[REVIEW]: High-performance neural population dynamics modeling enabled by scalable computational infrastructure

[editorialbot]

Submitting author: @a9p (Aashish Patel)
Repository: https://github.com/TNEL-UCSD/autolfads-deploy
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @emdupre
Reviewers: @richford, @tachukao
Archive: 10.5281/zenodo.7719505

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d2a1ec960ccd6200efd60f5b131de2f1/status.svg)](https://joss.theoj.org/papers/d2a1ec960ccd6200efd60f5b131de2f1)

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

@richford & @tachukao, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emdupre 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 @richford

📝 Checklist for @tachukao

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.35 s (751.3 files/s, 252409.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                           956            816           3611         332355
Python                          10            208            286           1386
Markdown                        29            441              0           1118
Bourne Shell                    12            133            200            496
TeX                              1             14              0            141
make                             5             25             14             58
JSON                             3              0              0             51
-------------------------------------------------------------------------------
SUM:                          1016           1637           4111         335605
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2035

[editorialbot]

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

OK DOIs

- 10.1038/nn.3776 is OK
- 10.1101/2021.01.13.426570 is OK
- 10.1038/s41592-018-0109-9 is OK
- 10.48550/arXiv.1711.09846 is OK
- 10.48550/arXiv.1712.05889 is OK
- 10.48550/arXiv.2006.02085 is OK
- 10.48550/arXiv.2109.04463 is OK
- 10.1038/s41586-021-03506-2 is OK
- 10.7554/eLife.66410 is OK
- 10.1146/annurev-neuro-092619-094115 is OK
- 10.1038/s41593-018-0095-3 is OK
- 10.1523/JNEUROSCI.0508-17.2018 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[emdupre]

👋 Hi @richford and @tachukao !

Thank you again for agreeing to review this submission ! The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @\editorialbot generate my checklist.

⭐ I know that the holiday season is here, so just to flag : We ask that reviewers provide their feedback within six weeks. If you anticipate any difficulties in working with this timeline, please let me know !

Otherwise, in working through the checklist, you're likely to have specific feedback on autolfads-deploy. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

[richford]

Review checklist for @richford

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/TNEL-UCSD/autolfads-deploy?
• 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 (@a9p) 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?

[tachukao]

@\editorialbot generate my checklist

[emdupre]

Sorry @tachukao , you'll need to remove the slash ! I just included it so that I didn't trigger the bot myself 🙂

If you enter the updated text in a new comment in-thread, it should trigger your checklist creation !

[tachukao]

Review checklist for @tachukao

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/TNEL-UCSD/autolfads-deploy?
• 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 (@a9p) 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?

[emdupre]

Hi @richford and @tachukao,

I just wanted to check-in on how this review process is going for you. Please let me know if you're having any difficulties in working through your reviewer checklist or interacting with autolfads-deploy.

[yarikoptic]

note: if reviewers do not emerge -- I would be happy to review, let me know @emdupre . Cheers.

[tachukao]

I just wanted to check-in on how this review process is going for you. Please let me know if you're having any difficulties in working through your reviewer checklist or interacting with autolfads-deploy.

Hi @emdupre, thanks for following up. Still working through the checklist

[tachukao]

Hi @emdupre, the citations look good to me in the proofs, but I'm a bit confused about how I should be checking the citation syntax in the text? Thanks for your help!

[richford]

Hi @emdupre, thanks for following up with me as well. I'm still working through the checklist and will aim to have it completed by Feb 10.

[emdupre]

Hi everyone,

Thanks for your updates !

@yarikoptic I appreciate the offer, and I will certainly keep you in mind for future reviews. Though I'm sure that the authors would appreciate your feedback regardless 😸

Hi @emdupre, the citations look good to me in the proofs, but I'm a bit confused about how I should be checking the citation syntax in the text? Thanks for your help!

Thanks for your attention on this, @tachukao ! If the citations are rendering appropriately in the proof, then they're in the appropriate syntax. As an editor, I'll make sure that all of the formatting information in the actual References section is correct once you and @richford can confirm that all of the relevant work is cited !

[cpandar]

Thanks very much! I wasn't sure if this message was for the authors or editors, but just FYI the proofs look great to the authors!

[cpandar]

@emdupre @richford @tachukao we appreciate all your efforts. This has been a fun review/editing process! I wish they were all this straightforward and clear.

[Kevin-Mattheus-Moerman]

@a9p I am the AEiC in this track and here to help process this work for acceptance. I have reviewed the archive and the paper and have the following remaining items that require your attention:

On the paper:

• Please complete the affiliations with the country, e.g. United States of America (do not abbreviate as USA).
• Is the word containerd okay or should that be containered?

On the archive:

• Please ensure the archive listed license matches your software license, it currently says "Other(Open)" so you'll have to manually edit this.

[a9p]

Hi @Kevin-Mattheus-Moerman! Thank you for your suggestions; they should all be addressed now -

• Country added to all affiliations
• containerd is the name of the container d[aemon] solution (ref)
• Archive updated with the appropriate license

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@a9p thanks. All looks good now.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05023 joss-papers#4066
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05023
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]

Congratulations on this JOSS paper @a9p !!

And thank you to @emdupre for editing this work, and to @richford and @tachukao for their review efforts! Thanks!

[editorialbot]

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

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