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

whedon commented 4 years ago

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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Reviewers and authors:

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.)

Reviewer instructions & questions

@tomsing1, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @tomsing1

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] 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.)

[x] 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

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

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

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

fboehm commented 4 years ago

@whedon check references

whedon commented 4 years ago

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

fboehm commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

fboehm commented 4 years ago

@anwarbio - Can you fix the references so that the words "Journal Article." are not in them?

Also, can you double-check that the hyperlinks for dois direct you to the correct articles? Right now, I'm unsuccessful in following the link to the Wang, et al. (2012) paper. It might just be a problem with my internet connection or browser, so please check this and confirm that you are directing readers to the correct article.

anwarbio commented 4 years ago

@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 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

fboehm commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

fboehm commented 4 years ago

@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 commented 4 years ago

@fboehm - Figures are now corrected. Thanks

fboehm commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

fboehm commented 4 years ago

@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 commented 4 years ago

@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 commented 4 years ago

@whedon set 10.5281/zenodo.4075110 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4075110 is the archive.

fboehm commented 4 years ago

@whedon set v1.0.1 as version

whedon commented 4 years ago

OK. v1.0.1 is the version.

fboehm commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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 commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1795

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 4 years ago

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 commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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 commented 4 years ago

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

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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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