[REVIEW]: Molearn: a Python package streamlining the design of generative models of biomolecular dynamics

[editorialbot]

Submitting author: !--author-handle-->@degiacom<!--end-author-handle-- (Matteo Degiacomi) Repository: https://github.com/Degiacomi-Lab/molearn Branch with paper.md (empty if default branch): Version: v2.0.3 Editor: !--editor-->@richardjgowers<!--end-editor-- Reviewers: @rmeli, @JoaoRodrigues Archive: 10.5281/zenodo.8284102

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217"><img src="https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217/status.svg)](https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217)

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

@rmeli & @JoaoRodrigues, 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 @richardjgowers 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 @RMeli

[richardjgowers]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1146/annurev-biochem-060614-034142 is OK
- 10.1146/annurev-biochem-013118-111947 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.str.2019.03.018 is OK
- 10.1103/PhysRevX.11.011052 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1110/ps.062416606 is OK
- 10.1093/bioinformatics/btx789 is OK
- 10.1063/5.0058639 is OK
- 10.1126/science.aaw1147 is OK
- 10.1063/1.5023804 is OK
- 10.1039/d0sc03635h is OK
- 10.1021/acs.jctc.2c00058 is OK
- 10.1021/acs.jctc.5b00255 is OK
- 10.1093/bioinformatics/btab785 is OK
- 10.1002/jcc.21787 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4516, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@degiacom I am the AEiC for this track and here to help process final steps. I have check this review, the repository, the paper, and the archive, and most seems in order. I only have the below points that require your attention:

• [ ] in your affiliations please spell out UK as United Kingdom.

[degiacom]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[degiacom]

Hello @Kevin-Mattheus-Moerman, I fixed the affiliation as indicated.

[Kevin-Mattheus-Moerman]

@degiacom thanks. All looks good now. I did notice that although you have contributing guidelines in an CONTRIBUTING.md file, you do not link to it in your README. We can proceed here but I would recommend that you also have a Contributing heading in the README and link to that file.

I'll now proceed to process this for acceptance in JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[degiacom]

Thank you for your feedback @Kevin-Mattheus-Moerman, I have edited the README file to point to CONTRIBUTING.md. Thank you also for accepting our work!

[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: Musson given-names: Samuel C. orcid: "https://orcid.org/0000-0002-2189-554X" - family-names: Degiacomi given-names: Matteo T. orcid: "https://orcid.org/0000-0003-4672-471X" contact: - family-names: Degiacomi given-names: Matteo T. orcid: "https://orcid.org/0000-0003-4672-471X" doi: 10.5281/zenodo.8284102 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Musson given-names: Samuel C. orcid: "https://orcid.org/0000-0002-2189-554X" - family-names: Degiacomi given-names: Matteo T. orcid: "https://orcid.org/0000-0003-4672-471X" date-published: 2023-09-05 doi: 10.21105/joss.05523 issn: 2475-9066 issue: 89 journal: Journal of Open Source Software publisher: name: Open Journals start: 5523 title: "Molearn: a Python package streamlining the design of generative models of biomolecular dynamics" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05523" volume: 8 title: "Molearn: a Python package streamlining the design of generative models of biomolecular dynamics" ```

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 :point_right: https://github.com/openjournals/joss-papers/pull/4529
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05523
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...

[RMeli]

Yay! Congratulations @degiacom and @SCMusson! 🎉

[degiacom]

Thank you @Rmeli! As instructed by @editorialbot, we will now party like we just published a paper :D

[Kevin-Mattheus-Moerman]

@degiacom congratulations on this publication!

Thanks for editing @richardjgowers

And a special thanks to the reviewers: @RMeli, @JoaoRodrigues !

[editorialbot]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.05523/status.svg)](https://doi.org/10.21105/joss.05523)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05523">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05523/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05523/status.svg
   :target: https://doi.org/10.21105/joss.05523

This is how it will look in your documentation:

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