[REVIEW]: jax-smfsb: A python library for stochastic systems biology modelling and inference

[editorialbot]

Submitting author: @darrenjw (Darren James Wilkinson)
Repository: https://github.com/darrenjw/jax-smfsb
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @jromanowska
Reviewers: @antoineruzette, @cthoyt
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/714db278d0aae77efbf0fe7a98679890/status.svg)](https://joss.theoj.org/papers/714db278d0aae77efbf0fe7a98679890)

Reviewers and authors:

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Reviewer instructions & questions

@antoineruzette & @cthoyt, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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

@antoineruzette, please create your checklist typing: @editorialbot generate my checklist

@cthoyt, please create your checklist typing: @editorialbot generate my checklist

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1538.3 files/s, 130522.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40            659           1136           1707
TeX                              1             25              0            130
reStructuredText                 4            147            306            114
Markdown                         2             35              0             67
make                             3             27             11             42
TOML                             1              4              0             29
YAML                             2             11             20             27
-------------------------------------------------------------------------------
SUM:                            53            908           1473           2116
-------------------------------------------------------------------------------

Commit count by author:

   121	Darren Wilkinson
     1	Charles Tapley Hoyt

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 690

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1111/j.1467-9868.2009.00736.x is OK
- 10.1016/j.cpc.2022.108527 is OK
- 10.1093/bioinformatics/btn051 is OK
- 10.1098/rsfs.2011.0047 is OK
- 10.1007/s11222-011-9288-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/bioinformatics/btab669 is OK
- 10.15252/msb.20199110 is OK
- 10.1088/1742-5468/ac3ae9 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1098/rsif.2008.0172 is OK
- 10.1093/bioinformatics/btac770 is OK
- 10.1038/nrg2509 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: On Neural Differential Equations
- No DOI given, and none found for title: An overview of the Scala programming language
- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: scala-smfsb
- No DOI given, and none found for title: python-smfsb

❌ MISSING DOIs

- 10.1201/9781351000918 may be a valid DOI for title: Stochastic Modelling for Systems Biology, third ed...
- 10.32614/cran.package.smfsb may be a valid DOI for title: smfsb: Stochastic Modelling for Systems Biology

❌ INVALID DOIs

- None

[editorialbot]

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

[jromanowska]

👋🏼 @darrenjw, @antoineruzette, @cthoyt, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

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as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

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We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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