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

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@menoliu@ppxasjsm<!--end-editor-- Reviewers: @dotsdl, @lohedges, @JenkeScheen, @sulstice Archive: 10.5281/zenodo.7887039

Status

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Markdown: [![status](https://joss.theoj.org/papers/6a56ce7708734f55141bcf61f5286b62/status.svg)](https://joss.theoj.org/papers/6a56ce7708734f55141bcf61f5286b62)

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

📝 Checklist for @dotsdl

📝 Checklist for @lohedges

📝 Checklist for @JenkeScheen

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 1626

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@editorialbot add @lohedges as reviewer

editorialbot commented 1 year ago

@lohedges added to the reviewers list!

ppxasjsm commented 1 year ago

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 commented 1 year ago

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

dotsdl commented 1 year ago

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 commented 1 year ago

no worries @dotsdl thanks for getting started with this!

ppxasjsm commented 1 year ago

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

lohedges commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

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

menoliu commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

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

lohedges commented 1 year ago

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 commented 1 year ago

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

menoliu commented 1 year ago

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

ppxasjsm commented 1 year ago

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

ppxasjsm commented 1 year ago

@editorialbot add @JenkeScheen to reviewers

editorialbot commented 1 year ago

@JenkeScheen added to the reviewers list!

ppxasjsm commented 1 year ago

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

Sulstice commented 1 year ago

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 commented 1 year ago

@editorialbot add @sulstice to reviewers

editorialbot commented 1 year ago

@sulstice added to the reviewers list!

ppxasjsm commented 1 year ago

Thank you @Sulstice!

JenkeScheen commented 1 year ago

Review checklist for @JenkeScheen

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?

editorialbot commented 1 year ago

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

ppxasjsm commented 1 year ago

@Sulstice are you able to do the review?

menoliu commented 1 year ago

@JenkeScheen Thanks for your review on #43. I have since updated the manuscript as well as included plotting functions for the modules shown as figures in the paper (rh, jc, noe, pre). I have also noticed your checkbox on Installation instructions: and have updated the documentation to include a clear list of dependencies as well.

editorialbot commented 1 year ago

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

JenkeScheen commented 1 year ago

Thanks @menoliu! The additional figures look great. I'll let @lohedges give his thoughts on the updated installation instructions.

lohedges commented 1 year ago

Many thanks @menoliu, I can confirm that the fixes work as expected and the installation process is now a lot more streamlined. Longer term, I still think it would be beneficial to make pip or conda packages for both SPyCi-PDB and IDPConformerGenerator, as it would make it easier to install your tools into larger environments alongside other packages.

I've left the references section unchecked at present since there is a minor formatting issue. I'll open an issue for that.

@JenkeScheen: Thanks for the comments regarding the additional examples and figures. The updates are really helpful.

Cheers.

menoliu commented 1 year ago

Thank you so much @lohedges for the comments. I have addressed them in the latest PR #47. The documentation is much cleaner now I think.

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

menoliu commented 1 year ago

@ppxasjsm thanks for organizing reviewers and keeping everyone up to date throughout this review process. I was just wondering since both Lester and Jenke have completed the checklist, what are the next steps moving forward?

editorialbot commented 1 year ago

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
- 10.1021/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

editorialbot commented 1 year ago

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
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 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
- 10.1021/acs.jpclett.6b00885 is OK
- 10.1073/pnas.1800690115 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.48550/ARXIV.2206.12667 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
- 10.1021/ja003724j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
- 10.1021/jacs.1c06264 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

ppxasjsm commented 1 year ago

I’ll now go through the submission make sure everything’s is in order. I may raise a couple more issues and then we can proceed with the publication. I probably will only get a chance to look at this properly next week though I am afraid. I’ll post anything I’ll need from you here or as an issue!

ppxasjsm commented 1 year ago

Sorry just to let you know that I didn't find time due to a looming deadline on Monday. I'll get to look at this for sure early next week. My apologies for the delay.

menoliu commented 1 year ago

Thanks for the heads up! Looking forwards to the next steps.

ppxasjsm commented 1 year ago

@menoliu, I've created a small issue for editorial suggestions of the paper: https://github.com/julie-forman-kay-lab/SPyCi-PDB/issues/51

Please read your publication again and create a new release of the software that reflects the paper version of it. Then deposit this version of the software on Zenodo or Figshare and post the DOI for it here.

openjournals / joss-reviews