Comments (22)
JasonJWilliamsNY
commented on June 16, 2024
1
Dear @nselem I'll pick this up this week apologies for the backlog.
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JasonJWilliamsNY
commented on June 16, 2024
1
@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.
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JasonJWilliamsNY
commented on June 16, 2024
1
@nselem we will recruit a single reviewer so that we can move swiftly.
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JasonJWilliamsNY
commented on June 16, 2024
1
@whedon start review
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whedon
commented on June 16, 2024
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
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
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whedon
commented on June 16, 2024
Wordcount for paper.md is 1504
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whedon
commented on June 16, 2024
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
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whedon
commented on June 16, 2024
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whedon
commented on June 16, 2024
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
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labarba
commented on June 16, 2024
Note: This metagenomics learning module has been peer reviewed by The Carpentries in the issue: carpentries-lab/reviews#11 (comment)
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labarba
commented on June 16, 2024
@whedon invite @JasonJWilliamsNY as editor
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whedon
commented on June 16, 2024
@JasonJWilliamsNY has been invited to edit this submission.
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nselem
commented on June 16, 2024
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.
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JasonJWilliamsNY
commented on June 16, 2024
@labarba I can reach out - This does not show up in my dashboard on the Jose website.
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labarba
commented on June 16, 2024
you need to accept the editor invitation first, with: @whedon assign me as editor
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JasonJWilliamsNY
commented on June 16, 2024
@whedon assign me as editor
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whedon
commented on June 16, 2024
OK, the editor is @JasonJWilliamsNY
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nselem
commented on June 16, 2024
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,
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nselem
commented on June 16, 2024
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: carpentries-lab/reviews#11 (comment)
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JasonJWilliamsNY
commented on June 16, 2024
@whedon add @enkera as reviewer
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whedon
commented on June 16, 2024
OK, @enkera is now a reviewer
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whedon
commented on June 16, 2024
OK, I've started the review over in #209.
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