Open editorialbot opened 3 months ago
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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
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
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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
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SUM: 44 768 647 2804
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Commit count by author:
92 Alessandro Gerada
29 agerada
2 Gerada
Paper file info:
📄 Wordcount for paper.md
is 626
✅ The paper includes a Statement of need
section
License info:
🟡 License found: GNU General Public License v3.0
(Check here for OSI approval)
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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.
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:
Plate
and PlateSet
classes (with respective methods), facilitating user extension.AIgarMIC
in a laboratory, with different use-cases (ranging from use as an MIC calculator to extension with custom models).We look forward to further comments and again thank @gchure and @ppxasjsm.
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.
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.
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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!).
@editorialbot generate pdf
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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!
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.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@editorialbot generate pdf
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@editorialbot check references
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
@agerada could you double check the above reference for me?
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).
@editorialbot generate pdf
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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.
@agerada Could you please update the references with a hyperlink? I think that would make sense to me.
@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.
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
Thanks for that @agerada!
@editorialbot set 10.5281/zenodo.13628882 as archive
Done! archive is now 10.5281/zenodo.13628882
@editoribot set v1.1.1 as version
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
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
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- None
❌ INVALID DOIs
- None
@editorialbot recommend accept
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Attempting dry run of processing paper acceptance...
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
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- None
❌ INVALID DOIs
- None
:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5842, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Minor change to avoid breaking python statement over two pages: https://github.com/agerada/AIgarMIC/pull/35
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: !--author-handle-->@agerada<!--end-author-handle-- (Alessandro Gerada) Repository: https://github.com/agerada/AIgarMIC Branch with paper.md (empty if default branch): Version: v1.1.1 Editor: !--editor-->@ppxasjsm<!--end-editor-- Reviewers: !--reviewers-list-->@gchure<!--end-reviewers-list-- Archive: 10.5281/zenodo.13628882
Status
Status badge code:
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
@gchure, 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:
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 ✨
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