Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @marouenbg, @krystophny it looks like you're currently assigned to review this paper :tada:.
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK
MISSING DOIs
- None
INVALID DOIs
- None
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@whedon generate pdf
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Hi @sjpfenninger , I finished my review, @Christopher-Khan addressed all of the comments either through additional experiments and implementation, new manuscript sections, and through point-by-point rebuttal.
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Hi @marouenbg. I just added one more result to the manuscript. The glmnet software package has two algorithm options to choose from, so I also included the benchmark result for the other option as well. It was slower than the option whose benchmark result I had already reported though. In addition, thank you again for doing this review! Your comments were very helpful in improving this submission!
Thanks @marouenbg for the extensive review and @Christopher-Khan for addressing everything thoroughly! krystophny's review is slightly delayed, but we expect by end of month, so stay tuned.
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@sjpfenninger I have finished reviewing the paper and testing the software and support the publication in JOSS after two minor changes in the README https://github.com/VU-BEAM-Lab/GENRE/issues/3 . As mentioned the package is relatively small (1000-2000 lines of code) and not very well known yet, but it looks very useful with its unique capability to solve multiple GLMs with elastic net regularization in parallel on GPUs and has the potential as a standard code for that task. The description is done well, and comparable software (without the special parallel feature) is referenced.
Hi @krystophny. Thank you for your review! In regards to the minor points, my responses are below.
For adding the folders to the MATLAB path, in the bullet point under Windows and Linux installation in the README, I have the following statement, "Assuming the repository is on your system, go to the MATLAB directory that contains the repository folders and add them to your MATLAB path."
In regards to not needing to specify the cuda path for Linux, I have the following statement in the second bullet point under Linux compilation in the README, "Note that mexcuda might find the CUDA toolkit library even if you do not explicitly type out its path. In addition, note that there might be differences in your path compared to the one shown above, such as in regards to the version of the CUDA toolkit that is being used."
Did you want me to still modify those statements?
@Christopher-Khan in that case it’s fine, now I understand that these things are correct already now. I was too hasty when reading. So all issues resolved!
@krystophny Great! Thank you!
@marouenbg @krystophny Thanks both for your reviews. Can you both confirm that you recommend to accept the submission? @krystophny can you close VU-BEAM-Lab/GENRE#3 if it is resolved?
@sjpfenninger everything resolved, I confirm the recommendation to accept the submission!
Hi @sjpfenninger, I have no further comments, I recommend the publication of the software.
@Christopher-Khan I have made some minor edits to the paper in VU-BEAM-Lab/GENRE#4 -- can you check and merge (ideally squash into single commit)? Also - could you adjust the table captions such that they differentiate what we see in the two tables rather than just saying "Benchmark times"?
Hi @sjpfenninger. I have squashed the edits into a single commit and merged them. I have also changed the title in the second table to differentiate it from the first table's title.
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@Christopher-Khan Great, we're ready to accept this. Can you make a tagged release on GitHub and archive that release, for example on Zenodo or figshare, then report the version number and archive DOI back here in the review issue?
Hi @sjpfenninger. Great! Here is the Zenodo information: DOI 10.5281/zenodo.4050385. Before archiving, I also made 3 minor edits to the paper unrelated to your edits (just reworded 3 sentences). Thank you!
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@Christopher-Khan great thanks. Can you edit the Zenodo item such that title and author list are the same as for the JOSS paper?
Hi @sjpfenninger. Sorry for the late response. I made one more edit to the paper. I forgot for the benchmarks to account for the fact that MATLAB code can sometimes run slower the first time it is called than subsequent calls due to MATLAB's execution engine. Therefore, I reran and updated the benchmarks in order to account for this. The times didn't change much, but I still wanted to update them in the paper. I made a new release on Zenodo and detailed the change on there. I have also updated the metadata. Here is the new Zenodo DOI. DOI: 10.5281/zenodo.4057940
Thank you!
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Hi @sjpfenninger. I was just following up. Was there anything else on my end that you needed me to do regarding the submission or the Zenodo archive? Thank you!
@whedon set doi as 10.5281/zenodo.4057940
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@whedon set 10.5281/zenodo.4057940 as archive
OK. 10.5281/zenodo.4057940 is the archive.
@whedon set v1.0.1 as version
OK. v1.0.1 is the version.
Submitting author: @Christopher-Khan (Christopher Khan) Repository: https://github.com/VU-BEAM-Lab/GENRE Version: v1.0.2 Editor: @sjpfenninger Reviewer: @marouenbg, @krystophny Archive: 10.5281/zenodo.4076520
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Review checklist for @marouenbg
Conflict of interest
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Software paper
Review checklist for @krystophny
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper