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[PRE REVIEW]: PGFinder — A Python package and web tool for peptidoglycomics #5904
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Five most similar historical JOSS papers: Phylen: automatic phylogenetic reconstruction using the EggNOG database PyGModels: A Python package for exploring Probabilistic Graphical Models with Graph Theoretical Structures Cocktail Shaker: An open source drug expansion and enumeration library for peptides CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices. |
@TheLostLambda thanks for this submission. I am the AEiC for this track and here to help with initial steps. |
Hi @Kevin-Mattheus-Moerman! Sounds good! I'm happy to help out however I can! Between the Python, Svelte, and Typescript (where the proper code is — as opposed to other data and documentation files), I think things should come out at around 1800 lines or so (going off of the In terms of citations, I think it helps that we've already got one paper out in eLife on the original version of the software, and we're working on another paper built on results from this tool at the moment! When it comes to use and citation by peers in the field, the existing PGFinder paper should have a couple of citations, and we recently presented this new and improved version at a conference where there seemed to be some decent interest! I there is any more information that would be helpful for the editorial board, just let me know! |
Oh, and perhaps to adjust the labels for this review, it might be good to remove TeX and Makefile tags (as those files are just part of the Sphinx documentation generation), and it would be good to add someone to take a look at the web side of things! A Svelte specialist would be best, but it's pretty close to regular HTML, CSS, and Java/Typescript :) |
@TheLostLambda thanks for the additional information. If in addition, you could summarise/clarify what significant changes were made since the elife paper (https://doi.org/10.7554/eLife.70597) that would be helpful. |
Hi @Kevin-Mattheus-Moerman ! Sorry for the glacial delay! In rough order of effort / impact / importance:
Beyond user features, substantial effort has gone into refactoring the codebase and bringing it in line with good open-source practices:
These are just the highlights and I've almost certainly missed out on some details, but when the eLife paper was published, the v0.02 tag was created, so you can see all of the changes we've made since using this link: Mesnage-Org/pgfinder@v0.02...main Looks like it's currently around 677 commits by 4 developers over the past two years or so :) Sorry again for the delay and hopefully this information is helpful! Please let me know if you'd like any more detail or clarification :) |
@Kevin-Mattheus-Moerman Hi Kevin! I don't mean to pester, but do you know how long we should expect the pre-review process to take / is there anything you still need from us? Thanks a ton, |
@TheLostLambda apologies for the delay encountered so far. We are combating a bit of a backlog in submissions and the board, as a consequence, has not been responding as fast as we'd like. I have spurred them on just now with a reminder and will conclude the scope review this week. Once again sorry for how long this has been going on. |
@TheLostLambda Once again my apologies for the delay in processing this scope review. The editorial board has now concluded this scope review. Unfortunately the conclusion is that this work is not at present in scope in JOSS. Although the software itself is scientifically interesting, the core functionality has already been published through the recent eLife publication (https://doi.org/10.7554/eLife.70597). The advancement on top of that work was not deemed sufficient enough to warrant a JOSS publication. We will now proceed to reject this submission. Note that the above conclusion does not mean the software is not useful or not of a high quality. We do hope you will consider JOSS for any future (re-)submissions. Once again, my sincere apologies for the much slower than usual scope review process. |
@editorialbot reject |
Paper rejected. |
Hi @Kevin-Mattheus-Moerman, and other editors - thanks for taking the time to look at our work. We're very proud of the eLife paper, which demonstrates the scientific merit and usefulness of pgfinder via an excellent journal. I encouraged my co-authors to submit to JOSS as well in order to obtain a review of the software (i.e. the code etc.), which I felt was not something the eLife process (nor that of many other journals) covered in detail. We've done quite a bit of PR reviewing within the team, but it's not quite the same as an independant perspective. I hadn't spotted any review criteria around novelty or previous publication - if anyone has time to direct me to the right bit of the criteria, I'd appreciate it! Or maybe it should have been obvious to me. If this is the wrong place for me to make a comment like this, please let me know. I'm comfortable with the rejection, just thinking what to do with future work. I will continue to point to the JOSS criteria as the best available set for reviewing research software (I'm happy that pgfinder was improved by making changes to meet these) and I appreciate the work you're doing. |
Submitting author: @TheLostLambda (Brooks Rady)
Repository: https://github.com/Mesnage-Org/pgfinder
Branch with paper.md (empty if default branch): ns-rse/109-joss
Version: v1.0.3
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman
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