[REVIEW]: MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes #5380

editorialbot · 2023-04-17T17:21:14Z

Submitting author: @amiralih (Amirali Hossein)
Repository: https://github.com/amiralih/MembraneAnalysis.jl
Branch with paper.md (empty if default branch):
Version: v0.3.2
Editor: @majensen
Reviewers: @tonigi, @davidnsousa
Archive: 10.5281/zenodo.8084178

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Checklists

📝 Checklist for @davidnsousa

📝 Checklist for @tonigi

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-04-17T17:21:16Z

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editorialbot · 2023-04-17T17:21:18Z

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

OK DOIs

- 10.1103/PhysRevE.103.042413 is OK
- 10.1016/j.bpj.2022.07.036 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-04-17T17:21:18Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (991.8 files/s, 175218.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                            9            804            188           2167
TOML                             3            211              1            961
Markdown                        10             82              0            239
YAML                             4              4              4             86
TeX                              1              1              0             22
-------------------------------------------------------------------------------
SUM:                            27           1102            193           3475
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-04-17T17:21:19Z

Wordcount for paper.md is 375

editorialbot · 2023-04-17T17:22:37Z

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

majensen · 2023-04-17T21:45:20Z

@editorialbot add @davidnsousa as reviewer

editorialbot · 2023-04-17T21:45:21Z

@davidnsousa added to the reviewers list!

davidnsousa · 2023-04-22T21:14:47Z

Review checklist for @davidnsousa

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/amiralih/MembraneAnalysis.jl?
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 (@amiralih) 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?

davidnsousa · 2023-04-22T22:24:27Z

Concerning functionality and documentation:

Not all documented core functions have automated tests that confirm the functional claims.
Tutorial is insufficient to understand the software usage: it does not provide example input data/files along with an explanation of how to structure input data; example data that allows to test every core function would be useful to confirm functional claims and tutor users along.
The peptide_radial_distribution function lacks a documentation entry.

tonigi · 2023-04-25T12:47:27Z

Review checklist for @tonigi

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/amiralih/MembraneAnalysis.jl?
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 (@amiralih) 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?

tonigi · 2023-04-25T13:38:12Z

There are a couple of areas that could benefit from a bit more polish. First, the tutorial. I would recommend a self-standing working simple example with example data. It does not start with using, which means that one gets an error out of the box

UndefVarError: DOPC_aa not defined

From what I can tell, it tries to open s.pdb, which is not in the repository. Could it be provided, and the tutorial made to analyze just one trajectory, for the sake of clarity?

In general, both the paper and the documentation are quite short. One could supplement the other, but in this case a lot of context is missing. For one, there is basically no mention of any other membrane analysis tools (state of the field), and there are many.

majensen · 2023-05-23T00:06:37Z

@amiralih how are your responses coming along to the editors' comments here?
Thanks

amiralih · 2023-05-24T00:31:32Z

@majensen I have tagged version 0.3.0 that addresses the issues raised by the reviewers:

The paper has been updated to emphasize key functionality of the package that distinguishes it from existing alternatives.
The tutorial has been updated with a set of accompanying trajectory files to be self-sufficient.
Test coverage has been expanded.

amiralih · 2023-05-25T17:08:18Z

@editorialbot commands

editorialbot · 2023-05-25T17:08:20Z

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


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amiralih · 2023-06-01T20:50:14Z

@majensen Hi, do I need to take any action to update the submission to the latest version of the repository, or to notify the reviewers about the changes? Thanks.

majensen · 2023-06-02T13:07:53Z

@amiralih they should be following the thread here -- @tonigi @davidnsousa please have a look. Thanks

tonigi · 2023-06-03T12:50:49Z

What about @editorialbot generate pdf

tonigi · 2023-06-03T12:52:08Z

@editorialbot generate pdf

editorialbot · 2023-06-03T12:53:22Z

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

tonigi · 2023-06-03T13:28:21Z

Trying to run the tutorial I get

julia> for i in traj_inds
           traj_file = traj_dir * traj_name * string(i) * traj_ext
           output_file = output_dir * "fs_$(i).h5"

           fluctuation_spectrum(;
               pdb_file=pdb_file,
               traj_file=traj_file,
               output_file=output_file,
               lipids=lipids,
               L_grid=L_grid
           )
       end
ERROR: SystemError: opening file "s.pdb": No such file or directory

Where is s.pdb?

amiralih · 2023-06-03T14:15:42Z

@tonigi The file s.pdb is available (along with the trajectory files) at the link provided in the tutorial:
https://zenodo.org/record/7908906

davidnsousa · 2023-06-03T21:44:43Z

Regarding the improvements I have updated the checklist above.

A statement of need is still missing in the documentation.
A description of how to structure/generate input data would improve the documentation to a more satisfactory level.
The functional claims cannot yet be confirmed from the tutorial.

I tested the tutorial with the example files from the link provided: s.pdb and two trajectory files t1.nc and t2.nc.

Calculating mean sampled curvature of heavy atoms of the lipids fails with:

ERROR: LoadError: UndefVarError: 'traj_id' not defined

I have corrected traj_id to traj_inds which solves the problem. The tutorial should be corrected.

Transverse curvature bias analysis fails with:

ERROR: LoadError: ArgumentError: Cannot open './A.dat': not a file

tonigi · 2023-06-04T08:05:53Z

Uhm... isn't >14 GB of files excessive for a tutorial? Also considering that there doesn't seems to be a way to download all the 100 files at once from Zenodo.

amiralih · 2023-07-04T16:19:32Z

Hi @majensen The changes are done.

majensen · 2023-07-04T19:38:42Z

@editorialbot generate PDF

editorialbot · 2023-07-04T19:38:43Z

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

@editorialbot commands

majensen · 2023-07-04T19:40:21Z

@editorialbot generate pdf

editorialbot · 2023-07-04T19:41:51Z

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

majensen · 2023-07-04T19:46:34Z

@editorialbot recommend-accept

editorialbot · 2023-07-04T19:46:35Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-07-04T19:46:37Z

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

OK DOIs

- 10.1103/PhysRevE.103.042413 is OK
- 10.1016/j.bpj.2022.07.036 is OK
- 10.1002/jcc.21172 is OK
- 10.1021/ci400172g is OK
- 10.1093/bioinformatics/btu037 is OK
- 10.1093/bioinformatics/btw563 is OK
- 10.1021/acs.jctc.9b00453 is OK
- 10.1021/acs.jctc.1c00447 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-04T19:48:19Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4378, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2023-07-06T14:34:35Z

Kevin-Mattheus-Moerman · 2023-07-06T14:36:25Z

@majensen thanks for editing this one. One minor note, you can now use @editorialbot create post-review checklist to create this list ☝️ , and it helps detect things we might sometimes miss, e.g. the archive title here. So something to consider for the future.

Kevin-Mattheus-Moerman · 2023-07-06T14:42:21Z

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

On the archive:

Please manually edit the ZENODO archive title to match your paper title
Please manually edit the ZENODO archive listed license to match your software license

On the paper:

In your affiliations. You may remove the zip code if you like (no need to have a complete postal address), and you can consider using United States of America (as this seems more common in JOSS). But both of these suggestions are optional.
Check spontanous which should probably be spontaneous

majensen · 2023-07-06T14:42:50Z

That is super helpful @Kevin-Mattheus-Moerman thanks!

majensen · 2023-07-06T14:44:07Z

@amiralih can you review the unchecked items in the "Additional author tasks" above?

amiralih · 2023-07-06T15:07:03Z

Hi @Kevin-Mattheus-Moerman I have fixed the issues mentioned.

Kevin-Mattheus-Moerman · 2023-07-06T15:16:48Z

@editorialbot generate pdf

editorialbot · 2023-07-06T15:18:09Z

⚠️ An error happened when generating the pdf.

Kevin-Mattheus-Moerman · 2023-07-06T15:19:46Z

@editorialbot generate pdf

editorialbot · 2023-07-06T15:21:13Z

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

Kevin-Mattheus-Moerman · 2023-07-06T15:25:46Z

@editorialbot accept

editorialbot · 2023-07-06T15:25:48Z

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

editorialbot · 2023-07-06T15:27:42Z

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

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cff-version: "1.2.0"
authors:
- family-names: Hossein
  given-names: Amirali
  orcid: "https://orcid.org/0000-0002-2580-3577"
- family-names: Sodt
  given-names: Alexander J.
  orcid: "https://orcid.org/0000-0002-5570-8212"
doi: 10.5281/zenodo.8084178
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hossein
    given-names: Amirali
    orcid: "https://orcid.org/0000-0002-2580-3577"
  - family-names: Sodt
    given-names: Alexander J.
    orcid: "https://orcid.org/0000-0002-5570-8212"
  date-published: 2023-07-06
  doi: 10.21105/joss.05380
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5380
  title: "MembraneAnalysis.jl: A Julia package for analyzing molecular
    dynamics simulations of lipid membranes"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05380"
  volume: 8
title: "MembraneAnalysis.jl: A Julia package for analyzing molecular
  dynamics simulations of lipid membranes"

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editorialbot · 2023-07-06T15:27:47Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-07-06T15:27:48Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

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Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05380 joss-papers#4385
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Kevin-Mattheus-Moerman · 2023-07-06T21:47:41Z

@amiralih congratulations on this paper in JOSS!

Thanks for editing @majensen !

And a special thanks to the reviewers: @tonigi, @davidnsousa !!!

editorialbot · 2023-07-06T21:47:43Z

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editorialbot added Julia review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 17, 2023

editorialbot assigned majensen Apr 17, 2023

editorialbot mentioned this issue Apr 17, 2023

[PRE REVIEW]: MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes #5140

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 4, 2023

editorialbot added accepted published Papers published in JOSS labels Jul 6, 2023

Kevin-Mattheus-Moerman closed this as completed Jul 6, 2023

[REVIEW]: MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes #5380

[REVIEW]: MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes #5380

Comments

editorialbot commented Apr 17, 2023 • edited

Status

Reviewer instructions & questions

Checklists

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davidnsousa commented Apr 22, 2023 • edited

Review checklist for @davidnsousa

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

davidnsousa commented Apr 22, 2023

tonigi commented Apr 25, 2023 • edited

Review checklist for @tonigi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tonigi commented Apr 25, 2023

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Kevin-Mattheus-Moerman commented Jul 6, 2023 • edited

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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editorialbot commented Apr 17, 2023 •

edited

davidnsousa commented Apr 22, 2023 •

edited

tonigi commented Apr 25, 2023 •

edited

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edited

Kevin-Mattheus-Moerman commented Jul 6, 2023 •

edited

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edited

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edited