[PRE 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: V1.0.0
Editor: @prashjha
Reviewers: @rmndrs89, @Aravind-Sundararajan
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Author instructions

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Software report:

github.com/AlDanial/cloc v 1.98  T=2.27 s (142.5 files/s, 372285.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                               30           1938           1849         728820
XML                             10              9          20035          38663
MATLAB                         239           6132          16734          28163
Perl                            14            174              6           1415
Markdown                         8            189              0            843
C/C++ Header                    11            109             98            543
TeX                              1             15              0            149
SVG                              1              1              1            100
Text                             2             41              0             87
YAML                             3             13             19             67
make                             3             19              3             53
Bourne Shell                     2             11             35             46
-------------------------------------------------------------------------------
SUM:                           324           8651          38780         798949
-------------------------------------------------------------------------------

Commit count by author:

    22	Anne Koelewijn
     1	scam_goudi

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.jbiomech.2019.07.022 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Practical methods for optimal control and estimati...
- No DOI given, and none found for title: Change the direction: 3D optimal control simulatio...
- No DOI given, and none found for title: Estimating 3D kinematics and kinetics from virtual...
- No DOI given, and none found for title: Predictive simulations to replicate human gait ada...

❌ MISSING DOIs

- 10.1007/bf00430237 may be a valid DOI for title: Optimization of energy expenditure during level wa...
- 10.1016/j.piutam.2011.04.021 may be a valid DOI for title: OpenSim: a musculoskeletal modeling and simulation...
- 10.1016/j.jbiomech.2009.12.012 may be a valid DOI for title: Optimality principles for model-based prediction o...
- 10.1080/10255842.2018.1490954 may be a valid DOI for title: A metabolic energy expenditure model with a contin...
- 10.1038/s41598-020-73856-w may be a valid DOI for title: Efficient trajectory optimization for curved runni...
- 10.1109/tnsre.2010.2047592 may be a valid DOI for title: A muscle-reflex model that encodes principles of l...
- 10.1007/s10107-004-0559-y may be a valid DOI for title: On the implementation of an interior-point filter ...
- 10.1016/j.gaitpost.2016.07.007 may be a valid DOI for title: Joint contact forces can be reduced by improving j...
- 10.1101/2023.05.25.542228 may be a valid DOI for title: Comparing sparse inertial sensor setups for sagitt...
- 10.1080/10255842.2019.1601179 may be a valid DOI for title: Optimal control simulation predicts effects of mid...
- 10.1098/rsif.2019.0402 may be a valid DOI for title: Rapid predictive simulations with complex musculos...

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1843

✅ 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 📄 👈

[editorialbot]

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Similarity score: 0.6987

⚠️ 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.

[Kevin-Mattheus-Moerman]

@adkoele Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• In your affiliations please spell out country names in full (no acronyms).
• Please can you confirm this project features automated testing? I cannot see a reference to it in the README.
• Can you confirm the documentation is complete enough, or complete it if not done already. I tried to look at some but found it empty looking:
  

In addition, please note that we're currently managing a large backlog of submissions and the editors most appropriate for your area are all already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[adkoele]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.jbiomech.2019.07.022 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Practical methods for optimal control and estimati...
- No DOI given, and none found for title: Change the direction: 3D optimal control simulatio...
- No DOI given, and none found for title: Estimating 3D kinematics and kinetics from virtual...
- No DOI given, and none found for title: Predictive simulations to replicate human gait ada...

❌ MISSING DOIs

- 10.1007/bf00430237 may be a valid DOI for title: Optimization of energy expenditure during level wa...
- 10.1016/j.piutam.2011.04.021 may be a valid DOI for title: OpenSim: a musculoskeletal modeling and simulation...
- 10.1016/j.jbiomech.2009.12.012 may be a valid DOI for title: Optimality principles for model-based prediction o...
- 10.1080/10255842.2018.1490954 may be a valid DOI for title: A metabolic energy expenditure model with a contin...
- 10.1038/s41598-020-73856-w may be a valid DOI for title: Efficient trajectory optimization for curved runni...
- 10.1109/tnsre.2010.2047592 may be a valid DOI for title: A muscle-reflex model that encodes principles of l...
- 10.1007/s10107-004-0559-y may be a valid DOI for title: On the implementation of an interior-point filter ...
- 10.1016/j.gaitpost.2016.07.007 may be a valid DOI for title: Joint contact forces can be reduced by improving j...
- 10.1101/2023.05.25.542228 may be a valid DOI for title: Comparing sparse inertial sensor setups for sagitt...
- 10.1080/10255842.2019.1601179 may be a valid DOI for title: Optimal control simulation predicts effects of mid...
- 10.1098/rsif.2019.0402 may be a valid DOI for title: Rapid predictive simulations with complex musculos...

❌ INVALID DOIs

- None

[adkoele]

@editorialbot check references

[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

[Kevin-Mattheus-Moerman]

@editorialbot invite @prashjha as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@adkoele I see some points are addressed. Are you able to address the others too? 👆

[adkoele]

Hi @Kevin-Mattheus-Moerman,

We do not have automatic testing.

Regarding the documentation, I am still working on it. It worked on my own computer before, but it seems that the code that we are using is not compatible with the Doxygen Action workflow that we have set up on git, so it requires a larger overhaul. I have not yet had time to look at this in more detail unfortunately. This week is however the final week of teaching, so hopefully I can be fixed soon. Is it required to finish that before moving on to the review?

[Kevin-Mattheus-Moerman]

@adkoele okay thanks for the update. If you can make these changes in a timely manor we can wait. However if you think you need more than a month then I suggest we retract this submission at this point and that you resubmit when the changes are implemented. Let me know what you think.

Fyi my GIBBON project features basic automated testing (a script triggering the test scripts). If you need an example.

[adkoele]

I don't think that it would take that long at this point.

Would it be necessary to have automatic testing? If so, why?

[adkoele]

@Kevin-Mattheus-Moerman hello again!
The documentation is now working. https://mad-lab-fau.github.io/BioMAC-Sim-Toolbox/

We do not have automatic testing, as I mentioned in the previous comment. I looked into it a bit. If I understand correctly, it would be required to either have automatic testing or to have manual steps that check the correctness of the code. Automatic testing is not really feasible, as the tests in src/tests rely on visual inspection.

How to run tests is explained in the documentation, for example: https://mad-lab-fau.github.io/BioMAC-Sim-Toolbox/class_gait2dc_test.html

Is that sufficient or should I still make an addition to the ReadMe or so?

[Kevin-Mattheus-Moerman]

@adkoele you are right fully automated testing is not a strict requirement. If you have or could add unit tests (not requiring human interactions) that would be recommended. I think we have enough to proceed here from what you describe but again having automated testing is recommended so perhaps you can consider adding some as this review processes.

[prashjha]

@editorialbot assign me as editor

[editorialbot]

Assigned! @prashjha is now the editor

[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

[prashjha]

Howdy! @anmuller, @felixchenier, @romainmartinez, and @tgeijten, would you be interested in reviewing the JOSS submission above (pdf link)? The corresponding software is at this link.

This link covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[prashjha]

Hi @adkoele, could you suggest names of potential reviewers from this reviewer database?

[adkoele]

Hi @prashjha,

Perhaps these
@rmndrs89
@I don't have GitHub.
@alcantarar

[tgeijten]

Hi @prashjha, I don't use MATLAB, sorry!

[prashjha]

@tgeijten, thank you for letting me know!

[prashjha]

Howdy! @rmndrs89 and @alcantarar, would you be interested in reviewing the JOSS submission above (pdf link)? The corresponding software is at this link.

This link covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[felixchenier]

Hi @prashjha
I don't use Matlab anymore either, I'd be quite rusty trying to test this software. But ping me again if you struggle to find someone.

[rmndrs89]

Hi @prashjha ,

Thanks for the opportunity!
I can review the toolbox.

[prashjha]

Hi @felixchenier, thank you for the response. I will ping if I still need you. Best, Prashant.

[prashjha]

Hi @rmndrs89, thank you for agreeing.

[prashjha]

@editorialbot add @rmndrs89 as reviewer

[editorialbot]

@rmndrs89 added to the reviewers list!

[romainmartinez]

Howdy! @anmuller, @felixchenier, @romainmartinez, and @tgeijten, would you be interested in reviewing the JOSS submission above (pdf link)? The corresponding software is at this link.

This link covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

Hello, thank you for the opportunity but unfortunately I do not use Matlab anymore. All the best!

[rmndrs89]

Hi @prashjha, do I start reviewing in this thread, or will a new thread [REVIEW]: BioMAC-Sim-Toolbox: A MATLAB toolbox for biomechanical motion analysis and creation through simulation be opened for the review itself?

[rmndrs89]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue

[rmndrs89]

Hi @prashjha how do we proceed with the review?

[prashjha]

HI @rmndrs89, please wait for me to find another reviewer. The review will take place in another GitHub issue, and you will be pinged and notified. Best, Prashant.

[prashjha]

Hi @mprib and @Aravind-Sundararajan, I am looking for another reviewer for the above JOSS submission. Would you be interested in reviewing this? You can find pdf at this link pdf link, and the corresponding software is at this link.

This reviewer guidelines covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[mprib]

Hi @prashjha,

I have minimal experience with MATLAB and am fairly slammed over the next couple of months. If no other reviewers are available I may be able to take this on in the summer, but can't commit to it at this time.

[Aravind-Sundararajan]

Hi @mprib and @Aravind-Sundararajan, I am looking for another reviewer for the above JOSS submission. Would you be interested in reviewing this? You can find pdf at this link pdf link, and the corresponding software is at this link.

This reviewer guidelines covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

Hello @prashjha, I would be happy to review this paper

[prashjha]

@Aravind-Sundararajan, thank you for agreeing to review!

[prashjha]

@editorialbot add @Aravind-Sundararajan as reviewer

[editorialbot]

@Aravind-Sundararajan added to the reviewers list!

[prashjha]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7945.