[REVIEW]: proteusPy: A Python Package for Protein Structure and Disulfide Bond Modeling and Analysis

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@suchanek@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @AnjaConev, @hmacdope 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

@JoaoRodrigues & @AnjaConev, 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 @richardjgowers 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 @AnjaConev

📝 Checklist for @hmacdope

richardjgowers commented 1 month ago

pinging @openjournals/bcm-eics again - I've hit a bit of a problem with this review as only one reviewer has completed. I've gone through the review process and agree with the sole reviewer here. Could we move forward with one review?

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot remove @JoaoRodrigues as reviewer

editorialbot commented 1 month ago

@JoaoRodrigues removed from the reviewers list!

Kevin-Mattheus-Moerman commented 1 month ago

@richardjgowers please feel free to tag me directly in the future.

Kevin-Mattheus-Moerman commented 1 month ago

@richardjgowers I do think we need a second reviewer to complete the review process. So please find an additional reviewer.

Kevin-Mattheus-Moerman commented 1 month ago

@RMeli do you think you could help suggest another reviewer for this one?

RMeli commented 1 month ago

Hello, I think the following people could be interested in reviewing this submission (GitHub handle without @):

joaomcteixeira (listed at reviewers.joss.theoj.org)
hmacdope
cbouy

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

Kevin-Mattheus-Moerman commented 1 month ago

@joaomcteixeira @hmacdope @cbouy would you be interested in reviewing this submission ("proteusPy: A Python Package for Protein Structure and Disulfide Bond Modeling and Analysis"), for JOSS: the journal of open source software? JOSS reviews focus on evaluation of the software as well as a short paper.

This here is a review issue, where a set of check-boxes guide reviewers through our GitHub based review process. As you can see :point_up:, one reviewer has completed their review already. However, we require one more review to be completed so your help would be greatly appreciated!

You can let us know here if you are interested in helping. Thanks!

suchanek commented 1 month ago

Thank you for moving this along!Eric G. Suchanek, PhD On Jun 5, 2024, at 5:00 AM, Kevin Mattheus Moerman @.***> wrote: @joaomcteixeira @hmacdope @cbouy would you be interested in reviewing this submission ("proteusPy: A Python Package for Protein Structure and Disulfide Bond Modeling and Analysis"), for JOSS: the journal of open source software? JOSS reviews focus on evaluation of the software as well as a short paper. This here is a review issue, where a set of check-boxes guide reviewers through our GitHub based review process. As you can see ☝️, one reviewer has completed their review already. However, we require one more review to be completed so your help would be greatly appreciated! You can let us know here if you are interested in helping. Thanks!

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 1 month ago

@suchanek you are welcome. Apologies this review has been taking longer than usual. Let me know if you want to suggest any additional reviewers too at this point. You may mention their GitHub handles, but leave out the @ symbols.

joaomcteixeira commented 1 month ago

Dear all, I am sorry but I am unable to review this paper due to time constraints. Best wishes!

suchanek commented 2 weeks ago

Hi all, any progress on reviewers? I don't have any prospects I'm afraid...

hmacdope commented 1 week ago

I can review the paper. :+1:

hmacdope commented 1 week ago

I believe I have to be formally assigned first though @Kevin-Mattheus-Moerman ?

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot add @hmacdope as reviewer

editorialbot commented 1 week ago

@hmacdope added to the reviewers list!

Kevin-Mattheus-Moerman commented 1 week ago

@hmacdope thanks for your help! You can get started by calling: @editorialbot generate my checklist

hmacdope commented 1 week ago

Review checklist for @hmacdope

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] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Repository: Is the source code for this software available at the https://github.com/suchanek/proteusPy?
[x] Contribution and authorship: Has the submitting author (@suchanek) 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?

suchanek commented 1 week ago

@hmacdope Thank you for your help!

hmacdope commented 5 days ago

Congrats on a wonderful piece of work @suchanek! The paper and software are well written and will be impactful.

Just a queries and things I would like fixed up:

In the paper

While I understand what you mean with this sentence "Disulfide bonds represent the sole naturally occurring covalent bond in proteins". It is not scientifically accurate. Please fix up.
When you say "freely accessible database" could you provide a link to a zenodo archive with said database in a public format?
You should reference the RCSB PDB publication(s) when referring to it.

Code changes:

Address these two issues:

Kevin-Mattheus-Moerman commented 3 days ago

@editorialbot remove @richardjgowers as editor

editorialbot commented 3 days ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman commented 3 days ago

@editorialbot assign me as editor

editorialbot commented 3 days ago

Assigned! @Kevin-Mattheus-Moerman is now the editor

openjournals / joss-reviews