front?

[will-rowe]

Hi @kescobo. Thanks for the ping and sorry for the delay.

Thanks to @aguang and @adRn-s for some excellent reviews. Given both have recommended acceptance, I'm happy to move forward. (That being said if you can respond @adRn-s regarding the two unchecked boxes, that would be great).

Let me give it another check over and then we can move on to acceptance.

[will-rowe]

@whedon generate pdf

[whedon]

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

[will-rowe]

Looks good to me.

@kescobo - can you please create a new tagged release and archive it (in zenodo) and then post back here with the version number and archive DOI

[kescobo]

@will-rowe

• Microbiome.jl
  • v0.8.2
  • doi: 10.5281/zenodo.5682344
• BiobakeryUtils.jl
  • v0.5.4
  • doi: 10.5281/zenodo.5682350

[will-rowe]

Hi @kescobo. I'm afraid the author list on the zenodo repository needs to match that of your paper - would you mind updating them?

[kescobo]

Ah, no sweat. Should be set @will-rowe

[will-rowe]

Great - thanks! All looks good to me. The one thing I'd say is that I've not come across a JOSS paper with 2 repositories/archives associated with the paper. I'll tag this submission with the Microbiome.jl archive but the EiC may have some suggestion on how this is usually handled.

[will-rowe]

@whedon set 10.5281/zenodo.5682344 as archive

[whedon]

OK. 10.5281/zenodo.5682344 is the archive.

[will-rowe]

@whedon set v0.8.2 as version

[whedon]

OK. v0.8.2 is the version.

[will-rowe]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3390/nu13082833 is OK
- 10.3390/microorganisms9081608 is OK
- 10.3389/fmicb.2021.670336 is OK
- 10.1186/s13059-017-1359-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/joss.03349 is OK
- 10.7554/eLife.65088 is OK
- 10.5281/zenodo.5566503 is OK

MISSING DOIs

- 10.1186/s13059-017-1359-z may be a valid DOI for title: Experimental design and quantitative analysis of microbial community multiomics

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2750

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2750, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kescobo]

PDF looks good to me! Thanks again everyone :-)

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03876 joss-papers#2755
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03876
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...

[arfon]

@adRn-s, @aguang – many thanks for your very speedy reviews here and to @will-rowe for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@kescobo – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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