[PRE REVIEW]: flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics

[editorialbot]

Submitting author: !--author-handle-->@marjanalbouye<!--end-author-handle-- (Marjan Albooyeh) Repository: https://github.com/cmelab/flowerMD Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @csadorf, @LIVazquezS, @abhishektiwari Managing EiC: Kevin M. Moerman

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (714.7 files/s, 195639.4 lines/s)
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1188

[editorialbot]

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

OK DOIs

- 10.1038/s41524-022-00906-4 is OK
- 10.1080/00268976.2020.1742938 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.2978177 is OK
- 10.1021/ct0502864 is OK
- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jcim.3c00081 is OK
- 10.1007/978-981-10-1128-3_5 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.5281/zenodo.8370982 is OK
- 10.1088/1361-651X/ab6a44 is OK
- 10.1126/sciadv.abg9763 is OK
- 10.1063/1.470016 is OK
- 10.3390/polym13132162 is OK

MISSING DOIs

- 10.1016/j.commatsci.2019.109363 may be a valid DOI for title: HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations
- 10.1021/acs.macromol.8b00011 may be a valid DOI for title: pyPRISM: a computational tool for liquid-state theory calculations of macromolecular materials

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine Submitting author: @RainierBarrett Handling editor: @richardjgowers (Active) Reviewers: @malramsay64, @rmeli Similarity score: 0.8359

pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics Submitting author: @ArtVoro Handling editor: @jgostick (Active) Reviewers: @janash, @rosecers, @jarvist Similarity score: 0.8335

BioSimSpace: An interoperable Python framework for biomolecular simulation Submitting author: @lohedges Handling editor: @will-rowe (Retired) Reviewers: @amritagos, @richardjgowers Similarity score: 0.8249

FHI-vibes: Ab Initio Vibrational Simulations Submitting author: @flokno Handling editor: @jgostick (Active) Reviewers: @keipertk, @ajjackson Similarity score: 0.8167

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows Submitting author: @AndreWeiner Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg Similarity score: 0.8142

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@marjanAlbouye thanks for this submission. I am the EiC for this track and here to help with initial steps. I will start looking for a handling editor. For the moment can you try work on the following:

• [x] Can you please try to address the above :point_up: potentially missing DOI's
• [x] In your affiliations, can you please spell out USA as United States of America
• [x] Please add clear contributing guidelines to your repository. We recommend adding a CONTRIBUTING.md file and to link to it in your readme. Here is a useful site showing examples of such a file: https://contributing.md/example/

[Kevin-Mattheus-Moerman]

@editorialbot invite @lucydot as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lucydot do you think you can help edit this work? I think @danielskatz has offered to review so that is a nice start.

[danielskatz]

Sorry @Kevin-Mattheus-Moerman - I did not mean to volunteer to review. This is not in my expertise at that level.

[marjanalbooyeh]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41524-022-00906-4 is OK
- 10.1080/00268976.2020.1742938 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.2978177 is OK
- 10.1021/ct0502864 is OK
- 10.1016/j.commatsci.2019.109363 is OK
- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jcim.3c00081 is OK
- 10.1021/acs.macromol.8b00011 is OK
- 10.1007/978-981-10-1128-3_5 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.5281/zenodo.8370982 is OK
- 10.1088/1361-651X/ab6a44 is OK
- 10.1126/sciadv.abg9763 is OK
- 10.1063/1.470016 is OK
- 10.3390/polym13132162 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[marjanalbooyeh]

@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:

[editorialbot]

Five most similar historical JOSS papers:

HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine Submitting author: @RainierBarrett Handling editor: @richardjgowers (Active) Reviewers: @malramsay64, @rmeli Similarity score: 0.8371

pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics Submitting author: @ArtVoro Handling editor: @jgostick (Active) Reviewers: @janash, @rosecers, @jarvist Similarity score: 0.8320

BioSimSpace: An interoperable Python framework for biomolecular simulation Submitting author: @lohedges Handling editor: @will-rowe (Retired) Reviewers: @amritagos, @richardjgowers Similarity score: 0.8213

FHI-vibes: Ab Initio Vibrational Simulations Submitting author: @flokno Handling editor: @jgostick (Active) Reviewers: @keipertk, @ajjackson Similarity score: 0.8145

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows Submitting author: @AndreWeiner Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg Similarity score: 0.8114

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[marjanalbooyeh]

@Kevin-Mattheus-Moerman Thank you. I addressed the comments in your last message.

Here is the list of our suggested reviewers:

• LIVazquezS
• srmnitc
• csadorf
• ptmerz
• rosecers

[lucydot]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lucydot is now the editor

[lucydot]

Hi @LIVazquezS @csadorf @rosecers - are you available to review this submission to JOSS? It is molecular dynamics + Python + reproducible workflows, which appears in-line with some of your interests...

[LIVazquezS]

Hi @lucydot , Yes, I am available to review this work.

[csadorf]

@lucydot Yes, I can review this.

[rosecers]

@lucydot as it might be a COI to have @csadorf and I both reviewing, I'll opt out of this review. Let me know if you end up needing another round.

[abhishektiwari]

@lucydot I will be open to review this submission. Have worked with scientific workflow systems.

[lucydot]

Thanks @rosecers for your update, we now have three reviewers so your expertise won't be needed (for this one!).

Thanks @csadorf @LIVazquezS @abhishektiwari - I'll add you now as reviewers, and then ask our editorialbot to start a new thread for the review itself. There will be instructions generated at the top of the new thread. If you have any questions about the process please do contact me, the best place to do that will be over in that new thread.

[lucydot]

@editorialbot add @csadorf as reviewer

[editorialbot]

@csadorf added to the reviewers list!

[lucydot]

@editorialbot add @LIVazquezS as reviewer

[editorialbot]

@LIVazquezS added to the reviewers list!

[lucydot]

@editorialbot add @abhishektiwari as reviewer

[editorialbot]

@abhishektiwari added to the reviewers list!

[lucydot]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5989.