[REVIEW]: Tyssue, en Epithelium simulation library

[whedon]

Submitting author: @glyg (Guillaume Gay)
Repository: https://github.com/damcb/tyssue
Version: 0.9.0
Editor: @pdebuyl
Reviewer: @fcooper8472, @SergeDmi
Archive: 10.5281/zenodo.4817609

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Reviewers and authors:

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@fcooper8472 & @SergeDmi, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @fcooper8472

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

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?

Review checklist for @SergeDmi

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

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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fcooper8472, @SergeDmi it looks like you're currently assigned to review this paper 🎉.

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[whedon]

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

OK DOIs

- 10.1101/2020.01.06.896266 is OK
- 10.1038/s41467-019-10720-0 is OK
- 10.1101/704932 is OK
- 10.1038/s41467-018-06497-3 is OK
- 10.1242/dev.146761 is OK
- 10.1098/rstb.2015.0520 is OK
- 10.1038/nphys3471 is OK
- 10.1038/nature14152 is OK
- 10.1007/s10237-015-0724-7 is OK
- 10.1007/s10237-012-0430-7 is OK
- 10.1016/J.CUB.2010.06.075 is OK
- 10.1016/J.CUB.2007.11.049 is OK
- 10.1016/S0021-9290(02)00006-4 is OK
- 10.1016/S0074-7696(08)62339-6 is OK
- 10.1016/0022-5193(78)90315-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[pdebuyl]

@fcooper8472 @SergeDmi make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines linked to at the top of this review page.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

[whedon]

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

[SergeDmi]

Review

Software structure and installation

I have actually little to say about the software. It is open source, well documented, easy to install with conda (although conda may have its pitfalls, it worked at first try for me).

Scholar effort

I think tyssue is a fantastic effort that really fills a need for well defined, reproducible physical models in the field, while allowing a lot of freedom for the user. It is clearly a fully-featured sofware.

Software usage

Tyssue is an API, which allows a broad use, at the expense of simplicity for the non-programmer. My main concern is the lack of gradual difficulty in the tutorials : reproducing research results is great, but gently steering the user might be missing.
While example 5 is simple as claimed, example 2 is rather complex. To engage scientists to use the software, step-by-step tutorial, or a better gradation of difficulty in the notebook examples, seem required to smoothen the steep learning curve.

Article

Statement of need

The statement of need does a good job of explaining the context, but lacks in describing the actual need for the software. A mention of existing software is also lacking. Instead, this paragraph gives a short description of Tyssue.

Software description

I think the article fails to convey the organization of Tyssue, that "Separates structure, geometry and models" (better explained in the readme). As a consequence, it is not clear that the models (referenced in the paragraph mechanics) can be chosen at will between Euler, Gradient descent, Quasi-static, and possibly other and user defined ; the same applies to topology.

Recommendation

The software and article definitely should be published in JOSS. Usage examples should be streamlined. Article should highlight the need for this software as well as software organisation and capabilities. A link to the examples and doc should be provided.

[pdebuyl]

@SergeDmi thank you very much for the review.

@glyg you can choose to address directly @SergeDmi 's review or to wait for @fcooper8472 's review. Let us know how you wish to proceed.

[glyg]

Hi @pdebuyl and @SergeDmi

Thank you a lot for your review Serge. @sophietheis and I are giving a workshop on tyssue next week, which will allow to test in the field a better tutorial.

If this is ok with you, we will answer Serge's remarks only after that (within the next 2 weeks).

[whedon]

👋 @SergeDmi, please update us on how your review is going.

[whedon]

👋 @fcooper8472, please update us on how your review is going.

[pdebuyl]

@SergeDmi our bot is sometimes a bit zealous, sorry :-)

[pdebuyl]

Hi @glyg , any update?

[glyg]

Hi @pdebuyl we meet with Sophie on Friday to workout a revision plan, we gave a workshop last week that should help address Serge's remarks. I'll update on Monday

[glyg]

Hi @pdebuyl - The update to the doc is going on under this issue: DamCB/tyssue-demo#4 - we are going back through the notebooks and trying to follow @SergeDmi 's advice to be more progressive. Also some newest notions as the EventManager haven't been documented properly yet.

As for the paper itself, we thought it might be better to have the comments from the second reviewer before we undertake the revisions.

[pdebuyl]

@fcooper8472 can you address the "code" part of the review already (general checks, functionality, and documentation)?

[pdebuyl]

@glyg you can proceed along DamCB/tyssue-demo#4 . You can also address @SergeDmi 's paper comments as that won't intersect yet with the review of @fcooper8472

[glyg]

ok, I'll try to make some progress at the end of the week, then Sophie (who's absent this week) will relay

[pdebuyl]

@sophietheis ping

[sophietheis]

Hi,
I am working on demo notebook, and I am also starting to improve the manuscript according to @SergeDmi comments.
Modifications are on my remote, I will start a PR tomorrow.

[pdebuyl]

@fcooper8472 ping

[sophietheis]

Hi @SergeDmi

You can find in the PR the modification made to our manuscript according to your comments.

1. Statement of need
   The statement of need does a good job of explaining the context, but lacks in describing the actual need for the software. A mention of existing software is also lacking. Instead, this paragraph gives a short description of Tyssue.

We are agree that there is a lack of information about the need and the existing software. We have expanded this part with reference with several publish work :

Several vertex models have been developed in the past few years to describe the physics of epithelia (for a review, see [@alt:2017]), and common features can be identified. Several kinds of models have already been published. The apical vertex model has been used several times to study topology changes during morphogenetic movement in Drosophila, Hydra and Xenopus([@staple:2010], [@farhadifar:2007], [@Aegerter:2012]). Associated with protein dynamics, it has been used to study the effect of protein position on tissue organisation in zebrafish retina ([@salbreux:2012]). 3D vertex model have been used to study epithelium deformation due to normal development or to cancer development ([@okuda:2015], [@Eritano:2020]).
Most of the time, models are developed for a specific biological question and are difficult to adapt to an other system, for severals reasons. With the tyssue library, we propose models which are adaptable and scalable with the fied research and the biological question. Topology and mechanics are implement independantly to improve the versatility of models.

2. Software description
   I think the article fails to convey the organization of Tyssue, that "Separates structure, geometry and models" (better explained in the readme). As a consequence, it is not clear that the models (referenced in the paragraph mechanics) can be chosen at will between Euler, Gradient descent, Quasi-static, and possibly other and user defined ; the same applies to topology.

We add a scheme into the manuscript to highlight the modularity of our library (new scheme).

[sophietheis]

@whedon check references

[sophietheis]

Fixed parentheses & some typos

@whedon generate pdf

Also fixed missing references.

[pdebuyl]

Hi @glyg and @sophietheis . I opened PR DamCB/tyssue#244 with the remaining syntax issues. I added a section title for the "not statement of need" part of the paper and fix a minor grammatical error.

Can you have a look at it and let me know if it is suitable for you? A final request: in the acknowledgments, you include one of the co-authors. Can you change it to "We wish to thank the team of Magali Suzanne (...)"? The current situation is a bit weird.

Apart from these issues, I am good for approving the paper.

[glyg]

Thanks a lot @pdebuyl - I thought I did remove the tags here but I guess there was some merge problem, sorry you had to do it again.

The current situation is a bit weird.

Ha yes good point, I saw it and was not sure how to get around it. I rephrased it now.

[pdebuyl]

@whedon check references

[whedon]

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

OK DOIs

- 10.1016/j.devcel.2021.01.005 is OK
- 10.2139/ssrn.3378007 is OK
- 10.21105/joss.01848 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41467-019-10720-0 is OK
- 10.1101/704932 is OK
- 10.1038/s41467-018-06497-3 is OK
- 10.1242/dev.146761 is OK
- 10.1098/rstb.2015.0520 is OK
- 10.1038/nphys3471 is OK
- 10.1038/nature14152 is OK
- 10.1007/s10237-015-0724-7 is OK
- 10.1007/s10237-012-0430-7 is OK
- 10.1371/journal.pcbi.1002618 is OK
- 10.1242/dev.082800 is OK
- 10.1016/j.cell.2010.07.042 is OK
- 10.1016/J.CUB.2010.06.075 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/J.CUB.2007.11.049 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/S0021-9290(02)00006-4 is OK
- 10.1016/S0074-7696(08)62339-6 is OK
- 10.1016/0022-5193(78)90315-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[pdebuyl]

@whedon generate pdf

[whedon]

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

[pdebuyl]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.devcel.2021.01.005 is OK
- 10.2139/ssrn.3378007 is OK
- 10.21105/joss.01848 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41467-019-10720-0 is OK
- 10.1101/704932 is OK
- 10.1038/s41467-018-06497-3 is OK
- 10.1242/dev.146761 is OK
- 10.1098/rstb.2015.0520 is OK
- 10.1038/nphys3471 is OK
- 10.1038/nature14152 is OK
- 10.1007/s10237-015-0724-7 is OK
- 10.1007/s10237-012-0430-7 is OK
- 10.1371/journal.pcbi.1002618 is OK
- 10.1242/dev.082800 is OK
- 10.1016/j.cell.2010.07.042 is OK
- 10.1016/J.CUB.2010.06.075 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/J.CUB.2007.11.049 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/S0021-9290(02)00006-4 is OK
- 10.1016/S0074-7696(08)62339-6 is OK
- 10.1016/0022-5193(78)90315-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2365

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2365, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[pdebuyl]

Thanks all for the submission and review! The editor-in-chief in rotation will pick up the process soon for finalizing the publication.

[glyg]

Great!!! Thanks a lot :)

[kthyng]

@glyg I see a small fix in your paper to make: in the parenthetical statement "for a review, see", the reference there should be in-line, not parenthetical. So, you should remove the [] around that reference.

[glyg]

Thanks @kthyng good catch, I fixed it

[glyg]

@whedon generate pdf

[whedon]

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

[kthyng]

Ok I think everything looks good!

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02973 joss-papers#2369
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02973
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @glyg! Thanks to @pdebuyl for editing and to reviewers @fcooper8472 and @SergeDmi for your time, hard work, and expertise!!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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HTML:
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reStructuredText:
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[glyg]

this is really great!!! Thank you all for the great review process!!!