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[REVIEW]: Tyssue, en Epithelium simulation library #2973
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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 🎉. 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:
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@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. |
ReviewSoftware structure and installationI 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 effortI 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 usageTyssue 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. ArticleStatement of needThe 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 descriptionI 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. RecommendationThe 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. |
@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. |
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). |
👋 @SergeDmi, please update us on how your review is going. |
👋 @fcooper8472, please update us on how your review is going. |
@SergeDmi our bot is sometimes a bit zealous, sorry :-) |
Hi @glyg , any update? |
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 |
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 As for the paper itself, we thought it might be better to have the comments from the second reviewer before we undertake the revisions. |
@fcooper8472 can you address the "code" part of the review already (general checks, functionality, and documentation)? |
@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 |
ok, I'll try to make some progress at the end of the week, then Sophie (who's absent this week) will relay |
@sophietheis ping |
Hi, |
@fcooper8472 ping |
Hi @SergeDmi You can find in the PR the modification made to our manuscript according to your comments.
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]).
We add a scheme into the manuscript to highlight the modularity of our library (new scheme). |
@whedon check references |
Also fixed missing references. |
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. |
@whedon check references |
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@whedon generate pdf |
@whedon recommend-accept |
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👋 @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
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Thanks all for the submission and review! The editor-in-chief in rotation will pick up the process soon for finalizing the publication. |
Great!!! Thanks a lot :) |
@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. |
Thanks @kthyng good catch, I fixed it |
@whedon generate pdf |
Ok I think everything looks good! |
@whedon accept deposit=true |
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Congrats on your new publication @glyg! Thanks to @pdebuyl for editing and to reviewers @fcooper8472 and @SergeDmi for your time, hard work, and expertise!! |
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this is really great!!! Thank you all for the great review process!!! |
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
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.
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