editorialbot commented 3 months ago

Submitting author: !--author-handle-->@agerada@ppxasjsm@gchure<!--end-reviewers-list-- Archive: 10.5281/zenodo.13628882

Status

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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

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@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 @gchure

editorialbot commented 3 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 3 months ago

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

OK DOIs

- 10.1046/j.1469-0691.2000.00142.x is OK
- 10.1128/spectrum.04209-23 is OK
- 10.17638/DATACAT.LIVERPOOL.AC.UK/2631 is OK
- 10.2144/000112257 is OK
- 10.1038/nprot.2007.521 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1295.9 files/s, 124263.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            448            508           1952
Markdown                         4            115              0            269
reStructuredText                 9            176            110            266
YAML                             3              6             21            165
TeX                              1              4              0             76
TOML                             1              7              0             41
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            44            768            647           2804
-------------------------------------------------------------------------------

Commit count by author:

    92  Alessandro Gerada
    29  agerada
     2  Gerada

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 626

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 3 months ago

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

gchure commented 3 months ago

Review checklist for @gchure

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/agerada/AIgarMIC?
[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 (@agerada) 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?

gchure commented 3 months ago

Hi @ppxasjsm, I have a quick editorial question. It seems like the software is already published in another peer reviewed journal ASM Spectrum. From my read of that paper, the software is described and validated on a novel dataset generated solely to train and test the software (i.e., the software isn't used in the paper to facilitate discovery). Given the JOSS guidelines for copublication, it's not clear to me that this software by itself merits a separate JOSS paper, even though the ASM paper doesn't cover the API or structure of the software itself.

Could you please let me know your opinion on this? I'm happy to continue to review the software (which seems quite good), but I noticed that almost all of my comments on the software paper itself are covered in the ASM publication.

agerada commented 3 months ago

Thank you @gchure for your comments and for reviewing our software. Although I appreciate the question is for @ppxasjsm, I will leave some comments to help with the decision.

Our JOSS submission for AIgarMIC was alongside a technical paper (in ASM Microbiology Spectrum) which we reference in the JOSS draft paper. The primary focus of the ASM Spectrum paper was to report and validate the use of machine learning approaches to interpret minimimum inhibitory concentration (MIC) experiments, delivered through our AIgarMIC software. Within the paper, we describe the laboratory experiments that generated the training images, the specifications of the artificial neural networks that were used to label images, and the validation of the predictions by comparing against a gold standard method (manual interpretation). The results are reported in the domain-standard format for MIC validation studies (e.g., essential and categorical agreement). Within the methods, we included a paragraph outlining the high-level features of AIgarMIC, to demonstrate a practical implementation of our approach.

Since the focus of the ASM Spectrum paper was the microbiological validation of our methods, we submitted our software to JOSS on the basis that our implementation contains software-specific scientific efforts (which are not explained or discussed in the ASM Spectrum paper). These include, for example:

the algorithms that split images, calculate the MIC, and perform quality assurance of the results.
the abstraction of agar dilution plates and experiments into Plate and PlateSet classes (with respective methods), facilitating user extension.
the use of a black over- or underlying grid for reliable software splitting of images.
tutorials that explain how to implement AIgarMIC in a laboratory, with different use-cases (ranging from use as an MIC calculator to extension with custom models).
command-line scripts that allow users without Python scripting experience to generate their own labelled images, train and test models, and perform MIC predictions.
the testing suite focused on the software implementation and algorithms (which complements the technical validation reported in ASM Spectrum).

We look forward to further comments and again thank @gchure and @ppxasjsm.

gchure commented 3 months ago

Thanks @agerada, that is really helpful context and I appreciate the effort here. Just to overcommunicate, I'm happy to give it a full JOSS review and just wanted to check with @ppxasjsm as I thought it may be in conflict with the JOSS guidelines.

As to the algorithms for splitting, are there tutorials/derivations of the splitting algorithms? I couldn't find details in the documentation beyond the API reference and source code. It may be worthwhile to write a tutorial outlining in some detail the algorithms and math behind the MIC calculation, for example.

agerada commented 3 months ago

Thank you @gchure – fair points on the documentation and algorithms. I have reviewed the documentation and the tutorials don't include use of the splitting alogirthm, which would be helpful. Also agree an overview of how the MIC and QC algorithms are implemented would be helpful. I will likely do this in pseudocode as the implementations are in software rather than in formal math.

Pending further input from @ppxasjsm I have opened two issues (agerada/AIgarMIC#10 and agerada/AIgarMIC#11 respectively) for the two points raised.

gchure commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:warning: An error happened when generating the pdf.

agerada commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

gchure commented 2 months ago

Hi @agerada and @ppxasjsm, I can just about close out my review of this work. There's two small outstanding issues(see #11 and #16), but I don't think they will require further review. Thanks @agerada for being collaborative and prompt with your responses to things (and sorry my review took longer than I had anticipated!).

gchure commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

gchure commented 2 months ago

Hi @ppxasjsm , now that @agerada has completed the aforementioned issues, I'm happy to say my review is complete and the work has my stamp of approval. Thanks again to @agerada for being highly communicative throughout the process!

ppxasjsm commented 2 months ago

Thank you @gchure and @agerada for all your work on the submission. I am sorry I missed some of the communication due to holidays and somehow not getting notifications. I think the paper submission here and the previous publication are ok. I'll now proceed with the editorial process.

ppxasjsm commented 2 months ago

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 references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

ppxasjsm commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

ppxasjsm commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- 10.1046/j.1469-0691.2000.00142.x is OK
- 10.1128/spectrum.04209-23 is OK
- 10.17638/DATACAT.LIVERPOOL.AC.UK/2631 is OK
- 10.2144/000112257 is OK
- 10.1038/nprot.2007.521 is OK

MISSING DOIs

- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras
- No DOI given, and none found for title: Open Source Computer Vision Library

INVALID DOIs

- None

ppxasjsm commented 2 months ago

@agerada could you double check the above reference for me?

agerada commented 2 months ago

Hi @ppxasjsm - thank you for the update. The DOI suggested for keras does not appear to be a valid one for keras. I have double checked and both keras and opencv do not provide DOIs for citations.

I have also re-reviewed the proof and made some minor corrections https://github.com/agerada/AIgarMIC/pull/31 (mainly typos).

agerada commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

agerada commented 3 weeks ago

Hi @ppxasjsm - just checking whether there there are any outsanding issues for me on this? If JOSS prefers all references to have an associated DOI, then I am happy to remove the references for keras and opencv and use hyperlinks to the packages within the text instead.

ppxasjsm commented 4 days ago

@agerada Could you please update the references with a hyperlink? I think that would make sense to me.

ppxasjsm commented 4 days ago

@agerada can you also please provide a DOI for a Zenodo archive of the version of the software that is associated with this paper? Can you also post the version number here? The last thing I would like you to double-check is that all names and ORCIDs are correct.

I am really sorry about being quite slow with processing this over the summer but I ended up much busier than anticipated.

agerada commented 3 days ago

Hi @ppxasjsm -- no need to apologise; I'm very grateful your editorial of our work, and for @gchure's constructive review.

I have merged https://github.com/agerada/AIgarMIC/pull/33 with a couple of minor edits from another read of the manuscript draft (@gchure had previously correctly flagged up that "assay" is a more apprpriate term than "test" with regards to the laboratory procdure of agar dilution MIC).

I can confirm that the author names and ORCIDs are correct.

Finally, here is a zenodo archive of the latest release (v1.1.1): https://zenodo.org/doi/10.5281/zenodo.13628882