[REVIEW]: STReNGTHS, a Python package to model and simulate complex reaction-diffusion systems

[editorialbot]

Submitting author: @ThibaultFillion (Thibault Fillion)
Repository: https://github.com/ThibaultFillion/strengths
Branch with paper.md (empty if default branch): main
Version: v0.0.16.6
Editor: @Nikoleta-v3
Reviewers: @parikshitbajpai, @jakryd
Archive: 10.5281/zenodo.11300235

Status

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Markdown: [![status](https://joss.theoj.org/papers/6ab8888e81d77b4c8b30be118c67d484/status.svg)](https://joss.theoj.org/papers/6ab8888e81d77b4c8b30be118c67d484)

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

@parikshitbajpai & @jakryd, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Nikoleta-v3 know.

✨ 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 ✨

Checklists

📝 Checklist for @parikshitbajpai

📝 Checklist for @jakryd

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.71.041103 is OK
- 10.1063/1.1378322 is OK
- 10.1371/journal.pcbi.1006830 is OK
- 10.1093/bioinformatics/bti431 is OK
- 10.1049/sb:20045021 is OK
- 10.1093/bioinformatics/btw469 is OK
- 10.3389/neuro.11.015.2009 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1143.4 files/s, 195700.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35           1889           2207           5036
C/C++ Header                     8            212            216           1155
JSON                             8              0              0           1100
reStructuredText                29            691            765            925
C++                              1             92             36            464
Markdown                         1             33              0            258
TeX                              1             19              0            136
CSS                              1             11              1             56
DOS Batch                        1              8              1             26
YAML                             2              1              4             25
make                             1              4              7              9
JavaScript                       1              1              0              8
TOML                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            90           2961           3237           9206
-------------------------------------------------------------------------------

Commit count by author:

    69	ThibaultFillion

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2346

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[Nikoleta-v3]

Hey @parikshitbajpai, @jakryd this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements ✅ As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6454 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3) if you have any questions/concerns. 😄 🙋🏻

[editorialbot]

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

[parikshitbajpai]

Review checklist for @parikshitbajpai

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 https://github.com/ThibaultFillion/strengths?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ThibaultFillion) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[ThibaultFillion]

@editorialbot commands

[editorialbot]

Hello @ThibaultFillion, here are the things you can ask me to do:

# List all available commands
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@editorialbot list editors

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@editorialbot generate my checklist

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@editorialbot check repository

# Check the references of the paper for missing DOIs
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# Get a link to the complete list of reviewers
@editorialbot list reviewers

[Nikoleta-v3]

Hello @parikshitbajpai @jakryd 👋🏻 I hope you are well! Any updates on your reviews? 😄

[parikshitbajpai]

Any updates on your reviews? 😄

Hello @Nikoleta-v3, hope you're doing well. Sorry for the time this is taking, I was a bit caught up at work the last couple of weeks. I should be able to finish the review by the end of this week.

[parikshitbajpai]

Hello @ThibaultFillion,

I am almost done with the review but have a few doubts I hope you can clarify.

1. Are the other similar tools specific to certain applications? I feel there are other general purpose PDE solvers which could be used for modelling reaction-diffusion system, e.g. FEM codes. Could you please clarify the criteria you used.
2. Are the examples meant to be original results or are they demonstrating the capability? I might have missed it in the manuscript if they were meant to be original results, and, if not, can you please clarify if the examples are based on some previously available models / results since that was not referenced?
3. Would you consider adding the examples scripts to the repo? It will enable users and people reading the article to quickly be able to verify the showcased capabilities.

Thanks!

[jakryd]

Review checklist for @jakryd

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 https://github.com/ThibaultFillion/strengths?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ThibaultFillion) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[jakryd]

The limitations of the package are explained in the paper, but I think that it can still be useful, especially for students who are starting to learn about such algorithms. The examples shown in @ThibaultFillion's paper are particularly compelling, and it would be great to make them available as Jupyter Notebooks so that users can experiment with them. But this can be done after publication. Overall, I did not come across any issues with the current version, and I am happy to recommend publication without any further modifications.

[ThibaultFillion]

@editorialbot generate pdf

[editorialbot]

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

[ThibaultFillion]

Thank you for your reviews @parikshitbajpai and @jakryd .

@parikshitbajpai Thank you for raising your concerns.

1. The similar tools evoked in the paper are all tools applied to the modeling and simulation of biochemical systems, providing an abstract interface above the lower level considerations such as ODE or PDE solving.
2. The figures in the paper are original results but are solely here for the purpose of illustrating some of the different features of the package. The first considers a fictive signal transduction scheme.
   The reaction rates are reasonable guesses but the diffusion coefficients are set from the literature and represent the correct order of magnitude, based on how and where the different species diffuse.
   We have added references for this in the manuscript.
   The second model applies some generic pattern-forming network to systems with various shapes.
   We added references to the documentation of the package as similar pattern-forming reaction-diffusion networks are used there.
3. Indeed, we added the simulation scripts to the paper repository.

@jakryd Thank you for your review. Making examples available as Jupyter notebooks would be a good idea. For now, we added the simulation scripts for the two examples to the paper repository.

[parikshitbajpai]

@ThibaultFillion Thanks for addressing those and adding the example scripts. Everything looks great and the paper can be accepted as it is.

[Nikoleta-v3]

Thank you to both reviewers for your time and efforts! @ThibaultFillion, please give me one week to also have a final look over the submission, and then we can move forward to the next steps!

[editorialbot]

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

[ThibaultFillion]

@editorialbot generate pdf

[editorialbot]

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

[ThibaultFillion]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@ThibaultFillion as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

• The version tag listed for this review should both match one of the tags for your repository, as well as match the version listed on the ZENODO archive. Currently you have 6 versions on ZENODO but I cannot see one for v0.0.16.2. Should you edit the ZENODO listed version tag? Or should be edit the one listed for this review to be the latest archived version/tag e.g. v0.0.16.5, please advise.

[Kevin-Mattheus-Moerman]

@jakryd thanks for your help with this review. One of your review tickboxes, i.e. the one for "performance" is unticked. Can you clarify if this is untensional? If not, can you please tick the box at this point? Thanks!

[ThibaultFillion]

Hello @Kevin-Mattheus-Moerman.

We would like to switch to the version v0.0.16.6.
Here is the corresponding Zenodo archive:

https://zenodo.org/records/11300235

The corresponding DOI is:

DOI: 10.5281/zenodo.11300235

Compared to the previous versions, we fixed some typos and made a minor change in a paragraph (commit fd38361 in the main branch of the software repository), and rectified author affiliations.

Also, we would like to slightly change the title, previously:

"STReNGTHS, a Python package to model and simulate reaction-diffusion systems"

to:

"STReNGTHS, a Python package to model and simulate complex reaction-diffusion systems"

Sorry for all those last-minute changes.

[ThibaultFillion]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.11300235 as archive

[editorialbot]

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

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot set archive as 10.5281/zenodo.11300235

[editorialbot]

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

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.11300235 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11300235

[Kevin-Mattheus-Moerman]

@editorialbot set v0.0.16.6 as version

[editorialbot]

Done! version is now v0.0.16.6

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Fillion
  given-names: Thibault
- family-names: Piazza
  given-names: Francesco
doi: 10.5281/zenodo.11300235
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Fillion
    given-names: Thibault
  - family-names: Piazza
    given-names: Francesco
  date-published: 2024-05-25
  doi: 10.21105/joss.06495
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6495
  title: STReNGTHS, a Python package to model and simulate complex
    reaction-diffusion systems
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06495"
  volume: 9
title: STReNGTHS, a Python package to model and simulate complex
  reaction-diffusion systems

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06495 joss-papers#5386
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06495
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...

[Kevin-Mattheus-Moerman]

@ThibaultFillion congratulations on this JOSS publication!

@Nikoleta-v3 thanks for editing!

And a special thank you to the reviewers: @parikshitbajpai, @jakryd !!!!

[editorialbot]

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

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[ThibaultFillion]

Great news! Thank you @Kevin-Mattheus-Moerman, @Nikoleta-v3, @parikshitbajpai and @jakryd!
It was a pleasure publishing in JOSS!