[REVIEW]: A Data Carpentry- Style Metagenomics Workshop

[whedon]

Submitting author: @nselem (Nelly Selem)
Repository: https://github.com/carpentries-lab/metagenomics-workshop
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @JasonJWilliamsNY
Reviewers: @enkera
Archive: 10.5281/zenodo.8306876
Paper kind: learning module

Status

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HTML: <a href="https://jose.theoj.org/papers/0b49e5dbfe3fadb4743408dc3d6fb99f"><img src="https://jose.theoj.org/papers/0b49e5dbfe3fadb4743408dc3d6fb99f/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/0b49e5dbfe3fadb4743408dc3d6fb99f/status.svg)](https://jose.theoj.org/papers/0b49e5dbfe3fadb4743408dc3d6fb99f)

Reviewers and authors:

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@enkera, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @enkera

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• Repository: Is the source for this learning module available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release (v1.0.0)?
• Authorship: Has the submitting author (@nselem) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

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@whedon commands

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

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[whedon]

Wordcount for paper.md is 1504

[whedon]

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (498.6 files/s, 48211.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        26            372              0           1427
Python                           7            342            230           1063
TeX                              1             22              0            233
R                                4             52             39            161
YAML                             3             30             54            126
make                             1             28             29             67
JSON                             1              0              0             57
Ruby                             1              3              1              7
Bourne Shell                     1              2              2              4
-------------------------------------------------------------------------------
SUM:                            45            851            355           3145
-------------------------------------------------------------------------------


Statistical information for the repository '1ac5fffa9be4e8bd17f6359c' was
gathered on 2023/06/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andy Boughton                    1             5              4            0.03
Francois Michonneau              1          2306              0            6.45
François Michonneau              5            22            130            0.43
Gabriel A. Devenyi               1             5              3            0.02
Greg Wilson                     47         12802          13284           73.01
Joseph Stachelek                 1             1              1            0.01
Katrin Leinweber                 3             6              6            0.03
Maxim Belkin                    14            55             55            0.31
Michael R. Crusoe                1            74             70            0.40
Raniere Silva                   20           262            687            2.66
Rémi Emonet                      2            49             17            0.18
Tracy Teal                       4          3817           1950           16.14
W. Trevor King                   1             0              1            0.00
William L. Close                 3            53             56            0.31
naught101                        1             4              2            0.02

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Andy Boughton                 3           60.0         10.3                0.00
François Michonneau          95          431.8          9.8                0.00
Greg Wilson                 506            4.0         32.1               11.26
Joseph Stachelek              1          100.0         10.2                0.00
Katrin Leinweber              1           16.7         10.0                0.00
Maxim Belkin                 46           83.6         10.3                2.17
Michael R. Crusoe            62           83.8         11.2                4.84
Raniere Silva                58           22.1         13.4               10.34
Tracy Teal                  873           22.9         20.1               12.37
naught101                     1           25.0         16.3                0.00

[whedon]

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

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.5281/ZENODO.3585993 is OK
- 10.1101/2021.06.17.448726 is OK
- 10.1101/2021.06.15.448091 is OK
- 10.21105/jose.00049 is OK
- 10.7554/eLife.49816 is OK
- 10.5281/ZENODO.3260309 is OK
- 10.3389/fmicb.2020.578600 is OK

MISSING DOIs

- 10.21105/jose.00049 may be a valid DOI for title: A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
- 10.21105/jose.00027 may be a valid DOI for title: An Introduction to Applied Bioinformatics: a free, open, and interactive text.
- 10.21105/jose.00021 may be a valid DOI for title: CFD Python: the 12 steps to Navier-Stokes equations
- 10.3389/fmicb.2020.578600 may be a valid DOI for title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
- 10.1002/bmb.21387 may be a valid DOI for title: Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
- 10.1525/abt.2021.83.1.33 may be a valid DOI for title: Introducing Python Programming into Undergraduate Biology

INVALID DOIs

- None

[whedon]

👋 @enkera, please update us on how your review is going (this is an automated reminder).

[nselem]

Hello @JasonJWilliamsNY and @enkera
Please could you share if there is any news in the review process?

[enkera]

Hello @JasonJWilliamsNY. I've had a look at the workshop and it satisfies most of the criteria needed for publication. There seem to be several broken or indirect URL links, in particular the Instructor Notes, Setup, and Metagenomics Workshop Setup page links are dead or not working properly. Other than that, everything looks good.

[nselem]

Hello @enkera ,
We have updated Setup and instructor notes in Metagenomics Workshop, I think they broke when we change the repo from carpentries-incubator to carpentries-lab, thank you for noticing that.

[nselem]

Hello, @enkera and @JasonJWilliamsNY
Is it something else needed for the workshop to be accepted?

[JasonJWilliamsNY]

Hi @nselem I'll take one last look so we can move to the acceptance step. Thanks @enkera for review!

[JasonJWilliamsNY]

@enkera can you check off the items in the checklist at the top of this page; don't worry if some don't apply.

[JasonJWilliamsNY]

@whedon unassign @enkera as reviewer

[JasonJWilliamsNY]

@editorialbot remove @enkera from reviewers

[editorialbot]

@enkera added to the reviewers list!

[JasonJWilliamsNY]

@enkera I removed and added you - if that does not work, I will consult with @labarba

[enkera]

I still can't check the boxes unfortunately.

…

On Wed, Jul 26, 2023 at 11:00 AM Jason Williams ***@***.***> wrote: @enkera <https://github.com/enkera> I removed and added you - if that does not work, I will consult with @labarba <https://github.com/labarba> — Reply to this email directly, view it on GitHub <#209 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETX4ADNFYTE4C4CCAZXHA3XSEWJTANCNFSM6AAAAAAYXBTHXI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[JasonJWilliamsNY]

@labarba can you help us out here?

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.5281/ZENODO.3585993 is OK
- 10.1101/2021.06.17.448726 is OK
- 10.1101/2021.06.15.448091 is OK
- 10.21105/jose.00049 is OK
- 10.7554/eLife.49816 is OK
- 10.5281/ZENODO.3260309 is OK
- 10.3389/fmicb.2020.578600 is OK

MISSING DOIs

- 10.21105/jose.00049 may be a valid DOI for title: A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
- 10.21105/jose.00027 may be a valid DOI for title: An Introduction to Applied Bioinformatics: a free, open, and interactive text.
- 10.21105/jose.00021 may be a valid DOI for title: CFD Python: the 12 steps to Navier-Stokes equations
- 10.3389/fmicb.2020.578600 may be a valid DOI for title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
- 10.1002/bmb.21387 may be a valid DOI for title: Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
- 10.1525/abt.2021.83.1.33 may be a valid DOI for title: Introducing Python Programming into Undergraduate Biology

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/jose-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/jose-papers#138, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[JasonJWilliamsNY]

pinging @labarba with a reminder to review

[nselem]

Hi Lorena, @labarba ,
Do you need anything else from us to go ahead with the review?

[JasonJWilliamsNY]

Pinging @labarba via email as well

[JasonJWilliamsNY]

Email ping sent to @labarba in addition to notification here.

[labarba]

Hi everybody — I apologize for the long neglect. I was slammed with editorial load from another publication in the last few months, but I have stepped down from that role. This will allow me to come back to JOSE and attend to various neglected submissions. Thank you for your patience.

I have checked the submission repository, and do not find a tagged v1.0.0 – could you please check that?

[nselem]

Welcome back Lorena!
I have added a tag to the workshop repository
https://github.com/carpentries-lab/metagenomics-workshop/tree/v1.0.0

[nselem]

Hello @labarba ,
Did you have the chance to look at the version? Is anything else needed?

[JasonJWilliamsNY]

Also pinging @labarba

[labarba]

@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.

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CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Zirión-Martínez
  given-names: Claudia
- family-names: Garfias-Gallegos
  given-names: Diego
- family-names: Arellano-Fernandez
  given-names: Tania Vanessa
- family-names: Espinosa-Jaime
  given-names: Aarón
- family-names: Bustos-Díaz
  given-names: Edder D
- family-names: Lovaco-Flores
  given-names: José Abel
- family-names: Tejero-Gómez
  given-names: Luis Gerardo
- family-names: Avelar-Rivas
  given-names: J Abraham
- family-names: Sélem-Mojica
  given-names: Nelly
  orcid: "https://orcid.org/0000-0003-1697-3862"
doi: 10.5281/zenodo.8306876
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zirión-Martínez
    given-names: Claudia
  - family-names: Garfias-Gallegos
    given-names: Diego
  - family-names: Arellano-Fernandez
    given-names: Tania Vanessa
  - family-names: Espinosa-Jaime
    given-names: Aarón
  - family-names: Bustos-Díaz
    given-names: Edder D
  - family-names: Lovaco-Flores
    given-names: José Abel
  - family-names: Tejero-Gómez
    given-names: Luis Gerardo
  - family-names: Avelar-Rivas
    given-names: J Abraham
  - family-names: Sélem-Mojica
    given-names: Nelly
    orcid: "https://orcid.org/0000-0003-1697-3862"
  date-published: 2024-02-14
  doi: 10.21105/jose.00209
  issn: 2577-3569
  issue: 72
  journal: Journal of Open Source Education
  publisher:
    name: Open Journals
  start: 209
  title: A Data Carpentry- Style Metagenomics Workshop
  type: article
  url: "https://jose.theoj.org/papers/10.21105/jose.00209"
  volume: 7
title: A Data Carpentry- Style Metagenomics Workshop

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.

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[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00209 jose-papers#140
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00209
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...

[labarba]

Congratulations, @nselem, your JOSE paper is published! 🚀

Huge thanks to the Editor: @JasonJWilliamsNY and Reviewers: @enkera — your contributions make this possible 🙏

And thank you all for your patience, as I dig up of a months-long backlog 😞

[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:

Markdown:
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HTML:
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  <img src="https://jose.theoj.org/papers/10.21105/jose.00209/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00209/status.svg
   :target: https://doi.org/10.21105/jose.00209

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[tobyhodges]

Congratulations @nselem et al 🎉, and thank you @JasonJWilliamsNY, @enkera, and @labarba for supporting this lesson review

[JasonJWilliamsNY]

Thanks all!