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[REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF
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 Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc"><img src="https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc)
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
@naik-aakash & @RiesBen, 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 @phibeck 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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.90 T=0.11 s (394.5 files/s, 145376.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 11 1081 1961 10109
XML 4 2 10 597
TeX 3 31 6 373
reStructuredText 13 240 278 262
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 1510 2267 12067
-------------------------------------------------------------------------------
Commit count by author:
186 bc118
50 pre-commit-ci[bot]
37 Brad Crawford
28 CalCraven
28 Co Quach
10 Jeffrey Potoff
6 GOMC
Paper file info:
📄 Wordcount for paper.md is 1354
✅ The paper includes a Statement of need section
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Review checklist for @naik-aakash
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/?
- [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@jpotoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- [x] 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.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] 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?
Review checklist for @RiesBen
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/?
- [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@jpotoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- [x] 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.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] 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?
Thanks @naik-aakash and @RiesBen for getting your reviews started! I see there's lots of activity also on the side of the authors in the respective issues, but please send us an note here when you have completed your updates or if any questions come up @jpotoff, thanks.
Hi @jpotoff just checking in. When you have a moment, could you please let us know the status of addressing the reviewers' comments? Thank you.
@phibeck We have addressed all of the reviewers comments and are good to go!
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @jpotoff thank you for letting us know you've completed working through the reviewers' comments. :tada: I saw your change to the authorlist (#131), which does not seem to be reflected in the latest proof. Could you cross-check that please? Thanks.
@RiesBen I see you've completed your checklist, thank you! :tada: Could you please confirm that you agree to the publication of this software in its current form? @naik-aakash, could you please let me know if the changes are satisfactory, and if so, tick off the relevant items on your checklist?
Hi @phibeck, Thanks. I forgot to update the checklist. I have just a few things left to go through the changes. I will try to wrap it up by the end of this week and update you here.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @naik-aakash when you have a moment, please let us know if there's any other issues the authors need to address, thanks.
Hi @phibeck , I Had a look at the changes that I wanted to check and am happy with the changes and agree for the publication of the manuscript on JOSS
And I apologize for the delays from my end @phibeck , @jpotoff with this final checks
Thank you @naik-aakash for completing your review and many thanks to all reviewers (@RiesBen) for your help with this submission! 🎉
@jpotoff the reviewers have recommended the submission for publication. There are a few more steps before we finalize the publication.
Post-Review Checklist for Editor and Authors
Additional Author Tasks After Review is Complete
- Double check authors and affiliations (including ORCIDs)
- Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
- Archive the release on Zenodo/figshare/etc and post the DOI here.
- Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
- Make sure that the license listed for the archive is the same as the software license.
Editor Tasks Prior to Acceptance
- [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
- [x] Check that the archive title, author list, version tag, and the license are correct
- [x] Set archive DOI with
@editorialbot set <DOI here> as archive - [x] Set version with
@editorialbot set <version here> as version - [x] Double check rendering of paper with
@editorialbot generate pdf - [x] Specifically check the references with
@editorialbot check referencesand ask author(s) to update as needed - [x] Recommend acceptance with
@editorialbot recommend-accept
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.1002/jcc.23422 is OK
- 10.1021/acs.jcim.2c01153 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
- 10.1021/acs.jctc.1c00302 is OK
- 10.1002/andp.19033160802 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
- 10.1021/jp048581s is OK
- 10.1021/acs.jpca.0c10845 is OK
- 10.1038/s41598-018-21070-0 is OK
- 10.1038/s42004-023-00944-z is OK
- 10.1002/jcc.23422 is OK
- 10.1007/s00249-011-0700-9 is OK
- 10.1021/ct4003477 is OK
- 10.1002/jcc.20082 is OK
- 10.1002/jcc.21367 is OK
- 10.2174/13816128113199990600 is OK
- 10.1007/978-3-030-26837-4_6 is OK
- 10.1007/978-3-658-07529-3_1 is OK
- 10.1080/23746149.2023.2235060 is OK
- 10.1140/epjs/s11734-022-00569-8 is OK
- 10.1007/s13202-020-01003-2 is OK
- 10.1016/j.neuron.2018.08.011 is OK
- 10.1039/c4fd90024c is OK
- 10.1007/978-981-19-3092-8_1 is OK
- 10.1038/s41563-021-01015-1 is OK
🟡 SKIP 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 ...
- No DOI given, and none found for title: VMD-python
- No DOI given, and none found for title: Computer Simulation of Liquids (2nd ed.)
- No DOI given, and none found for title: Understanding Molecular Simulation From Algorithms...
❌ MISSING DOIs
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
❌ INVALID DOIs
- doi.org/10.1002/jcc.23808 is INVALID because of 'doi.org/' prefix
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@phibeck Ok, working on the checklist. We will attempt to update any missing DOIs, however, some of the materials cited (in many cases software) do not have DOIs, so those will have to remain as they are.
Hi @jpotoff just sending a friendly reminder to go through the items in your checklist when you have a moment, thanks.