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Reviews for the Journal of Open Source Education (JOSE)
http://jose.theoj.org
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[PRE REVIEW]: Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples #128

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @ethanwhite (Ethan P. White) Repository: https://github.com/datacarpentry/semester-biology/ Version: v4.1.0 Editor: @ShanEllis Reviewers: @smwindecker, @catherinehulshof 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

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/30d2d92728226af1e99f559f2f22b38f"><img src="https://jose.theoj.org/papers/30d2d92728226af1e99f559f2f22b38f/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/30d2d92728226af1e99f559f2f22b38f/status.svg)](https://jose.theoj.org/papers/30d2d92728226af1e99f559f2f22b38f)

Author instructions

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

@ethanwhite 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 commented 3 years ago

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 commented 3 years ago

Wordcount for paper.md is 2151

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1371/journal.pcbi.1005755 may be a valid DOI for title: Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
- 10.1146/annurev.ecolsys.37.091305.110031 may be a valid DOI for title: The new bioinformatics: integrating ecological data from the gene to the biosphere
- 10.1177/002248718703800308 may be a valid DOI for title: Explicit teaching and teacher training
- 10.2218/ijdc.v10i1.351 may be a valid DOI for title: Data Carpentry: Workshops to Increase Data Literacy for Researchers
- 10.1371/journal.pone.0224288 may be a valid DOI for title: Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction

INVALID DOIs

- None
whedon commented 3 years ago

PDF failed to compile for issue #128 with the following error: 

 ORCID looks to be the wrong length
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (0000-0001-6728-774) for Ethan P. White (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.37 s (1656.1 files/s, 107720.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                       541           5166              0          18723
SVG                              1              0              0           2694
JSON                             3              1              0           2085
CSS                              4            111            205            815
HTML                            13            106             14            671
Jupyter Notebook                31              0           8016            376
Python                           9            124            111            266
R                                7             42             61            206
TeX                              1              9              0             78
YAML                             2             18              4             55
XML                              1              4              0             24
JavaScript                       1              3              0             12
TOML                             1              0              0              2
-------------------------------------------------------------------------------
SUM:                           615           5584           8411          26007
-------------------------------------------------------------------------------

Statistical information for the repository '510782cd81c8ca2b9ee1dfdf' was
gathered on 2021/08/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ethan White                     17           645             29           86.86
Zack Brym                        2             1            101           13.14

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
Ethan White                 515           79.8         71.2               17.86
Zack Brym                     1          100.0         48.1                0.00
labarba commented 3 years ago

hey @ethanwhite — could you check that your ORCID is correct?

labarba commented 3 years ago

@whedon invite @ShanEllis as editor

whedon commented 3 years ago

@ShanEllis has been invited to edit this submission.

ethanwhite commented 3 years ago

@labarba - oops, looks like the last digit got deleted while editing. I've fixed the pushed the change to the repo.

@whedon generate pdf [UPDATE: doesn't look like whedon listens to me so someone else will need to try to regenerate the pdf]

labarba commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #128 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/author.rb:72:in `block in build_affiliation_string': Problem with affiliations for S. Ernest, perhaps the affiliations index need quoting? (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/author.rb:71:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/author.rb:71:in `build_affiliation_string'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/author.rb:17:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:205:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:205:in `block in parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:202:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:202:in `parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:93:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
labarba commented 3 years ago

@ethanwhite I think commands to @whedon need to be alone in a comment

ethanwhite commented 3 years ago

Thanks @labarba and sorry about the failures. I ran it through the test site before submitting, but apparently that wasn't enough. I'll work on getting everything passing here and ping you and @ShanEllis once it's passing.

ShanEllis commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @ShanEllis

ethanwhite commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

ethanwhite commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
ethanwhite commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1371/journal.pcbi.1005755 is OK
- 10.1093/biosci/bix025 is OK
- 10.1146/annurev.ecolsys.37.091305.110031 is OK
- 10.1177/002248718703800308 is OK
- 10.2218/ijdc.v10i1.351 is OK
- 10.1371/journal.pone.0224288 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.9790/7388-05616670 is INVALID
ethanwhite commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1371/journal.pcbi.1005755 is OK
- 10.1093/biosci/bix025 is OK
- 10.1146/annurev.ecolsys.37.091305.110031 is OK
- 10.1177/002248718703800308 is OK
- 10.2218/ijdc.v10i1.351 is OK
- 10.1371/journal.pone.0224288 is OK

MISSING DOIs

- None

INVALID DOIs

- None
ethanwhite commented 3 years ago

@ShanEllis - the article is now rendering properly and the reference checks are passing.

Possible reviewers include K8hertweck, jhollist, jsta, andrewmaclachlan.

ShanEllis commented 3 years ago

Thanks @ethanwhite! Looks ready to start the review process.

Hi @jsta and @jhollist, I have you both as interested reviewers for JOSE, and it appears you are each a good fit for this submission. Would you like to contribute a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing. Thanks!

ShanEllis commented 3 years ago

Hi @pschloss, given your interest in reviewing for JOSE (and previous review - thank you!), I wanted to reach out to see if you'd be interested in contributing a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing in the next couple of days. Thanks!

ShanEllis commented 3 years ago

Hi @K8hertweck, it looks like you've signed up previously to review for JOSE, and I think we have a recent submission that's a great fit for you. I wanted to reach out to see if you'd be interested in contributing a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing in the next couple of days. Thanks!

jhollist commented 3 years ago

@ShanEllis I am so sorry for not getting back to you on this sooner. No excuse... Just forgot.

Unfortunately, I am going to have to pass at this time. I'd really love to review this, but I am swamped. Keep me in mind for future submissions.

pschloss commented 3 years ago

Hi - thanks for reaching out. Unfortunately, I've been pretty swamped with other reviews and projects that I need to tend to.

Pat

On Mon, Sep 13, 2021 at 6:19 PM Shannon Ellis @.***> wrote:

Hi @pschloss https://github.com/pschloss, given your interest in reviewing for JOSE (and previous review - thank you!), I wanted to reach out to see if you'd be interested in contributing a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing in the next couple of days. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/128#issuecomment-918623736, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJUUBG4A5AIF25HRYYEEV3UBZ2FLANCNFSM5C4DMOTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

ShanEllis commented 3 years ago

Unfortunately, I am going to have to pass at this time. I'd really love to review this, but I am swamped. Keep me in mind for future submissions.

I have been there, @jhollist. Thanks for the reply, and good luck with all that's on your plate.

ShanEllis commented 3 years ago

Hi - thanks for reaching out. Unfortunately, I've been pretty swamped with other reviews and projects that I need to tend to.

Totally understand, @pschloss! Thanks for the quick reply.

ShanEllis commented 3 years ago

Hi @fmichonneau! I have you down as an interested reviewer for JOSE, and I think we have a recent submission that's a really good fit for you. I wanted to reach out to see if you'd be interested in contributing a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing in the next couple of days. Thanks!

fmichonneau commented 3 years ago

Hi @ShanEllis Thanks for the invitation but I think my affiliation with The Carpentries creates a conflict of interest for this submission.

ShanEllis commented 3 years ago

Hi @gvdr! I have you down as an interested reviewer for JOSE, and I think we have a recent submission that's a good fit for you. I wanted to reach out to see if you'd be interested in contributing a review for this submission? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". Please let me know if you're available and willing in the next couple of days. Thanks!

ShanEllis commented 3 years ago

Hi @karthik! I'm sure you're super busy (which is why I've held off thus far on bugging you for this), but I've been struggling to pin down reviewers. Any chance you have time for a JOSE review? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". I believe you've reviewed for JOSE before, so you know that the papers are not very long and the review process is open and happens entirely on GitHub. Let me know if you'll have time to complete this review!

labarba commented 3 years ago

I noticed on the paper it says these materials have been used in a number of university and college courses. Why not find someone among the instructors of those courses to act as reviewers? They would already have read the material and had direct experience teaching with them, perhaps finding areas that need improvement. I don't see that there would be any reason to think adopting the materials raises conflict-of-issue concerns, if the adopter did not collaborate with the original authors... What do you think, @ethanwhite ?

ShanEllis commented 3 years ago

That's a good idea, @labarba. I wasn't sure if there was a COI issue there, but if you and @ethanwhite think that's a possibility, I'll go ahead with that!

Also, we do have one reviewer on board now! I'll add @smwindecker to the official review issue once we find our second (unless you say otherwise/to start it before then, @labarba!)

karthik commented 3 years ago

Hi @karthik! I'm sure you're super busy (which is why I've held off thus far on bugging you for this), but I've been struggling to pin down reviewers. Any chance you have time for a JOSE review? The title is "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". I believe you've reviewed for JOSE before, so you know that the papers are not very long and the review process is open and happens entirely on GitHub. Let me know if you'll have time to complete this review!

Thanks for thinking of me. I'm out on family leave at the moment and am not taking on new reviews till the end of the year. Good luck with your reviewer search.

labarba commented 3 years ago

I'll add @smwindecker to the official review issue once we find our second (unless you say otherwise/to start it before then, @labarba!)

Yes, you add the reviewers here, in the Pre-review issue. Go ahead and run @whedon assign <user> as reviewer here for the first reviewer, then @whedon add <user> as reviewer for the second, then @whedon start review 😄

ethanwhite commented 3 years ago

I agree that folks who have used this material in their courses could be good reviewers. Of the courses on that list the only folks I'm aware of who have conflicts of interest are the University of Florida folks (institutional conflicts + one of them is an author on the paper).

One person on that list that comes to mind as a possibility is catherinehulshof.

ShanEllis commented 3 years ago

@whedon assign @smwindecker as reviewer

whedon commented 3 years ago

OK, @smwindecker is now a reviewer

ShanEllis commented 3 years ago

I agree that folks who have used this material in their courses could be good reviewers. Of the courses on that list the only folks I'm aware of who have conflicts of interest are the University of Florida folks (institutional conflicts + one of them is an author on the paper).

One person on that list that comes to mind as a possibility is catherinehulshof.

Excellent. Thank you, @ethanwhite. I will reach out to to this end, keeping the exceptions you noted in mind. I appreciate it!

ShanEllis commented 3 years ago

Hi @catherinehulshof! Reaching out to see if you're interested and able to review a submission to JOSE (Journal of Open Source Education) titled "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". I believe you are familiar with these materials, making you a good fit for the review and hopefully making the review process shorter for you. The review process for JOSE is open and happens on GitHub. If you're interested and able, please let me know!

catherinehulshof commented 3 years ago

Dear Shannon,

I would be interested and am familiar with the materials after learning more about the review process. What are the review criteria/format, etc?

Cheers,

Catherine

Catherine M. Hulshof, PhD (she/her: why I use pronouns https://www.mypronouns.org/what-and-why) Environmental Data Science Department of Biology Virginia Commonwealth University Richmond, VA, 23284 https://www.biodiversityresearchlab.com

On Fri, Oct 1, 2021 at 7:40 PM Shannon Ellis @.***> wrote:

Hi @catherinehulshof https://github.com/catherinehulshof! Reaching out to see if you're interested and able to review a submission to JOSE (Journal of Open Source Education) titled "Data Carpentry for Biologists: A semester long Data Carpentry course using ecological and other biological examples". I believe you are familiar with these materials, making you a good fit for the review and hopefully making the review process shorter for you. The review process for JOSE is open and happens on GitHub. If you're interested and able, please let me know!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/128#issuecomment-932635082, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEWIRHO4OOZNWGKKDZZ6S2LUEZBFVANCNFSM5C4DMOTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

ShanEllis commented 3 years ago

@catherinehulshof Oh excellent! To explain the process/steps a bit:

  1. Once agreed, I would add you officially as a reviewer.
  2. After this I would start the review officially (rather than this issue, which is "pre-review") where you and the other reviewer would begin your review.
  3. Upon starting the review, we would work from a new issue on GitHub. There would be a checklist here (to guide your review) and your review would be included as a comment there.
  4. Upon receipt of both reviews (ideally within a few weeks, but we understand people are busy), I would review your comments along with the other reviewer and communicate with the authors at that point in time.

To see an example of a review issue (of a paper that was subsequently published), have a look here: https://github.com/openjournals/jose-reviews/issues/115

Also, a note that whedon is the bot that helps make this process go as smoothly as possible, just so you know what it means whenever you see that pop up. Happy to answer any questions you may have if this doesn't clear things up!

Shannon

catherinehulshof commented 3 years ago

Hi Shannon,

I'd be happy to provide a review within the next several weeks.

Catherine

Catherine M. Hulshof, PhD (she/her: why I use pronouns https://www.mypronouns.org/what-and-why) Environmental Data Science Department of Biology Virginia Commonwealth University Richmond, VA, 23284 https://www.biodiversityresearchlab.com

On Mon, Oct 4, 2021 at 2:31 PM Shannon Ellis @.***> wrote:

@catherinehulshof https://github.com/catherinehulshof Oh excellent! To explain the process/steps a bit:

  1. Once agreed, I would add you officially as a reviewer.
  2. After this I would start the review officially (rather than this issue, which is "pre-review") where you and the other reviewer would begin your review.
  3. Upon starting the review, we would work from a new issue on GitHub. There would be a checklist here (to guide your review) and your review would be included as a comment there.
  4. Upon receipt of both reviews (ideally within a few weeks, but we understand people are busy), I would review your comments along with the other reviewer and communicate with the authors at that point in time.

To see an example of a review issue (of a paper that was subsequently published), have a look here: #115 https://github.com/openjournals/jose-reviews/issues/115

Also, a note that whedon is the bot that helps make this process go as smoothly as possible, just so you know what it means whenever you see that pop up. Happy to answer any questions you may have if this doesn't clear things up!

  • Shannon

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/128#issuecomment-933745219, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEWIRHI4EX2I3N67GVXBPZDUFHXGJANCNFSM5C4DMOTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

ShanEllis commented 3 years ago

@whedon add @catherinehulshof as reviewer

whedon commented 3 years ago

OK, @catherinehulshof is now a reviewer

ShanEllis commented 3 years ago

@whedon start review