[REVIEW]: SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures

[editorialbot]

Submitting author: @menoliu (Zi Hao Liu) Repository: https://github.com/julie-forman-kay-lab/SPyCi-PDB Branch with paper.md (empty if default branch): Version: v0.1.10 Editor: @ppxasjsm Reviewers: @dotsdl Archive: Pending

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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

@dotsdl, 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 @ppxasjsm 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

@dotsdl, please create your checklist typing: @editorialbot generate my checklist

[editorialbot]

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (816.0 files/s, 141155.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SQL                              2              2              0           4085
Python                          32            784           1177           2721
reStructuredText                12            286             84            496
TeX                              1             29              0            378
JSON                             5              0              0            268
YAML                             8             31             45            206
INI                              1             14              0            174
Markdown                         2             57              0            174
C Shell                          1             20             10             30
-------------------------------------------------------------------------------
SUM:                            64           1223           1316           8532
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1626

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK

MISSING DOIs

- 10.1021/acs.jpclett.6b00885.s001 may be a valid DOI for title: Multi-timescale dynamics in intrinsically disordered proteins from NMR relaxation and molecular simulation
- 10.1101/2020.08.09.243030 may be a valid DOI for title: DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
- 10.1021/jacs.1c06264.s001 may be a valid DOI for title: Quantitative description of intrinsically disordered proteins using single-molecule FRET, NMR, and SAXS

INVALID DOIs

- None

[menoliu]

@editorialbot commands

[editorialbot]

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

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[menoliu]

Just a minor note to the editor and reviewers that since v0.1.10, I've fixed some minor bugs and the most up-to-date version is v0.1.13. Thanks!

[ppxasjsm]

@editorialbot add @lohedges as reviewer

[editorialbot]

@lohedges added to the reviewers list!

[ppxasjsm]

Thank you @lohedges for agreeing to review this. If you have any questions at any point please let me know. You can generate your review checklist with the following command: @editorialbot generate my checklist.

[dotsdl]

Sorry folks for the delay, working against a deadline. Have this on my task list for later this week.

[dotsdl]

Review checklist for @dotsdl

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/julie-forman-kay-lab/SPyCi-PDB?
• [x] 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 (@menoliu) 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?

[ppxasjsm]

no worries @dotsdl thanks for getting started with this!

[ppxasjsm]

@dotsdl and @lohedges, I've just sent you a gentle reminder email for this review.

[lohedges]

Review checklist for @lohedges

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/julie-forman-kay-lab/SPyCi-PDB?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@menoliu) 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?

[menoliu]

Apologies Lester for the delayed response to the issues, I was not notified via E-mail... They will all be resolved in the first week* of January. Happy holidays!

Edit: by the end of the month*, I've rang in the new year with COVID-19.

[lohedges]

@menoliu: Thanks for your updates. I've not had a chance to look at these yet and won't for the next week or so since I'm working to some tight deadlines.

[ppxasjsm]

Thanks @lohedges and @menoliu for the updates. @dotsdl How are you getting on with your review?

[menoliu]

Thank you all for your notes and reviews. I am making improvements to SPyCi-PDB currently as well as one of my projects demand it. I will be modifying the chemical-shift (CS) back-calculator by adding another, more commonly used one, perhaps as the default to hopefully resolve some current/initial issues (I will be more than happy to edit the manuscript if needed later on). Cheers!

[ppxasjsm]

@dotsdl had to, unfortunately, drop out as a reviewer. @menoliu I am trying to secure a second reviewer. If you have any suggestions they'd be very welcome.

[ppxasjsm]

@lohedges did you manage to be able to take a look at the updates?

[lohedges]

Not yet, I'm afraid. I doubt I'll be able to do so until the middle/end of next week at the earliest, I'm afraid.

[menoliu]

Sorry for the late reply @ppxasjsm I was at a conference. I believe if nicksisco1932 or sulstice are available that would be great.

[menoliu]

Hi @ppxasjsm , hope you're doing well. Just wondering how is it securing another reviewer? Thanks in advance!

[ppxasjsm]

Hi @menoliu, now I had accidentally dropped the ball. Too many deadlines and then I got sick. On it now.

[ppxasjsm]

@editorialbot add @JenkeScheen to reviewers

[editorialbot]

@JenkeScheen added to the reviewers list!

[ppxasjsm]

@JenkeScheen thank you for agreeing to review this submission! You can generate your checklist using the command @editorialbot generate my checklist.

[Sulstice]

Sure

On Fri, Mar 24, 2023 at 10:46 AM Toni Mey @.***> wrote:

@JenkeScheen https://github.com/JenkeScheen thank you for agreeing to review this submission! You can generate your checklist using the command @editorialbot generate my checklist.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4861#issuecomment-1482923006, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2EAUUT3ZXWBPOPQ5C7RTTW5WXSTANCNFSM6AAAAAARHKVMVE . You are receiving this because you were mentioned.Message ID: @.***>

-- Suliman Sharif Ph.D. Candidate Pharmaceutical Sciences | University of Maryland, School of Pharmacy M.Sc Medicinal Chemistry | University of California, Riverside School of Medicine B.Sc. Biochemistry | University of Texas at Austin @.***

[ppxasjsm]

@editorialbot add @sulstice to reviewers