[REVIEW]: Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations

[editorialbot]

Submitting author: @jfaraudo (JORDI FARAUDO)
Repository: https://github.com/soft-matter-theory-at-icmab-csic/chitin_builder
Branch with paper.md (empty if default branch):
Version: v1.1
Editor: @majensen
Reviewers: @amoeba, @tonigi
Archive: 10.5281/zenodo.3274725

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c409d05d1e558827d1dea6275faf8965/status.svg)](https://joss.theoj.org/papers/c409d05d1e558827d1dea6275faf8965)

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

@amoeba & @WangKehan573, 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 @majensen 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 @amoeba

📝 Checklist for @tonigi

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (288.6 files/s, 64485.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             50              0            690
Tcl/Tk                           2             73            124            647
Markdown                         4            100              0            258
Bourne Shell                     1              8             16             22
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             9            232            144           1635
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3611

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

OK DOIs

- 10.1021/ma0477246 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK
- 10.1021/ma0477246 is OK
- 10.1016/S1381-5148(00)00038-9 is OK
- 10.1002/cben.201400025 is OK
- 10.1021/acssuschemeng.8b06372 is OK
- 10.1002/jcc.22959 is OK
- 10.1021/ct8002964 is OK
- 10.1021/ct200328p is OK
- 10.1081/MC-120006451 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1021/ct700301q is OK
- 10.1002/jcc.20291 is OK
- 10.1007/s12668-013-0097-2 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.jpcb.6b05999 is OK
- 10.1007/s10853-015-9271-y is OK
- 10.1016/J.CIS.2019.02.003 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1016/J.CARBPOL.2017.08.076 is OK
- 10.1002/pola.20176 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1002/jcc.20289 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1039/C6GC00628K is OK
- 10.1039/C6RA00107F is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[majensen]

@amoeba, @WangKehan573, have you been able to give some time to this review? Please let me know in the thread. Thanks!

[amoeba]

Hi @majensen, I hadn't noticed this review go from pre-review to review so thanks for the ping! I can get my review done in the next two weeks.

[amoeba]

Review checklist for @amoeba

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/soft-matter-theory-at-icmab-csic/chitin_builder?
• 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 (@jfaraudo) 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?

[amoeba]

Hi @majensen, while reviewing the "Substantial scholarly effort" checklist item, I find a could use some editorial help. Using the corresponding section in the Review criteria as a guide, I think this submission is borderline due to the size and apparent age of the codebase. I don't see that this was discussed in pre review but please let me know if I missed that

It seems to me the most important element of this checklist item is whether the work is of broad interest and likely to be cited which isn't something I can assess with my background. However, in the paper, the authors speak to this at the end of their Introduction and Statement of Need section and to me it sounds like they theorize this tool would be quite useful to others in their field. With that, I'm inclined to check "Substantial scholarly effort" so long as you agree.

[majensen]

Sorry for the long delay @amoeba and all. I am discussing this with one of the AEICs. @jfaraudo - can you comment here on your view of the effort put into this software, and on its usefulness to the community? I think it is a specialized community, and that is ok - how do you see this work contributing to the science?

[majensen]

@WangKehan573 - are you still able to review #5771? Please let me know if I can help- thanks

[WangKehan573]

I regret to inform you that I am unable to review the material you have submitted due to circumstances beyond my control. Unfortunately, I am experiencing unforeseen challenges that are preventing me from fulfilling my responsibility as a reviewer. I apologize for any inconvenience this may cause and I assure you that I am doing my best to resolve the situation. I hope you can understand and forgive my inability to meet my commitments at this time. Thank you for your understanding

…

---- Replied Message ---- | From | Mark ***@***.***> | | Date | 11/02/2023 22:56 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [openjournals/joss-reviews] [REVIEW]: Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations (Issue #5771) | @WangKehan573 - are you still able to review #5771? Please let me know if I can help- thanks — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jfaraudo]

@majensen Yes, sure, we can comment on this here.
Yes, the code is useful for a very specialized community. Our target are the VMD users that develop simulations of polymeric materials based on natural polymers. To make a comparison, it is an scope similar to that of the "cellulose builder" app, that generates structures cellulosic materials, but in our case for chitin based materials. The relevance of this is based on the fact that cellulose and chitin are the most abundant polymers in Earth and are both of natural origin and therefore interesting as "green" materials. They have also very interesting properties. Prediction by computer simulation of their properties and behaviour is relatively under-studied (compared with other less abundant materials or compared with other human-designed materials) due to practical difficulties in generating appropiate structures suitable for the simulations. The objective of this code is to solve this problem, providing interested researchers with a tool that is able to generate the necessary files to investigate by computer simulations the properties of materials based on different crsytall structures of chitin polymer. We hope that this app will help in the advancement of the understanding of chitin and rational design materials based on this natural polymer by computer simulation.

@jfaraudo - can you comment here on your view of the effort put into this software, and on its usefulness to the community? I think it is a specialized community, and that is ok - how do you see this work contributing to the science?

[majensen]

Thanks @jfaraudo - I have also spent some time getting a deeper understanding of the VMD framework, which it is very current use, with new plugins written for it frequently up to the present time (even though it was published first around 1996). @amoeba I would call it the "Emacs of Molecular Modeling". I have not heard any disagreement from the Associate Editor in Chief to this argument. So let's proceed with "Substantial scholarly effort".

[majensen]

@jfaraudo -- unfortunately one of our reviewers had to decline. I am sorry about the very long delay. Would you have any suggestions for reviewers with the right expertise who could fairly review your work? Much appreciated!

[amoeba]

So let's proceed with "Substantial scholarly effort".

Thanks for taking a look, @majensen. Works for me.

[jfaraudo]

Sorry for the delay in responding. I think apropiate referees could be developers of other VMD plugins. One example is Dr Toni Giorgino @tonigi [ https://github.com/tonigi | https://github.com/tonigi ] Let me think about others. jordi From: "Mark Jensen" ***@***.***> To: "openjournals/joss-reviews" ***@***.***> Cc: "Jordi Faraudo" ***@***.***>, "Mention" ***@***.***> Sent: Thursday, 16 November, 2023 23:15:28 Subject: Re: [openjournals/joss-reviews] [REVIEW]: Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations (Issue #5771) [ https://urldefense.com/v3/__https://github.com/jfaraudo__;!!D9dNQwwGXtA!SoVYcjZdOWxeXeN0LHD9qH4oQ6jNIU5hcjJUbM0yWsXZW_b9OuhoxRVV66y2u82gJIOXk1ZcVLfopsmGnCnIN695DQ$ | @jfaraudo ] -- unfortunately one of our reviewers had to decline. I am sorry about the very long delay. Would you have any suggestions for reviewers with the right expertise who could fairly review your work? Much appreciated! — Reply to this email directly, [ https://urldefense.com/v3/__https://github.com/openjournals/joss-reviews/issues/5771*issuecomment-1815400010__;Iw!!D9dNQwwGXtA!SoVYcjZdOWxeXeN0LHD9qH4oQ6jNIU5hcjJUbM0yWsXZW_b9OuhoxRVV66y2u82gJIOXk1ZcVLfopsmGnCkvMKOaXw$ | view it on GitHub ] , or [ https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AHFLNXQOV2VH55UJH6W5273YE2GABAVCNFSM6AAAAAA3XYVVACVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVGQYDAMBRGA__;!!D9dNQwwGXtA!SoVYcjZdOWxeXeN0LHD9qH4oQ6jNIU5hcjJUbM0yWsXZW_b9OuhoxRVV66y2u82gJIOXk1ZcVLfopsmGnCkvfQuctQ$ | unsubscribe ] . You are receiving this because you were mentioned. Message ID: ***@***.***>

…

-- Dr. Jordi Faraudo Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), [ https://icmab.es/faraudo-gener-jordi-permanent-researchers | https://icmab.es/faraudo-gener-jordi-permanent-researchers ] Associate Editor - Condensed Matter Physics @ "Heliyon" journal, [ http://www.heliyon.com/ | http://www.heliyon.com  ] Editorial Board member @ "Materials" journal, [ http://www.mdpi.com/journal/materials | http://www.mdpi.com/journal/materials ] "It's nice to know the computer understands the problem, but I would like to understand it too." (Attributed to Eugene Wigner)

[tonigi]

I'll be happy to review.

[majensen]

Thanks so much @tonigi !

[majensen]

@editorialbot add tonigi as reviewer

[majensen]

Once you create your archive, please let me know the version and the DOI created, here in this thread. Thanks

[jfaraudo]

@majensen Zenodo DOI https://doi.org/10.5281/zenodo.10517626
Zenodo record https://zenodo.org/records/10517626
Archived version 1.1

[majensen]

Thanks @jfaraudo - the journal prefers that the title and authors on the archive match those on the paper, if you can update those items.

[jfaraudo]

OK @majensen The zenodo archive was generated automatically after creating the new software version (we had an automatic update of our GitHub repo in Zenodo) and it takes as title the GitHub repo name and as authos everyone that contributed in the repo (including referees like @amoeba that did a pull request on GitHub). We will try to correct this today. If a correction is not possible we will create manually another Zenodo archive for the JOSS publication.

[jfaraudo]

@majensen Corrected, now authors and title matches that of JOSS submission and files correspond to latest repository version . Same DOI: https://zenodo.org/doi/10.5281/zenodo.3274725

[majensen]

@editorialbot set v1.1 as version

[editorialbot]

Done! version is now v1.1

[majensen]

@editorialbot set 10.5281/zenodo.3274725 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.3274725

[majensen]

@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

- 10.1021/ma0477246 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK
- 10.1021/ma0477246 is OK
- 10.1016/S1381-5148(00)00038-9 is OK
- 10.1002/cben.201400025 is OK
- 10.1021/acssuschemeng.8b06372 is OK
- 10.1002/jcc.22959 is OK
- 10.1021/ct8002964 is OK
- 10.1021/ct200328p is OK
- 10.1081/MC-120006451 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1021/ct700301q is OK
- 10.1002/jcc.20291 is OK
- 10.1007/s12668-013-0097-2 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.jpcb.6b05999 is OK
- 10.1007/s10853-015-9271-y is OK
- 10.1016/J.CIS.2019.02.003 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1016/J.CARBPOL.2017.08.076 is OK
- 10.1002/pola.20176 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1002/jcc.20289 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1039/C6GC00628K is OK
- 10.1039/C6RA00107F is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#4958, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jfaraudo]

@editorialbot accept

[editorialbot]

I'm sorry @jfaraudo, I'm afraid I can't do that. That's something only eics are allowed to do.

[jfaraudo]

Everything (pdf file, etc) looks good to me.

[Kevin-Mattheus-Moerman]

@jfaraudo As AEiC I will now help to process final steps towards acceptance in JOSS. I have just checked your repository, this review, the archive link, and the paper. All seems in order, so I will now proceed to accept this 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: Malaspina
  given-names: David
  orcid: "https://orcid.org/0000-0002-5420-9534"
- family-names: Faraudo
  given-names: Jordi
  orcid: "https://orcid.org/0000-0002-6315-4993"
contact:
- family-names: Faraudo
  given-names: Jordi
  orcid: "https://orcid.org/0000-0002-6315-4993"
doi: 10.5281/zenodo.3274725
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Malaspina
    given-names: David
    orcid: "https://orcid.org/0000-0002-5420-9534"
  - family-names: Faraudo
    given-names: Jordi
    orcid: "https://orcid.org/0000-0002-6315-4993"
  date-published: 2024-01-29
  doi: 10.21105/joss.05771
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5771
  title: "Chitin Builder: a VMD tool for the generation of structures of
    chitin molecular crystals for atomistic simulations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05771"
  volume: 9
title: "Chitin Builder: a VMD tool for the generation of structures of
  chitin molecular crystals for atomistic simulations"

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 👉 Creating pull request for 10.21105.joss.05771 joss-papers#4963
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05771
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]

@jfaraudo congratulations on this JOSS publication !
Thanks for editing @majensen

And a special thank you to the reviewers: @amoeba, @tonigi !!

[editorialbot]

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

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reStructuredText:
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[majensen]

Really great to finally get this out - thanks to all for thier perseverance!

[jfaraudo]

Thanks to all @majensen @tonigi @amoeba