[PRE REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF

[editorialbot]

Submitting author: @jpotoff (Jeffrey Potoff)
Repository: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/
Branch with paper.md (empty if default branch):
Version: 0.0.3
Editor: @phibeck
Reviewers: @naik-aakash, @RiesBen
Managing EiC: Kyle Niemeyer

Status

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Markdown: [![status](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc/status.svg)](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc)

Author instructions

Thanks for submitting your paper to JOSS @jpotoff. Currently, there isn't a JOSS editor assigned to your paper.

@jpotoff if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "pages" (NAME) ["@", #<BibTeX::Entry >, {:author=>["Mayne, C.G. Mayne and Saam, J, and Schulten, K. and Tajkhorshid, E. and Gumbart, J.C."], :journal=>["J. Comp. Chem."], :volume=>["34"], :issue=>["32"]}]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (395.7 files/s, 148136.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11           1081           1961          10109
XML                              4              2             10            597
TeX                              3             44             33            426
reStructuredText                13            272            278            392
DOS Batch                        1             29              1            212
YAML                             6             23              3            182
Markdown                         2             59              0            147
make                             1             28              6            143
Dockerfile                       1             15              2             33
Bourne Shell                     1              2              0              9
-------------------------------------------------------------------------------
SUM:                            43           1555           2294          12250
-------------------------------------------------------------------------------

Commit count by author:

   185	bc118
    50	pre-commit-ci[bot]
    37	Brad Crawford
    28	CalCraven
    28	Co Quach
     5	GOMC
     3	Jeffrey Potoff

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1360

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

⚠️ An error happened when generating the pdf.

[kyleniemeyer]

Hello @jpotoff, this pre-review issue is where we will sort out any issues, assign an editor, and find reviewers.

First, I noticed the unusual LICENSE in the software repo: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/blob/main/LICENSE.rst. Why are you including the license information for vmd-python and VMD, when these do not appear to be distributed in this software?

Second, the paper compilation issue appears to stem from a missing comma at the end of line 6 of paper.bib.

[kyleniemeyer]

@editorialbot invite @phibeck as editor

Hi @phibeck, could you edit this submission?

[editorialbot]

Invitation to edit this submission sent!

[phibeck]

Hi @kyleniemeyer yes I can edit this one

[phibeck]

@editorialbot assign @phibeck as editor

[editorialbot]

Assigned! @phibeck is now the editor

[phibeck]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1002/jcc.23422 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1002/jcc.21287 is OK
- 10.1021/acs.jctc.5b00935 is OK
- 10.1063/1.1674022 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK

MISSING DOIs

- 10.1021/ja9621760 may be a valid DOI for title: Development and Testing of the OPLS All-Atom Force...
- No DOI given, and none found for title: 
- No DOI given, and none found for title: Sur le mélange des gaz
- 10.1002/andp.18812480110 may be a valid DOI for title: Ueber die Anwendung des Satzes vom Virial in der k...
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: GMSO: General Molecular Simulation Object
- No DOI given, and none found for title: forcefield-utilities
- No DOI given, and none found for title: Open-Source Molecular Modeling Software in Chemica...
- No DOI given, and none found for title: MoSDeF-dihedral-fit: A simple software package to ...
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
- 10.1016/0263-7855(96)00018-5 may be a valid DOI for title: VMD – Visual Molecular Dynamics
- No DOI given, and none found for title: A System for Interactive Molecular Dynamics Simula...
- No DOI given, and none found for title: Multiple Alignment of protein structures and seque...
- No DOI given, and none found for title: \em An Efficient Library for Parallel Ray Tracing ...
- No DOI given, and none found for title: Knowledge-based secondary structure assignment
- No DOI given, and none found for title: Linearly Scalable Computation of Smooth Molecular ...
- 10.1145/220279.220324 may be a valid DOI for title: Fast and Robust Computation of Molecular Surfaces
- No DOI given, and none found for title: Speech/Gesture Interface to a Visual-Computing Env...
- No DOI given, and none found for title: vmd-python

INVALID DOIs

- None

[phibeck]

Hi @jpotoff, thanks for your submission. I'll be looking for reviewers next. A few things you can do to speed up the review process in addition to what was pointed out above by @kyleniemeyer:

• it would be helpful if you could identify a few potential reviewers from this list https://reviewers.joss.theoj.org/reviewers (without tagging them with an @)
• there are some missing DOIs, please add them and regenerate the pdf using @editorialbot generate pdf

[phibeck]

Hi @jpotoff could you please have a look and address these issues? I will wait with inviting reviewers until we have a working manuscript link.

[jpotoff]

@phibeck ok, will work on this today.

[jpotoff]

What is the preferred method of referring to software that does not have an associated DOI?

[jpotoff]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[jpotoff]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[jpotoff]

@editorialbot generate pdf

[editorialbot]

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

[phibeck]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1002/jcc.23422 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1021/ja9621760 is OK
- 10.1002/andp.19033160802 is OK
- 10.1002/jcc.21287 is OK
- 10.1021/acs.jctc.5b00935 is OK
- 10.1063/1.1674022 is OK
- 10.1002/andp.18812480110 is OK
- 10.1002/aic.17206 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1145/364338.364398 is OK

MISSING DOIs

- No DOI given, and none found for title: Sur le mélange des gaz
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: GMSO: General Molecular Simulation Object
- No DOI given, and none found for title: forcefield-utilities
- No DOI given, and none found for title: MoSDeF-dihedral-fit: A simple software package to ...
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
- No DOI given, and none found for title: vmd-python

INVALID DOIs

- None

[phibeck]

What is the preferred method of referring to software that does not have an associated DOI?

If the software is on GitHub, referencing by URL and with project name makes sense. Seems like this is what you did already.

[jpotoff]

@editorialbot generate pdf

[editorialbot]

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

[phibeck]

👋 @jkalayan, @richardjgowers & @mattwthompson, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[mattwthompson]

I'm one of the original authors of much of the MoSDeF software stack, but haven't been involves in a few years and didn't know about this project until now. I feel I can give an impartial review (and am happy to help) if you're comfortable with that context.

[phibeck]

Thanks @MatthewThompson! Could you please let me know whether you have a COI based on the following guideline (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy). It sounds like the answer is "no COI", but I just want to be sure.

As a reviewer (or editor), COIs are your present or previous association with any authors of a submission: recent (past four years) collaborators in funded research or work that is published; and lifetime for the family members, business partners, and thesis student/advisor or mentor. In addition, your recent (past year) association with the same organization of a submitter is a COI, for example, being employed at the same institution.

[mattwthompson]

Based on this criteria I think I would

recent (past four years) collaborators in funded research or work that is published

I have no COI with the first or corresponding authors but I had a funded software (i.e. producing a software product, not scientific research output) project with the middle five authors in 2021-2022. That project did not produce a publication but did contribute to a software project I'm still working on. (These people are in the lab in did my PhD in, 2014-2019, including my PI Peter Cummings)

The calls is yours, of course - and in either case I'm happy advertise this to some other experts in dihedral fitting

[phibeck]

Thanks @mattwthompson Because of the lifetime COI given your thesis advisor is a co-author, let's skip this one. If you have recommendations of other possible reviewers I would appreciate if you could let me know.

[phibeck]

👋 @masrul, @wongzit & @lancekavalsky, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[phibeck]

👋 @MartinBeseda, @RMeli & @naik-aakash, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[RMeli]

Hi @phibeck, thank you for the invitation. I'm rather busy editing a few JOSS submissions at the moment, therefore I don't have the bandwidth to take on a review as well. Sorry about that!

[phibeck]

Hi @RMeli no problem, thanks for letting me know. Somehow in the reviewer database it doesn't show your other commitments, otherwise I wouldn't have asked. Hope it's just a glitch this time.

[naik-aakash]

Hi @phibeck, I would be happy to review this submission for the JOSS.

[phibeck]

Great, thank you very much @naik-aakash

[phibeck]

@editorialbot add @naik-aakash as reviewer

[editorialbot]

@naik-aakash added to the reviewers list!

[RMeli]

@phibeck, no problem. I think the database only shows reviewing commitments and not editorial commitments.

[MartinBeseda]

Hi @phibeck ,
thank you very much for appointing me! Unfortunately, I'm really busy for the next two weeks, so I won't be able to review the code.

[phibeck]

👋 @JaafarMehrez, @Hsuchein & @RiesBen, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[RiesBen]

Hej @phibeck , I could have a look at the submission next week. :)

[phibeck]

Thank you very much @RiesBen!

[phibeck]

@editorialbot add @RiesBen as reviewer

[editorialbot]

@RiesBen added to the reviewers list!

[phibeck]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6970.