[REVIEW]: BioMAC-Sim-Toolbox: A MATLAB toolbox for biomechanical motion analysis and creation through simulation

[editorialbot]

Submitting author: @adkoele (Anne Koelewijn)
Repository: https://github.com/mad-lab-fau/BioMAC-Sim-Toolbox/
Branch with paper.md (empty if default branch):
Version: V1.0.1
Editor: @prashjha
Reviewers: @rmndrs89, @Aravind-Sundararajan
Archive: 10.5281/zenodo.17280081

Status

Status badge code:

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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

@rmndrs89 & @Aravind-Sundararajan, 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 @prashjha 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 @Aravind-Sundararajan

📝 Checklist for @rmndrs89

[editorialbot]

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:

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

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[editorialbot]

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

✅ OK DOIs

- 10.1137/1.9780898718577 is OK
- 10.1007/BF00430237 is OK
- 10.1016/j.piutam.2011.04.021 is OK
- 10.1016/j.jbiomech.2009.12.012 is OK
- 10.7717/peerj.14852 is OK
- 10.1080/10255842.2018.1490954 is OK
- 10.1038/s41598-020-73856-w is OK
- 10.3389/fbioe.2024.1285845 is OK
- 10.1016/j.jbiomech.2019.07.022 is OK
- 10.1109/TNSRE.2022.3189038 is OK
- 10.1109/tnsre.2010.2047592 is OK
- 10.1007/s10107-004-0559-y is OK
- 10.1016/j.gaitpost.2016.07.007 is OK
- 10.1101/2023.05.25.542228 is OK
- 10.1080/10255842.2019.1601179 is OK
- 10.1098/rsif.2019.0402 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=2.20 s (149.0 files/s, 385098.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                               31           1833           1783         729894
XML                             10              9          20035          38663
MATLAB                         239           6113          16718          28110
Perl                            15            171              6           1444
Markdown                        10            287             22           1305
C/C++ Header                    11            109             98            543
TeX                              1             15              0            164
SVG                              1              1              1            100
Text                             2             41              0             87
YAML                             3             14             23             75
make                             3             19              3             53
Bourne Shell                     2             11             35             46
-------------------------------------------------------------------------------
SUM:                           328           8623          38724         800484
-------------------------------------------------------------------------------

Commit count by author:

    44	Anne Koelewijn
     4	Ton van den Bogert
     2	scam_goudi
     1	adkoele

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1846

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[prashjha]

Dear @rmndrs89 and @Aravind-Sundararajan, please read the first couple of comments in this thread and create your review checklist. You can read the reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Good luck!

[Aravind-Sundararajan]

Review checklist for @Aravind-Sundararajan

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/mad-lab-fau/BioMAC-Sim-Toolbox/?
• 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 (@adkoele) 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?