[REVIEW]: Flint: a simulator for biological and physiological models in ordinary and stochastic differential equations

[whedon]

Submitting author: @tabe (Takeshi Abe)
Repository: https://github.com/flintproject/Flint
Version: Flint-2.4.0RC1-JOSS
Editor: @majensen
Reviewers: @mstimberg, @dawbarton
Archive: 10.5281/zenodo.4017040

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Status

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Markdown: [![status](https://joss.theoj.org/papers/ba63c7df89b7f27f5d8003bc42cdf5e5/status.svg)](https://joss.theoj.org/papers/ba63c7df89b7f27f5d8003bc42cdf5e5)

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.)

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

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

Review checklist for @dawbarton

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 (@tabe) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @mstimberg

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 (@tabe) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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. @funasoul, @mstimberg it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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[whedon]

👉 Check article proof 📄 👈

[majensen]

@whedon remind @majensen in 5 days

[whedon]

Reminder set for @majensen in 5 days

[majensen]

@arfon - should I remind @whedon to remind me? 😄

[arfon]

:-) we'll see...

[mstimberg]

I've started reviewing but I have to say that I had some difficulties to get things going. I'm on Ubuntu, so none of the provided binary packages applies to my situation. I had a look into installing from source, but it seems to require many dependencies that are non-standard and would have to be installed from source as well. Since I did not want to go down that rabbit hole I installed CentOS 8 in a Virtual Machine and used the provided binaries instead. I can confirm that the installation works, but then again things get a bit difficult: the only concrete example file mentioned in the user documentation (I did not look at the Youtube videos, though) is a file "distributed as part of the PhysioDesigner installation". PhysioDesigner seems to be a related project, but it is not mentioned in the JOSS article. The Flint website has a link to www.physiodesigner.org, but this website seems to be down. Same for https://physiome.jp, the other link to an external source on the website (without any explanation what it refers to). I finally got the simulator running with an SMBL file from elsewhere and I will continue to do the review, but as first suggestions for improvement @tabe:

• Give some details about related projects such as PhysioDesigner or physiome.jp in the JOSS article
• Provide clear instructions how to get example files in the documentation, or distribute them with the software itself
• The website has packages for CentOS/RHEL and the github repository also mentions them, but the user guide only has instructions for Windows/OS X

[tabe]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[tabe]

Dear @mstimberg,

* Give some details about related projects such as PhysioDesigner or  physiome.jp in the JOSS article

I've mentioned the physiome.jp project and related tools in the last revision of paper.md.
Confirmed their sites are out of reach now, I'm not sure when they will come back though.

* Provide clear instructions how to get example files in the documentation, or distribute them with the software itself

I'm going to reconsider the examples in the user guide, and include the model files in the distribution, too.

* The website has packages for CentOS/RHEL and the github repository also mentions them, but the user guide only has instructions for Windows/OS X

I will update the user guide in order to include descriptions specific to CentOS/RHEL.
Thank you for your suggestions.

[mstimberg]

Thanks for the changes so far, I was now able to install Flint from source on Ubuntu 18.04. I opened two issues in the project's repository:

• Installation instructions: [JOSS review] Suggestions for installation docs flintproject/Flint#15
• User manual: [JOSS review] Suggestions for user manual flintproject/Flint#16

Here a few general comments about the article, the software, and the website:

• The last sentence of the first paragraph of the introduction ("As a consequence, ...") is rather unclear and would benefit from rewriting, I think.
• Still in the introduction, the authors states "aims to establish a computational platform for multiscale in silico studies on physiome". I have to admit that I have not come across the term "physiome" so far, so it might benefit from a little explanation/reference for the general audience.
• The main weakness of the introduction is that the unique contribution of Flint remains a bit unclear. Is it that it can not only simulate SBML models (as many other simulators), but also models on a higher level defined in PHML that include low-level descriptions in SBML? Does it offer benefits for users only interested in SBML models?
• It seems a bit odd that the implementation section only focusses on the parameter fitting functionality. From what I understood, this is more of a "bonus feature" (which is not even mentioned in the user manual). Of course the paper is not meant to replace technical documentation, but maybe there is something to say about the high level functionality of the general software here (e.g. how it leverages existing libraries for its functionality, or how it uses multi-threading, etc.)?
• The README mentions that the project's website contains "its user manual and tutorials", but the "Tutorial videos on YouTube" linked on that site seem to be tutorials for PhysioDesigner, not for Flint (at least judging from their titles).

Minor issues:

• In the last sentence of the first paragraph, the abbrevations that are directly followed by citations (e.g. "(SBML) (Hucka et al., 2003)") look a bit ugly. I think you can use [SBML; @hucka_systems_2003] instead of (SBML) [@hucka_systems_2003] (did not test this, though).

[tabe]

Dear @mstimberg,

* Installation instructions: [flintproject/Flint#15](https://github.com/flintproject/Flint/issues/15)

* User manual: [flintproject/Flint#16](https://github.com/flintproject/Flint/issues/16)

Thank you for opening the above issues, we've started working to solve them.

Here a few general comments about the article, the software, and the website:

They are all reasonable, so revising our paper to amend the weakness you pointed out.

* The README mentions that the project's website contains "its user manual and tutorials", but the ["Tutorial videos on YouTube"](https://www.youtube.com/user/PhysioDesigner) linked on that site seem to be tutorials for `PhysioDesigner`, not for `Flint` (at least judging from their titles).

The videos do include how to simulate PHML models by Flint while the focus is how to edit them with PhysioDesigner.
We will prepare a new tutorial dedicated to Flint soon.

[tabe]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[mstimberg]

Dear @tabe: given that you left the issues open, I assume you are still working on them? Let me/us know when you want us to have another look.

I am afraid I will be out of office from July 13th to July 31st, though, so I cannot guarantee any timely response during that period.

[majensen]

@mstimberg, just want to thank you for your work so far. @funasoul -- have you had an opportunity to take a look at this software? Thanks very much -

[tabe]

@mstimberg,

Dear @tabe: given that you left the issues open, I assume you are still working on them? Let me/us know when you want us to have another look.

Yes, I will add a comment on each of the issues once it is done, to let you know.

[majensen]

Hello @dawbarton - I know you are engaged in another JOSS review at the moment, but I wondered if this work would be interesting to you. We could use your assistance! Thanks for your consideration, and any suggestions for alternative reviewers. --@majensen

[dawbarton]

Hello @dawbarton - I know you are engaged in another JOSS review at the moment, but I wondered if this work would be interesting to you. We could use your assistance! Thanks for your consideration, and any suggestions for alternative reviewers. --@majensen

I'd be happy to take a look at this but realistically I won't get chance to take a look until w/c 8 August (or slightly after depending on what is happening in that week). If that's fine with you, I'll do it.

[majensen]

Thanks @dawbarton that would be great.

[majensen]

@whedon add @dawbarton as reviewer

[whedon]

👉 Check article proof 📄 👈

[majensen]

@tabe we are ready to move forward. Can I ask you to create an archive of the Flint repository (using Zenodo, FigShare, or similar)? The title of your archive should match the title of the paper. Then please report back the DOI of the archive in this thread.
Please let me know if you have any questions -

[tabe]

@majensen, uploaded an archive to Zenodo:
https://doi.org/10.5281/zenodo.4017040
I hope this works for you.

[majensen]

@whedon set Flint-2.4.0RC1-JOSS as version

[whedon]

OK. Flint-2.4.0RC1-JOSS is the version.

[majensen]

@whedon set 10.5281/zenodo.4017040 as archive

[whedon]

OK. 10.5281/zenodo.4017040 is the archive.

[majensen]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3389/fphys.2015.00251 is OK
- 10.14326/abe.3.50 is OK
- 10.1109/SAINT.2012.40 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.3389/fphys.2010.00164 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1126/science.290.5495.1358 is OK
- 10.1073/pnas.0406841102 is OK
- 10.1016/j.imr.2015.12.004 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#1713

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1713, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

👋 @tabe - this looks good, and I'm working on the final processing.
Can you merge flintproject/Flint#24, which has some minor changes to the paper?
Also, I think the SUNDIALS TOMS paper should have 10.1145/1089014.1089020 added as the DOI.

[tabe]

Dear @danielskatz,

👋 @tabe - this looks good, and I'm working on the final processing.
Can you merge flintproject/Flint#24, which has some minor changes to the paper?

Done.

Also, I think the SUNDIALS TOMS paper should have 10.1145/1089014.1089020 added as the DOI.

Added at flintproject/Flint@c90b99a.

[danielskatz]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3389/fphys.2015.00251 is OK
- 10.14326/abe.3.50 is OK
- 10.1109/SAINT.2012.40 is OK
- 10.1137/S0036144500378302 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.1145/1089014.1089020 is OK
- 10.3389/fphys.2010.00164 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1126/science.290.5495.1358 is OK
- 10.1073/pnas.0406841102 is OK
- 10.1016/j.imr.2015.12.004 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#1717

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1717, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@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.02331 joss-papers#1718
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02331
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...

[danielskatz]

Thanks to @mstimberg, @dawbarton for reviewing, and @majensen for editing!

And congratulations to @tabe (Takeshi Abe) and co-author!!

[whedon]

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

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.02331/status.svg)](https://doi.org/10.21105/joss.02331)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02331">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02331/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02331/status.svg
   :target: https://doi.org/10.21105/joss.02331

This is how it will look in your documentation:

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