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[REVIEW]: BlueCelluLab: Biologically Detailed Neural Network Experimentation API #7026
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
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Paper file info: 📄 Wordcount for ✅ The paper includes a |
License info: 🟡 License found: |
Hi @anilbey and reviewers @finsberg and @ryEllison - this is the review thread for the submission. All of our communications will happen here from now on. Meanwhile, please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package. Please feel free to ping me (@mooniean) if you have any questions or concerns. Thanks! |
Review checklist for @finsbergConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@mooniean I am done with my review on this software and can recommend it for publication in JOSS. The authors did an excellent job preparing this software for JOSS. |
@finsberg thank you so much, that is great to hear! As soon as @ryEllison also checks the paper/software, I'll then make final checks! |
Review checklist for @ryEllisonConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Good morning, @mooniean! I have now finished my review of the paper/software. It's a rather nice frontend API to the NEURON simulation engine, facilitating quick neuron-model development. There's certainly an off-the-shelf compatibility during installation for Unix-like OS over Windows. With that said, however, I can make the recommendation for publication in JOSS. |
This is excellent, thank you both for your reviews! Before going to the post-review checklist, @anilbey: in the paper, can you add a small explanation for Figure 1? It is not mentioned at any point in the text, it's only for clarification! After, I'll be happy to advance to the next steps. |
Thanks reviewers for taking your time and reviewing BlueCelluLab. @mooniean I just added it the explanation here BlueBrain/BlueCelluLab#199 let me regenerate the pdf. |
@editorialbot generate pdf |
Post-Review Checklist for Editor and AuthorsAdditional Author Tasks After Review is Complete
Editor Tasks Prior to Acceptance
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@editorialbot check references |
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@anilbey I've started the post-review checklist. Can you please follow the tasks in my previous comment?
Furthermore, there seems to be 3 DOIs missing, could you try to address those please? |
Here is the DOI for the latest release on zenodo: https://doi.org/10.5281/zenodo.13304365 |
Hi @mooniean
This was also mentioned during the pre-review #6956 (comment). Those 3 references do not have the DOI. If all references require a DOI, can we turn those three into footnotes instead (if the markdown template supports it)? |
That's ok! I knew I had seen it somewhere. I'll proceed now with the next steps |
@editorialbot set https://doi.org/10.5281/zenodo.13304365 as archive |
Done! archive is now 10.5281/zenodo.13304365 |
@editorialbot set v2.6.28 as version |
Done! version is now v2.6.28 |
@editorialbot generate pdf |
@editorialbot recommend-accept |
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👋 @openjournals/bcm-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5761, then you can now move forward with accepting the submission by compiling again with the command |
@editorialbot set 2.6.28 as version |
Done! version is now 2.6.28 |
@anilbey as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:
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Hi @Kevin-Mattheus-Moerman, yes please update the version to be 2.6.32 since it contains changes related to the copyright and citation. |
I totally agree. Especially because those 3rd party code/data are not part of the package. Those are only used in the example directory to demonstrate some real world use cases. I created this issue here to address it. BlueBrain/BlueCelluLab#206 |
@editorialbot set 2.6.32 as version |
Done! version is now 2.6.32 |
@editorialbot set 10.5281/zenodo.13325726 as archive |
Done! archive is now 10.5281/zenodo.13325726 |
@anilbey I think all looks good to proceed now. |
@editorialbot accept |
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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? Notify your editorial technical team... |
@anilbey congratulations on this JOSS publication! Thanks for editing @mooniean ! And a special thank you to the reviewers: @finsberg, @ryEllison !! |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
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That is great news, thanks a lot @Kevin-Mattheus-Moerman @mooniean @finsberg @ryEllison for editing and reviewing this work. |
Submitting author: @anilbey (Mustafa Anıl Tuncel)
Repository: https://github.com/BlueBrain/BlueCelluLab
Branch with paper.md (empty if default branch): joss-paper
Version: 2.6.32
Editor: @mooniean
Reviewers: @finsberg, @ryEllison
Archive: 10.5281/zenodo.13325726
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
@finsberg & @ryEllison, 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 @mooniean 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 @finsberg
📝 Checklist for @ryEllison
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