[PRE 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: v0.8.0
Editor: @will-rowe
Reviewers: @adRn-s, @aguang
Managing EiC: Kevin M. Moerman

⚠️ 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.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/450fa18f47932c5fd3b837edeac91440/status.svg)](https://joss.theoj.org/papers/450fa18f47932c5fd3b837edeac91440)

Author instructions

Thanks for submitting your paper to JOSS @kescobo. Currently, there isn't an JOSS editor assigned to your paper.

@kescobo if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ 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.

For a list of things I can do to help you, just type:

@whedon commands

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=0.05 s (741.6 files/s, 148387.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              2              2           4024
Julia                           10            282             53           1178
Markdown                        10            295              0            952
TeX                              1             17              0            180
YAML                             7              4             10            154
TOML                             4              4              0             46
-------------------------------------------------------------------------------
SUM:                            36            604             65           6534
-------------------------------------------------------------------------------


Statistical information for the repository '5aa6f9e15e63d2a740f5b4d1' was
gathered on 2021/10/21.
No commited files with the specified extensions were found.

[whedon]

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

[Kevin-Mattheus-Moerman]

@kescobo thanks for this submission. I will be helping to look for a handling editor.

@kescobo Note that in the readme for Microbiome.nl you point to: https://github.com/EcoJulia/BiobakeryUtils which gives a 404 error since the .jl part is missing, the correct URL seems to be: https://github.com/EcoJulia/BiobakeryUtils.jl

[Kevin-Mattheus-Moerman]

@whedon check repository https://github.com/EcoJulia/BiobakeryUtils.jl

[whedon]

Wordcount for paper.md is 963

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (457.9 files/s, 91615.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              2              2           4024
Julia                           10            282             53           1178
Markdown                        10            295              0            952
TeX                              1             17              0            180
YAML                             7              4             10            154
TOML                             4              4              0             46
-------------------------------------------------------------------------------
SUM:                            36            604             65           6534
-------------------------------------------------------------------------------


Statistical information for the repository 'c7bc34945e30b0a74b634f87' was
gathered on 2021/10/21.
No commited files with the specified extensions were found.

[Kevin-Mattheus-Moerman]

@openjournals/dev I think the above is for the Microbiome.jl package alone. Is there an easy way for me to also check the BiobakeryUtils.jl package? I tried the below but it seems to ignore the URL:

@whedon check repository https://github.com/EcoJulia/BiobakeryUtils.jl

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

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

OK DOIs

- 10.3390/nu13082833 is OK
- 10.3390/microorganisms9081608 is OK
- 10.1137/141000671 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
- 10.5334/jors.151 may be a valid DOI for title: Differentialequations.jl–a performant and feature-rich ecosystem for solving differential equations in julia

INVALID DOIs

- 10.3389/fmicb.2021.670336 is INVALID

[Kevin-Mattheus-Moerman]

@kescobo can you check these DOI's? ☝️ Note that if you'd like to update the paper you can call @whedon generate pdf, and you can also call @whedon check references.

[Kevin-Mattheus-Moerman]

@whedon invite @will-rowe as editor

[whedon]

@will-rowe has been invited to edit this submission.

[kescobo]

@Kevin-Mattheus-Moerman Thanks for getting this ball rolling! Just tagging my co-authors, @annelle-abatoni @anikaluo @vanjakle

Re: link in readme: fixed here

Re: DOIs:

• missing DOIs found by Whedon were correct - added here
• Invalid doi is bizarre - this is the paper, and the DOIs listed there match what's included here, but the links even from the publisher's website are invalid. I'll reach out to them to see what the issue is.

[kescobo]

@whedon check references

[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

[kescobo]

Unclear on the missing one - does this need to be in curly braces?

[Kevin-Mattheus-Moerman]

@kescobo I think that DOI looks fine. Our system for checking these isn't always correct. I'll inform @openjournals/dev about this one too in case it helps make the system better.

[Kevin-Mattheus-Moerman]

@will-rowe could you help edit this one?

[will-rowe]

Hi. Sorry for the delay. Yes, I can take it

[will-rowe]

Hi @Adrianzo and @aguang - would either of you be able to review this please?

[Kevin-Mattheus-Moerman]

@whedon assign @will-rowe as editor

[whedon]

OK, the editor is @will-rowe

[danielskatz]

👋 @will-rowe - if you want, you can always do this yourself when you agree to edit a paper

@whedon assign @will-rowe as editor

[kescobo]

Excellent, thanks @will-rowe!

[aguang]

Hi @Adrianzo and @aguang - would either of you be able to review this please?

Yes, I can review.

[adRn-s]

Nice paper!

@kescobo I couldn't find the docs

[will-rowe]

Thanks @aguang ! I'll find one more reviewer and then we will kick off the review process.

[will-rowe]

Hi @adRn-s - just on the off chance seeing as you've commented here, would you be willing to review this paper for JOSS?

[adRn-s]

Yes. Sorry for the misunderstanding, I'm no longer using the other account (@Adrianzo), but I got here because of the e-mail/ mention.

[kescobo]

Nice paper!

Thanks!

I couldn't find the docs

Oops! Looks like that link didn't get fixed - we recently moved from BioJulia to EcoJulia github org and those ones slipped through. Fixed here, but for easy reference:

• Microbiome docs: stable | latest
• BiobakeryUtils docs: stable | latest

"Stable" points to the docs for the latest release, and "latest" points to docs for the main branch, even if unreleased. Looking just now, the BiobakeryUtils stable version is actually pointing to very old docs, but "latest" is working correctly. I will investigate.

[kescobo]

Alright! Finally got the "stable" docs for BiobakeryUtils to build correctly.

@adRn-s and @aguang thanks for agreeing to review! It's up to you of course, but I suggest starting here in the docs

[adRn-s]

Great!

PS. I had some issue, but apparently it was my connectivity

[will-rowe]

Hi all. I'm having some Github difficulties with this thread for some reason. I will assign our reviewers and move this to a review issue. Thank you for agreeing to review and to @kescobo for getting the docs ready

[will-rowe]

@whedon assign @adRn-s as reviewer

[whedon]

OK, @adRn-s is now a reviewer

[will-rowe]

@whedon add @aguang as reviewer

[whedon]

OK, @aguang is now a reviewer

[will-rowe]

@whedon start review

[whedon]

OK, I've started the review over in #3876.