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[REVIEW]: BlueCelluLab: Biologically Detailed Neural Network Experimentation API #7026

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editorialbot opened this issue Jul 23, 2024 · 51 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Jul 23, 2024

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

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff"><img src="https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg)](https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff)

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:

@editorialbot generate my 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

@editorialbot
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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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Adapting dynamic object-oriented languages to mixe...
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.25 s (637.4 files/s, 182223.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            29              1              0          25703
Python                          99           2228           1809           8357
reStructuredText                 8            354            192           1939
Jupyter Notebook                 8              0           4422            576
YAML                             5             21             15            168
TeX                              1              9              0            152
Markdown                         5             34              0            100
TOML                             1              8              0             71
INI                              1              5              0             63
DOS Batch                        1              8              1             26
make                             2              4              7             17
CSV                              1              0              0             11
Bourne Shell                     1              4              0              8
-------------------------------------------------------------------------------
SUM:                           162           2676           6446          37191
-------------------------------------------------------------------------------

Commit count by author:

    74	Anil Tuncel
    56	anilbey
     9	Werner Van Geit
     6	dependabot[bot]
     5	ilkilic
     3	Alexis Arnaudon
     3	Aurélien Jaquier
     3	Eduard Šubert
     2	MikeG
     1	A Sato
     1	Darshan Mandge
     1	Kiliç Ilkan Fabrice
     1	eduard.subert

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Paper file info:

📄 Wordcount for paper.md is 1268

✅ The paper includes a Statement of need section

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License info:

🟡 License found: Other (Check here for OSI approval)

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@mooniean
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mooniean commented Jul 23, 2024

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!

@finsberg
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finsberg commented Jul 23, 2024

Review checklist for @finsberg

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/BlueBrain/BlueCelluLab?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@anilbey) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@finsberg
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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.

@mooniean
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@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!

@ryEllison
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ryEllison commented Aug 1, 2024

Review checklist for @ryEllison

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/BlueBrain/BlueCelluLab?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@anilbey) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@ryEllison
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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.

@mooniean
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mooniean commented Aug 5, 2024

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.

@anilbey
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anilbey commented Aug 9, 2024

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.

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anilbey commented Aug 9, 2024

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@mooniean
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mooniean commented Aug 9, 2024

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

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@mooniean
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mooniean commented Aug 9, 2024

@editorialbot check references

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

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Adapting dynamic object-oriented languages to mixe...
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None

@mooniean
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mooniean commented Aug 9, 2024

@anilbey I've started the post-review checklist. Can you please follow the tasks in my previous comment?

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.

Furthermore, there seems to be 3 DOIs missing, could you try to address those please?

@AurelienJaquier
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AurelienJaquier commented Aug 12, 2024

Here is the DOI for the latest release on zenodo: https://doi.org/10.5281/zenodo.13304365
Edit: I updated the link to have the list of authors consistent with the paper

@anilbey
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anilbey commented Aug 12, 2024

Hi @mooniean

Furthermore, there seems to be 3 DOIs missing, could you try to address those please?

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)?

@mooniean
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That's ok! I knew I had seen it somewhere. I'll proceed now with the next steps

@mooniean
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Done! archive is now 10.5281/zenodo.13304365

@mooniean
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@editorialbot set v2.6.28 as version

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Done! version is now v2.6.28

@mooniean
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@mooniean
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Mypy-optional static typing for python
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None

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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 accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 13, 2024
@Kevin-Mattheus-Moerman
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@editorialbot set 2.6.28 as version

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Done! version is now 2.6.28

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Aug 16, 2024

@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:

  • I see you have additional released created in the last couple of days, should we here update to 2.6.32 or is 2.6.28 still accurate for this review?
  • The following is a recommendation, not a requirement. I would remove the text at the top of you LICENSE (which mentions the 3rd party/dependency licenses), since you already mention this in your README. This way you LICENSE file can fully match the normal Apache 2.0 text and GitHub (and our systems too) would easily recognise it then as such.

@anilbey
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anilbey commented Aug 17, 2024

Hi @Kevin-Mattheus-Moerman, yes please update the version to be 2.6.32 since it contains changes related to the copyright and citation.

@anilbey
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anilbey commented Aug 17, 2024

The following is a recommendation, not a requirement. I would remove the text at the top of you LICENSE (which mentions the 3rd party/dependency licenses), since you already mention this in your README. This way you LICENSE file can fully match the normal Apache 2.0 text and GitHub (and our systems too) would easily recognise it then as such.

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

@Kevin-Mattheus-Moerman
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@editorialbot set 2.6.32 as version

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Done! version is now 2.6.32

@Kevin-Mattheus-Moerman
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@editorialbot set 10.5281/zenodo.13325726 as archive

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Done! archive is now 10.5281/zenodo.13325726

@Kevin-Mattheus-Moerman
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@anilbey I think all looks good to proceed now.

@Kevin-Mattheus-Moerman
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@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Tuncel
  given-names: Anıl
- family-names: Geit
  given-names: Werner Van
- family-names: Gevaert
  given-names: Mike
- family-names: Torben-Nielsen
  given-names: Benjamin
- family-names: Mandge
  given-names: Darshan
- family-names: Kılıç
  given-names: İlkan
- family-names: Jaquier
  given-names: Aurélien
- family-names: Muller
  given-names: Eilif
- family-names: Kanari
  given-names: Lida
- family-names: Markram
  given-names: Henry
doi: 10.5281/zenodo.13325726
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Tuncel
    given-names: Anıl
  - family-names: Geit
    given-names: Werner Van
  - family-names: Gevaert
    given-names: Mike
  - family-names: Torben-Nielsen
    given-names: Benjamin
  - family-names: Mandge
    given-names: Darshan
  - family-names: Kılıç
    given-names: İlkan
  - family-names: Jaquier
    given-names: Aurélien
  - family-names: Muller
    given-names: Eilif
  - family-names: Kanari
    given-names: Lida
  - family-names: Markram
    given-names: Henry
  date-published: 2024-08-17
  doi: 10.21105/joss.07026
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7026
  title: "BlueCelluLab: Biologically Detailed Neural Network
    Experimentation API"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07026"
  volume: 9
title: "BlueCelluLab: Biologically Detailed Neural Network
  Experimentation API"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07026 joss-papers#5778
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07026
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Aug 17, 2024
@Kevin-Mattheus-Moerman
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@anilbey congratulations on this JOSS publication!

Thanks for editing @mooniean !

And a special thank you to the reviewers: @finsberg, @ryEllison !!

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07026/status.svg)](https://doi.org/10.21105/joss.07026)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07026">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07026/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07026/status.svg
   :target: https://doi.org/10.21105/joss.07026

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@anilbey
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anilbey commented Aug 20, 2024

That is great news, thanks a lot @Kevin-Mattheus-Moerman @mooniean @finsberg @ryEllison for editing and reviewing this work.

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