[PRE REVIEW]: A Data Carpentry- Style Metagenomics Workshop

[whedon]

Submitting author: @nselem (Nelly Selem) Repository: https://github.com/carpentries-lab/metagenomics-workshop Version: v1.0.0 Editor: @JasonJWilliamsNY Reviewers: @enkera Managing EiC: Jordan Gorzalski

:warning: JOSE reduced service mode :warning:

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

Status

Status badge code:

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)

Author instructions

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

@nselem 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 JOSE and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSE 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.

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE 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 1504

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (429.8 files/s, 41560.0 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 '142466472d99117b315936ea' was
gathered on 2023/04/12.
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]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[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

[labarba]

Note: This metagenomics learning module has been peer reviewed by The Carpentries in the issue: https://github.com/carpentries-lab/reviews/issues/11#issuecomment-1451841516

[labarba]

@whedon invite @JasonJWilliamsNY as editor

[whedon]

@JasonJWilliamsNY has been invited to edit this submission.

[nselem]

Hello @JasonJWilliamsNY What about PaulaNietoG and fpsom, as reviewers, since they were the reviewers of the lesson, it could be easy for them to review the article.

[JasonJWilliamsNY]

@labarba I can reach out - This does not show up in my dashboard on the Jose website.

[labarba]

you need to accept the editor invitation first, with: @whedon assign me as editor

[JasonJWilliamsNY]

@whedon assign me as editor

[whedon]

OK, the editor is @JasonJWilliamsNY

[nselem]

Dear @JasonJWilliamsNY @whedon and @labarba I hope this message finds you well. I am writing to kindly inquire about the status of our article. I was wondering if the manuscript has been assigned to reviewers for the peer-review process yet. Any update on the progress of the review process would be greatly appreciated. We are excited about this manuscript. Thank you for your time and assistance. Best regards,

[JasonJWilliamsNY]

Dear @nselem I'll pick this up this week apologies for the backlog.

[JasonJWilliamsNY]

@nselem checking in with @labarba to see if we can fast track or what form this will take since it has already undergone a level of review.

[nselem]

Thanks @JasonJWilliamsNY yes, the lesson has been thoroughly reviewed, but the short paper describing it is not. That's what I was thinking that maybe PaulaNietoG and fpsom the reviewers of the lesson could review the manuscript. Or maybe other reviewers but pointing them to the previous review link here: The Carpentries issue: https://github.com/carpentries-lab/reviews/issues/11#issuecomment-1451841516

[JasonJWilliamsNY]

@nselem we will recruit a single reviewer so that we can move swiftly.

[JasonJWilliamsNY]

@whedon add @enkera as reviewer

[whedon]

OK, @enkera is now a reviewer

[JasonJWilliamsNY]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/jose-reviews/issues/209.