[REVIEW]: BioGears: A C++ library for whole body physiology simulations

whedon commented 4 years ago

Submitting author: @ajbaird (Austin Baird) Repository: https://github.com/BioGearsEngine/core Version: v7.3.2 Editor: @meg-simula Reviewer: @fcooper8472, @MiroK Archive: 10.5281/zenodo.4304604

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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

@fcooper8472 & @MiroK, 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
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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @fcooper8472

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 (@ajbaird) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

Review checklist for @MiroK

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 (@ajbaird) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

MiroK commented 4 years ago

Thanks @ajbaird! @meg-simula I am done with the review

ajbaird commented 3 years ago

Hi @meg-simula let me know if there is anything else I can do! Thanks again for all the edits!

meg-simula commented 3 years ago

@ajbaird This reminder was perfect!

@fcooper8472 @MiroK Could you confirm that you recommend this paper for acceptance at this point?

fcooper8472 commented 3 years ago

@meg-simula yes, absolutely recommended.

MiroK commented 3 years ago

@meg-simula Yes from me too

meg-simula commented 3 years ago

Ok @ajbaird - I will follow-up on this later tonight or tomorrow - will get back in touch.

meg-simula commented 3 years ago

@whedon generate pdf

meg-simula commented 3 years ago

@whedon check references

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:

whedon commented 3 years ago

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

OK DOIs

- 10.1089/end.2016.0613 is OK
- 10.1016/0022-2828(90)91460-o is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1002/psp4.12371 is OK
- 10.1117/12.2252510 is OK
- 10.3389/fphys.2019.01321 is OK
- 10.1109/EMBC.2019.8857686 is OK

MISSING DOIs

- 10.1016/j.pbiomolbio.2004.01.004 may be a valid DOI for title: CellML: its future, present and past

INVALID DOIs

- None

meg-simula commented 3 years ago

@ajbaird

Please address the following minor points in the paper:

[ ] Add space before reference to (Otto...)
[ ] This phrasing is unclear, please rephrase: "This work has extended the engine to support ..."
[ ] "New dugs" should probably be "New drugs" - please spell-check
[ ] Missing punctuation after reference to Figure 1
[ ] Should HowToFaciculation() be HowToFasciculation() ?

After these points have been addressed, could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

ajbaird commented 3 years ago

I will get to these today!

ajbaird 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:

ajbaird 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:

ajbaird 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:

ajbaird commented 3 years ago

Hi @meg-simula ! I think I got to all the edits you listed here with a few other minor things.

Software version is v7.3.2 https://github.com/BioGearsEngine/core/releases/tag/7.3.2
release is up on Zenodo, DOI is here 10.5281/zenodo.4304604, Author list and title should be the same as this paper.
Target DOI link is https://doi.org/10.5281/zenodo.4304604

I think that is everything, let me know if I got to it, sorry if I missed something.

Thanks!

Austin

meg-simula commented 3 years ago

@whedon generate pdf

meg-simula 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

- 10.1089/end.2016.0613 is OK
- 10.1016/0022-2828(90)91460-o is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1002/psp4.12371 is OK
- 10.1117/12.2252510 is OK
- 10.3389/fphys.2019.01321 is OK
- 10.1109/EMBC.2019.8857686 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

meg-simula commented 3 years ago

@whedon set 10.5281/zenodo.4304604 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4304604 is the archive.

meg-simula commented 3 years ago

@whedon set v7.3.2 as version

whedon commented 3 years ago

OK. v7.3.2 is the version.

meg-simula commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1089/end.2016.0613 is OK
- 10.1016/0022-2828(90)91460-o is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1002/psp4.12371 is OK
- 10.1117/12.2252510 is OK
- 10.3389/fphys.2019.01321 is OK
- 10.1109/EMBC.2019.8857686 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/1969

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1969, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1089/end.2016.0613 is OK
- 10.1016/0022-2828(90)91460-o is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1002/psp4.12371 is OK
- 10.1117/12.2252510 is OK
- 10.3389/fphys.2019.01321 is OK
- 10.1109/EMBC.2019.8857686 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/1981

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1981, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 3 years ago

@ajbaird - could you please add a little more information to the affiliation string? For example, city and country name.

ajbaird commented 3 years ago

Hi @arfon ! Just added city state and country, let me know if you want a more detailed address. Thanks!

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1089/end.2016.0613 is OK
- 10.1016/0022-2828(90)91460-o is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1002/psp4.12371 is OK
- 10.1117/12.2252510 is OK
- 10.3389/fphys.2019.01321 is OK
- 10.1109/EMBC.2019.8857686 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/1984

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1984, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 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/1985
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02645
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 3 years ago

@fcooper8472, @MiroK - many thanks for your reviews here and to @meg-simula for editing this submission. JOSS relies upon the volunteer efforts of folks like yourself - we simply couldn't do it without you ✨

@ajbaird - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 3 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.02645/status.svg)](https://doi.org/10.21105/joss.02645)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02645">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02645/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02645/status.svg
   :target: https://doi.org/10.21105/joss.02645

This is how it will look in your documentation:

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