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

[editorialbot]

Submitting author: !--author-handle-->@darrenjw<!--end-author-handle-- (Darren James Wilkinson) Repository: https://github.com/darrenjw/jax-smfsb Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: @antoineruzette, @cthoyt Managing EiC: Chris Vernon

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1617.4 files/s, 120350.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40            556           1140           1614
TeX                              1             23              0            128
Markdown                         2             29              0             69
make                             3             26             11             37
TOML                             1              4              0             29
reStructuredText                 3             25             42             29
YAML                             1              6             17             10
-------------------------------------------------------------------------------
SUM:                            51            669           1210           1916
-------------------------------------------------------------------------------

Commit count by author:

    89  Darren Wilkinson

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 682

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

:warning: An error happened when generating the pdf.

[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
- 10.15252/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
- 10.1038/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

[crvernon]

@editorialbot invite @jromanowska as editor

:wave: @jromanowska - are you available to take this one on?

[editorialbot]

Invitation to edit this submission sent!

[jromanowska]

@crvernon , I think I can take it :)

[jromanowska]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[darrenjw]

Searching the review database (for Python and Systems Biology), it seems like Manuel Razo-Mejia and Griffin Chure would be appropriate, along with Antoine Ruzette, Abhishek Tiwari, Yafei Wang, and many others.

[jromanowska]

Thank you, @darrenjw ! I'm sorry, I didn't have time to look at it yet. I'll come back to you this week.

[jromanowska]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[jromanowska]

Before we proceed, I've created an issue in your repo because the paper.md does not compile, please fix that. Also, I'd suggest to extend the paper just a bit by mentioning any software that has similar functionality to yours. You mention in the first paragraph of 'Statement of need' that there are some, perhaps it would be good to cite some of them that you think are worth mentioning.

[darrenjw]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[darrenjw]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

GPJax: A Gaussian Process Framework in JAX Submitting author: @thomaspinder Handling editor: @dfm (Active) Reviewers: @gpleiss, @theorashid Similarity score: 0.7394

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flowMC: Normalizing flow enhanced sampling package for probabilistic inference in JAX Submitting author: @kazewong Handling editor: @rkurchin (Active) Reviewers: @matt-graham, @Daniel-Dodd Similarity score: 0.7076

SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency Submitting author: @antoinediez Handling editor: @pdebuyl (Active) Reviewers: @lorenzo-rovigatti, @junghans Similarity score: 0.7046

PyNumDiff: A Python package for numerical differentiation of noisy time-series data Submitting author: @florisvb Handling editor: @christinahedges (Retired) Reviewers: @pmli, @billtubbs Similarity score: 0.7040

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[darrenjw]

Thanks. The build is fixed and I've added references to a couple of existing systems biology simulation libraries.

[jromanowska]

:wave: @cthoyt, @benlansdell, @ortega2247 & @antoineruzette, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[cthoyt]

I'd made some quick suggestions to @darrenjw to try and update the package to conform to Python community code standards (https://github.com/darrenjw/jax-smfsb/issues/7, https://github.com/darrenjw/jax-smfsb/issues/8) and to add some documentation for new users (https://github.com/darrenjw/jax-smfsb/issues/9)

I will consider reviewing the code further and the manuscript if these are addressed

[jromanowska]

I'd made some quick suggestions to @darrenjw to try and update the package to conform to Python community code standards (darrenjw/jax-smfsb#7, darrenjw/jax-smfsb#8) and to add some documentation for new users (darrenjw/jax-smfsb#9)

I will consider reviewing the code further and the manuscript if these are addressed

Thank you so much for looking into that so fast! We'll wait for the author to address these issues. :+1:

[benlansdell]

Hi @jromanowska , I'm happy to act as a reviewer, sure!

[jromanowska]

Thank you, @benlansdell. As you can see from previous comments in this thread, we're currently waiting for the author to address some issues raised by @cthoyt.

[antoineruzette]

Hi @jromanowska, happy to help reviewing this repo. Cheers!

[jromanowska]

Thank you, @antoineruzette. We'll wait some days for the response from @darrenjw to issues raised by @cthoyt.

In the meantime, if you or @benlansdell have any other comments, please write them here. Note that this is not yet the official review thread, so you don't need to look into the code yet.

[jromanowska]

@darrenjw, I can see you're working on the code - great work! Let us know when you feel you've addressed the issues so that we can start the real review process. @cthoyt, please, keep your expectations low because the review has not yet started.

[darrenjw]

The suggestions from @cthoyt are all good - just time-consuming. I've had a reasonable go at addressing most of them, so I think it's probably fine to start the real review process now. Thanks,

[jromanowska]

@editorialbot add @antoineruzette as reviewer

[editorialbot]

@antoineruzette added to the reviewers list!

[jromanowska]

@editorialbot add @cthoyt as reviewer

[editorialbot]

@cthoyt added to the reviewers list!

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7491.