[REVIEW]: ‘Bioassays’; a new package in R for analyzing cellular assays #2402

whedon · 2020-06-28T19:47:12Z

Submitting author: @anwarbio (ANWAR PALAKKAN)
Repository: https://github.com/anwarbio/bioassays
Version: v1.0.1
Editor: @fboehm
Reviewers: @tomsing1, @homonecloco
Archive: 10.5281/zenodo.4075110

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Markdown: [![status](https://joss.theoj.org/papers/68721e17fcb3d07413631c8d395dff5c/status.svg)](https://joss.theoj.org/papers/68721e17fcb3d07413631c8d395dff5c)

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Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

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Review checklist for @tomsing1

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@anwarbio) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
[x ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

The vignettes needed proofreading. I have suggested changes and submitted a pull request for the author to review. (I also included a few other minor suggestions in the pull request, which he might find useful.)

References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @homonecloco

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@anwarbio) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The text was updated successfully, but these errors were encountered:

whedon · 2020-06-28T19:47:15Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tomsing1 it looks like you're currently assigned to review this paper 🎉.

⚠️ 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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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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 · 2020-06-28T19:47:27Z

PDF failed to compile for issue #2402 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/2402/paper.md): mapping values are not allowed in this context at line 2 column 17 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:125:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:119:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

arfon · 2020-07-03T10:45:12Z

@anwarbio - your paper title needs quoting, i.e. change this:

title: Bioassays: a new package in R for analyzing cellular assays

to this:

title: "Bioassays: a new package in R for analyzing cellular assays"

in your paper.md.

anwarbio · 2020-07-03T11:22:58Z

@arfon - The above change is made in the title of paper.md

arfon · 2020-07-03T11:43:27Z

@whedon generate pdf

whedon · 2020-07-03T11:44:04Z

👉 Check article proof 📄 👈

anwarbio · 2020-07-03T12:48:17Z

@whedon, @arfon
Few mistakes were in the article proof, and is now corrected in paper.md.
Details of the correction are
1) Line 25 1st paragraph last line: high-throughput is corrected as High-throughput
2) Line 27 2nd paragraph 3rd line: us is corrected as use
3) Line 29 3rd paragraph 1st line: server is corrected as serve
4) Line 39 7th paragraph 1st line: An extra convert is deleted.
Thanking you,
Anwar

whedon · 2020-07-03T12:48:20Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

fboehm · 2020-07-03T13:03:43Z

Thanks, @anwarbio.

fboehm · 2020-07-03T18:52:07Z

@whedon remove homoneclocom as reviewer

whedon · 2020-07-03T18:52:11Z

OK, homoneclocom is no longer a reviewer

fboehm · 2020-07-03T18:52:32Z

@whedon add @homonecloco as reviewer

whedon · 2020-07-03T18:52:37Z

OK, @homonecloco is now a reviewer

tomsing1 · 2020-07-04T02:58:31Z

@fboehm I think I waited too long to accept the https://github.com/openjournals/joss-reviews/invitations invite. Would you mind refreshing it so I can edit the checklist? Many thanks!

danielskatz · 2020-07-04T12:56:53Z

@whedon re-invite @tomsing1 as reviewer

whedon · 2020-07-04T12:56:57Z

OK, the reviewer has been re-invited.

@tomsing1 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

homonecloco · 2020-07-04T21:49:44Z

Hi @anwarbio ,
I started the review with the documentation. I am still to read the paper, but I'll give you my comments of what I have reviewed so far, so you can consider them.

The API documentation (https://cran.r-project.org/web/packages/bioassays/bioassays.pdf) has the beginning looking incomplete or misformated. The documentation of the actual functions seems ok, but having so many NA at the beginning of the document is not recommended.
The vignette with examples (https://cran.r-project.org/web/packages/bioassays/vignettes/bioassays-examples.html) refers to some files, like “L DIFF P3 72HRS.csv”. I couldn’t find that file in the repository. I appreciate that the examples may be included as part of the package, but for this particular document, having the actual file used can help the users to format their tables.
In some packages, the documentation is in html and in PDF. It would be useful to have the same option for the vignettes of this packages. The PDFs are hard to copy and paste.

anwarbio · 2020-07-05T17:58:26Z

Hi @homonecloco

Thank you for reviewing the package and your suggestions are really helpful in improving the package. I have made the below changes in github files. Once all are happy with contents, then I can go for an update on CRAN with all changes.

The API documentation (https://cran.r-project.org/web/packages/bioassays/bioassays.pdf) has the beginning looking incomplete or misformated. The documentation of the actual functions seems ok, but having so many NA at the beginning of the document is not recommended.
comment: I have now corrected this
The vignette with examples (https://cran.r-project.org/web/packages/bioassays/vignettes/bioassays-examples.html) refers to some files, like “L DIFF P3 72HRS.csv”. I couldn’t find that file in the repository. I appreciate that the examples may be included as part of the package, but for this particular document, having the actual file used can help the users to format their tables.
comment: All the files used in the examples are now added in the exdata folder and is now mentioned in 'vignette with examples'
In some packages, the documentation is in html and in PDF. It would be useful to have the same option for the vignettes of this packages. The PDFs are hard to copy and paste.
comment: The vignettes are in html format. Adding both html and pdf file might be difficult as the images of 'heatplate' appear in different dimensions in pdf and html. I might need separate rmd files for html and pdf, I doubt if CRAN will allow this.

Thanking you,
Amwar

homonecloco · 2020-07-08T16:08:22Z

Hi @anwarbio ,
Thanks for making the updates so fast. Is there a way I can preview them? Specially I would like to see the NAs go away. In any case, I see you uploaded the file, and it is fine if you only have the html documentation. As long it is available in either format, in an easy to copy and paste (so you can test that the commands are working as expected), is fine.
Best,
Ricardo.

anwarbio · 2020-07-08T22:21:48Z

Hi @homonecloco ,
Thank you for the reply. I have made few more edits today to put each function in separate line (you can see them in the github). I do not know how to share the preview file, so I have shared you a screenshot showing the functions arranged neatly.
Thanking you,
Anwar

fboehm · 2020-07-19T17:03:43Z

@tomsing1 and @homonecloco - I hope that your reviews are going well. Please feel free to complete the checklists when you're satisfied with the submission and to suggest revisions until you're satisfied. Please let me know how I might help.

anwarbio · 2020-10-07T15:39:15Z

@fboehm - I have fixed this by removing the word "Journal Article".
Also I have double checked all the dois hyperlink. I can confirm you that all of them are working and directing to correct article.
Thanks

fboehm · 2020-10-07T16:07:13Z

@whedon generate pdf

whedon · 2020-10-07T16:07:45Z

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

fboehm · 2020-10-07T16:40:29Z

@whedon generate pdf

whedon · 2020-10-07T16:41:12Z

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

fboehm · 2020-10-07T16:47:43Z

@anwarbio - the figure labels for the 384-well plate figures should be fixed. Right now, the horizontal axis labels overlap each other. Can you fix this so that the labels are spaced apart a little more? Thanks again!

anwarbio · 2020-10-07T17:44:23Z

@fboehm - Figures are now corrected. Thanks

fboehm · 2020-10-07T18:08:22Z

@whedon generate pdf

whedon · 2020-10-07T18:09:07Z

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

fboehm · 2020-10-07T18:14:28Z

@anwarbio - the reviewers have recommended your submission for publication. Before we accept it, I need you to make an archive and a Github tagged release. Once you do that, please comment here with the doi of the archive and the version number for the tagged release. Please double-check that the archive has the same author and same title as your submission.

anwarbio · 2020-10-09T12:15:53Z

@fboehm - Thank you very much for the wonderful review and accepting the paper for publication. The doi and version number is given below.
doi: 10.5281/zenodo.4075110 , link: https://doi.org/10.5281/zenodo.4075110
version: v1.0.1

Thanks,
Anwar

fboehm · 2020-10-10T14:28:08Z

@whedon set 10.5281/zenodo.4075110 as archive

whedon · 2020-10-10T14:28:12Z

OK. 10.5281/zenodo.4075110 is the archive.

fboehm · 2020-10-10T14:28:35Z

@whedon set v1.0.1 as version

whedon · 2020-10-10T14:28:40Z

OK. v1.0.1 is the version.

fboehm · 2020-10-10T14:30:54Z

@whedon accept

whedon · 2020-10-10T14:30:57Z

Attempting dry run of processing paper acceptance...

whedon · 2020-10-10T14:31:09Z

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

OK DOIs

- 10.1007/s10295-006-0086-3 is OK
- 10.1002/em.22014 is OK
- 10.1007/978-1-4939-2742-5_11 is OK
- 10.1016/j.bios.2015.05.018 is OK
- 10.1038/srep42383 is OK
- 10.1093/bioinformatics/btr664 is OK
- 10.1186/s12859-019-2891-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-10-10T14:31:37Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1795

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1795, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng · 2020-10-10T17:03:41Z

Ok I can take over from here! I see that the version and Zenodo archive are taken care of! Paper looks good too. We can move forward.

kthyng · 2020-10-10T17:03:47Z

@whedon accept deposit=true

whedon · 2020-10-10T17:03:50Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2020-10-10T17:04:50Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-10-10T17:04:51Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02402 joss-papers#1796
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02402
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2020-10-10T17:12:11Z

Congrats on your new publication @anwarbio! Thanks to editor @fboehm and reviewers @tomsing1 and @homonecloco for your time and expertise!!

whedon · 2020-10-10T17:12:15Z

🎉🎉🎉 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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02402/status.svg)](https://doi.org/10.21105/joss.02402)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02402">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02402/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02402/status.svg
   :target: https://doi.org/10.21105/joss.02402

This is how it will look in your documentation:

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whedon added the review label Jun 28, 2020

whedon assigned fboehm Jun 28, 2020

whedon mentioned this issue Jun 28, 2020

[PRE REVIEW]: ‘Bioassays’; a new package in R for analyzing cellular assays #2326

Closed

whedon unassigned fboehm Jul 3, 2020

whedon assigned fboehm Jul 3, 2020

whedon assigned fboehm and unassigned fboehm Jul 3, 2020

homonecloco self-assigned this Jul 3, 2020

tomsing1 mentioned this issue Jul 5, 2020

[JOSS REVIEW]: R CMD check warning and note anwarbio/bioassays#1

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 10, 2020

whedon added accepted published Papers published in JOSS labels Oct 10, 2020

kthyng closed this as completed Oct 10, 2020

[REVIEW]: ‘Bioassays’; a new package in R for analyzing cellular assays #2402

[REVIEW]: ‘Bioassays’; a new package in R for analyzing cellular assays #2402

Comments

whedon commented Jun 28, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @tomsing1

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @homonecloco

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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