[REVIEW]: KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities #6842

editorialbot · 2024-06-05T09:01:13Z

Submitting author: @JuliusWelzel (Julius Welzel)
Repository: https://github.com/neurogeriatricskiel/NGMT
Branch with paper.md (empty if default branch):
Version: v0.0.5
Editor: @Kevin-Mattheus-Moerman
Reviewers: @aaa34169, @davidpagnon
Archive: 10.17605/OSF.IO/8M2SP

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Reviewer instructions & questions

@aaa34169 & @davidpagnon, 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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Checklists

📝 Checklist for @aaa34169

📝 Checklist for @davidpagnon

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editorialbot · 2024-06-05T09:01:16Z

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editorialbot · 2024-06-05T09:01:37Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.27 s (279.2 files/s, 492984.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              3              0              0         116689
Python                          25           1389           1919           4327
Markdown                        28            646              0           2153
Jupyter Notebook                11              0           3660            747
HTML                             1             32              1            396
TeX                              1             20              1            178
YAML                             4             20              6            166
TOML                             1              4              0             52
CSS                              1              2              0             10
-------------------------------------------------------------------------------
SUM:                            75           2113           5587         124718
-------------------------------------------------------------------------------

Commit count by author:

   161	masoudabedinifar
   160	Julius Welzel
    56	github-actions
    47	rmndrs89
    37	Robbin Romijnders
    34	jwelzel
    21	JuliusWelzel
     3	dependabot[bot]

editorialbot · 2024-06-05T09:01:43Z

Paper file info:

📄 Wordcount for paper.md is 1120

✅ The paper includes a Statement of need section

editorialbot · 2024-06-05T09:01:44Z

License info:

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

editorialbot · 2024-06-05T09:01:57Z

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

OK DOIs

- 10.3390/brainsci9020034 is OK
- 10.1016/j.medengphy.2020.11.005 is OK
- 10.21105/joss.01778 is OK
- 10.1016/S1474-4422(20)30033-8 is OK
- 10.1038/sdata.2016.44 is OK
- 10.3233/JPD-181498 is OK
- 10.1109/OJEMB.2024.3356791 is OK
- 10.1002/mds.28377 is OK
- 10.1186/s12984-023-01198-5 is OK
- 10.3389/fneur.2017.00135 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1016/S1474-4422(19)30397-7 is OK

MISSING DOIs

- 10.31234/osf.io/w6z79 may be a valid DOI for title: Motion-BIDS: extending the Brain Imaging Data Stru...
- 10.1371/journal.pone.0069627 may be a valid DOI for title: Prevalence and burden of gait disorders in elderly...
- No DOI given, and none found for title: Technical validation of real-world monitoring of g...
- 10.1186/s12984-019-0494-z may be a valid DOI for title: Locomotion and cadence detection using a single tr...
- 10.1109/embc44109.2020.9176281 may be a valid DOI for title: Real-world speed estimation using single trunk IMU...
- No DOI given, and none found for title: Estimate Gait Quality Composite
- No DOI given, and none found for title: Mobilise-D Technical Validation Study Recommended ...

INVALID DOIs

- None

editorialbot · 2024-06-05T09:02:31Z

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

Kevin-Mattheus-Moerman · 2024-06-05T09:02:33Z

@aaa34169, @davidpagnon thanks for agreeing to review this submission. This is where the review takes place. Please get started by calling @editorialbot generate my checklist. We hope you can provide your review within about 2-3 weeks but do let me know if you need more time. Thanks again!

aaa34169 · 2024-06-05T10:08:14Z

Review checklist for @aaa34169

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/neurogeriatricskiel/NGMT?
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 (@JuliusWelzel) 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?

davidpagnon · 2024-06-05T11:36:24Z

Review checklist for @davidpagnon

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/neurogeriatricskiel/NGMT?
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 (@JuliusWelzel) 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?

JuliusWelzel · 2024-06-12T07:45:01Z

No worries 😄 I will delete our comments as well

davidpagnon · 2024-06-12T09:36:09Z

Most of the example files not available --> neurogeriatricskiel/KielMAT#90

davidpagnon · 2024-06-12T11:53:08Z

Here is a first pass for the review:

General checks

License: Non-Profit Open Software License version 3.0" is OSI approved: https://opensource.org/license/nposl-3-0
Substantial scholarly effort: The tools offered by NGMT are useful in the field of gait analysis, and are straightforward to put into application thanks to this toolbox.
Data sharing: Two large datasets are natively supported (Keep Control and Mobilize-D), and tools are provided to load them.
Example files for tutorials are missing for now.
It would be good to add a line stating that it has been gathered in accordance with the Declaration of Helsinki.

Functionality

Installation: Installation ran properly on python 3.11 (on python 3.12, I had to add the --user flag: pip install ngmt --user)
Functionality: I could not test all tutorials yet, due to missing example files.
The theory behind each module is well explained on the website and in the docstrings.

Documentation

Statement of need: The statement of need is clear and the target audience (motion researchers) is also specified.
It may be worth specifying that the expected motion data are 3D accelerations (from the wrist or the lower-back depending on the module).
Note that the list is not rendered on the website (all items are on the same line).
Example usage: Example data files are currently missing
Code quality: The code is clearly documented (both on the website and in the docstrings), it is very well written, classes and functions are easy to read. Tests are extensive.
Community guidelines: Issues have been activated on the repository so the user can report issues or seek support; there are contribution guidelines on the website and in the paper, but it would be good to refer to them in the Readme.md file.

Software paper

Summary: It is not immediately clear from the paper what kind of data the toolbox uses: marker-based data? Video input? RGB-D? IMUs? I suppose any piece of hardware could be suitable as long as it can provide acceleration data (from the pelvis? the wrist?), but it is not stated. I would be more specific very early on, for example by specifying which type of motion data is expected L12: "NGMT offers a range of 12 algorithms for the processing of motion data in neuroscience and biomechanics".
Statement of need: I would like more detail to be given about each of the 4 modules. I feel like someone skimming the paper could easily miss that there are actually 4 main modules, and if they do, they may not understand what they consist in. Why are these 4 modules (+ the ones under development: "postural transition analysis" and "turns") specifically useful? I would also appreciate it if you provided the gist of the theory behind each module.

Why are accelerometers better than vision-based approaches in your context? Supposedly because unlike being filmed, one can wear accelerometers all day long and at any place.

I do not understand the end of the sentence L33: "DHT [...] offers a new dimension of measuring daily function, that is, performance"

One subsidiary remark: NGMT is just a sequence of letters that will not bear any meaning to anyone who comes across it; moreover, I think this toolbox could be useful to many more cases than the very specific field of neurogeriatric motion. For the sake of dissemination, would it be worth finding another name?
State of the field: It may be interesting to cite other approaches not using acceleration-based data, such as the Mobile gait-lab (paper and code): although it works from video input and focuses on different quantities (walking speed, cadence, maximum knee flexion, and gait deviation), the approach is globally similar in that it is open-source and meant to be easily accessible to non computer-science specialists. Sit2Stand and Sports2D are other repositories that could make it to this section.
Quality of writing: I am not a native English speaker but no obvious error jumps to mind.

Kevin-Mattheus-Moerman · 2024-07-16T15:11:21Z

@aaa34169 I hope you are doing well. Could you provide an update on where things stand? If you need more time let us know. Thanks again for your help!

Kevin-Mattheus-Moerman · 2024-07-16T15:12:07Z

@JuliusWelzel apologies for the delay with this review so far. We'll see if we here from @aaa34169, if they are still able to help we'll resume, if not we'll try to find an alternative reviewer.

JuliusWelzel · 2024-07-23T06:55:04Z

Thanks @davidpagnon for your comprehensive review.
We have updated the toolbox and made a new release, so the example datasets can now be fetched from public repos. Let us know if everything works.

Data sharing: Two large datasets are natively supported (Keep Control and Mobilize-D), and tools are provided to load them.
Example files for tutorials are missing for now.

Examples for ICD and GSD have been added as part of #102. They can be simply loaded as shown in this example.

It would be good to add a line stating that it has been gathered in accordance with the Declaration of Helsinki.

This has been added in neurogeriatricskiel/KielMAT@8fa81ad

It may be worth specifying that the expected motion data are 3D accelerations (from the wrist or the lower-back depending on the module).

A table with an overview has been added on the landing page in

Community guidelines: Issues have been activated on the repository so the user can report issues or seek support; there are contribution guidelines on the website and in the paper, but it would be good to refer to them in the Readme.md file.

We have added a link and statement about contributing in the README.

Software paper

Summary: It is not immediately clear from the paper what kind of data the toolbox uses: marker-based data? Video input? RGB-D? IMUs? I suppose any piece of hardware could be suitable as long as it can provide acceleration data (from the pelvis? the wrist?), but it is not stated. I would be more specific very early on, for example by specifying which type of motion data is expected L12: "NGMT offers a range of 12 algorithms for the processing of motion data in neuroscience and biomechanics".

We have updated the summary in neurogeriatricskiel/KielMAT@a62e731

Statement of need: I would like more detail to be given about each of the 4 modules. I feel like someone skimming the paper could easily miss that there are actually 4 main modules, and if they do, they may not understand what they consist in. Why are these 4 modules (+ the ones under development: "postural transition analysis" and "turns") specifically useful? I would also appreciate it if you provided the gist of the theory behind each module.
Why are accelerometers better than vision-based approaches in your context? Supposedly because unlike being filmed, one can wear accelerometers all day long and at any place.
I do not understand the end of the sentence L33: "DHT [...] offers a new dimension of measuring daily function, that is, performance"

We have updated the text in various commits to address these valuable comments

One subsidiary remark: NGMT is just a sequence of letters that will not bear any meaning to anyone who comes across it; moreover, I think this toolbox could be useful to many more cases than the very specific field of neurogeriatric motion. For the sake of dissemination, would it be worth finding another name?

We thank you for pointing this out. We have change the name of the toolbox to KielMotionAnalysisToolbox (KielMAT).

State of the field: It may be interesting to cite other approaches not using acceleration-based data, such as the Mobile gait-lab (paper and code): although it works from video input and focuses on different quantities (walking speed, cadence, maximum knee flexion, and gait deviation), the approach is globally similar in that it is open-source and meant to be easily accessible to non computer-science specialists. Sit2Stand and Sports2D are other repositories that could make it to this section.

We adapted the text in the following commit: neurogeriatricskiel/KielMAT@d8f471f

JuliusWelzel · 2024-07-23T06:56:00Z

@Kevin-Mattheus-Moerman We made a new release as parts of our responses to @davidpagnon. The available version is now 0.0.5.

davidpagnon · 2024-07-24T15:02:09Z

Thanks for addressing my points! I tried all the modules with the new version and they all work seamlessly.

Three last remarks:

It would be nice if there was a progress bar and/or message telling us that the mobilize dataset is being downloaded. I did not have any of it and it took a while, so I exited. When I relaunched it it did not work (invalid zip file) so I had to find where the dataset was stored, remove it, and type the command again. I believe you would just have to set this to True and it would show the progress bar:
https://github.com/neurogeriatricskiel/KielMAT/blob/a2b757a2f785aa3f43aba72dcfe357d363737dc2/kielmat/datasets/mobilised.py#L71
I had a timeout issue when downloading the keepcontrol dataset, but then the demo still worked so I would not worry. It may be on my end, my connection is not especially fast.
RuntimeError: Timeout when trying to download D:\softs\KielMAT\kielmat\datasets\_keepcontrol\sub-pp001\motion\sub-pp001_task-calibration3_tracksys-omc_motion.tsv.
The user needs to pip install kielmat, but then also to git clone https://github.com/neurogeriatricskiel/KielMAT.git, and to cd keilmat or this tutorial will not work. It may be worth specifying it.
I feel like the Installation section should be at the very beginning of the home page. Right now the user has to dig to find how to install it and that may add a small obstacle to the adoption of the software.

JuliusWelzel · 2024-07-25T09:17:16Z

Hi,

thanks for getting back so quickly. All three points have been addressed as follows:

It would be nice if there was a progress bar and/or message telling us that the mobilize dataset is being downloaded. I did not have any of it and it took a while, so I exited. When I relaunched it it did not work (invalid zip file) so I had to find where the dataset was stored, remove it, and type the command again. I believe you would just have to set this to True and it would show the progress bar.

We set the progressbar True as default in: 52a0386b1e4f2df6e8950db50abdf1f94aef5a7a

The user needs to pip install kielmat, but then also to git clone https://github.com/neurogeriatricskiel/KielMAT.git, and to cd keilmat or this tutorial will not work. It may be worth specifying it.

Good point, we now allow the data for the example to be downloaded form the online repo directly in: d79baaa419fa487ece3f0bbc3514817a07375075

I feel like the Installation section should be at the very beginning of the home page. Right now the user has to dig to find how to install it and that may add a small obstacle to the adoption of the software.

Agreed, we moved it up on the main page in: 3a001628f85c50405528c78cf5739f574d9c4c92

davidpagnon · 2024-07-25T09:25:07Z

It all looks good to me!

JuliusWelzel · 2024-07-25T14:30:38Z

It all looks good to me!

Amazing, thank you for your valuable comments :)

Kevin-Mattheus-Moerman · 2024-08-06T10:08:22Z

@aaa34169 I hope you are doing well. Could you provide an update on where things stand? If you need more time let us know. Thanks again for your help!

aaa34169 · 2024-08-07T06:24:51Z

yes, i recovered from my two broken arms :-) . I think i can do the review by the end of the week.

Kevin-Mattheus-Moerman · 2024-08-07T09:45:04Z

@aaa34169 good to hear you recovered. Sounds like quite the trauma you went through. Thanks for still being willing to help, greatly appreciated! Looking forward to your contribution!

aaa34169 · 2024-08-08T13:11:59Z

here is my review of NGMT: NeuroGeriatric Motion Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities

General

NGMT is implemented in Python (>=3.10) and is available under the Non-Profit Open Software License version 3.0. It can be installed from PyPI or from source on GitHub.

The documentation includes comprehensive installation instructions, a conceptual framework, and tutorial notebooks.

The code utilizes downloadable data from sources such as the Mobilised and OpenNeuro projects. However, it is important to note that these downloads may encounter SSL errors when accessed from a secure network, such as that of a hospital.

Functionality

The library is easily installable with Python 3.10. The local installation using the command

pip install -e .

works flawlessly.

The modules serve well-defined purposes.

The library employs data from projects such as Mobilised or OpenNeuro. However, when accessed on a secure network, an "SSLCertVerificationError" exception may be returned. It would be beneficial to mention this potential error and ideally provide information on how to resolve or circumvent it.
The library is intended for users such as rehabilitation center engineers or academic researchers who may want to use it on institutional workstations. It's important to prevent any potential reluctance from these users.

Regarding the data, I have also noted that the file "exAccelDataMobilise.csv" does not allow the example modules_03_pam to run successfully.

Documentation

The entirety of the library is documented and accessible .

To address common errors, I would recommend that the authors create a "Common Issues" or "Frequently Asked Questions" section.

In general, the documentation is intuitive and provides both high-level and low-level information. However, I find that the organization could be improved, particularly with a focus on the concept of DataClass and its usage.

First, I suggest that the horizontal menu place DataClass before modules. Additionally, on the Home page, it is pertinent to describe the "KielMATRecording" object thoroughly, accompanied specifically by an explanation demonstrating how to construct a KielMATRecording instance from the user’s own data, rather than from the Mobilised project dataset.

Moreover, on the Home page, the link https://neurogeriatricskiel.github.io/KielMAT/examples/00_tutorial_basics/ leads to a page with display errors.

In the Examples section, I find the title "Tutorial basics" to be somewhat misleading, as the content of this page explains how to load a dataset and does not explore the modules. I would propose the following organization for the examples:

Construct Your DataClass
- Load data into KielMAT
- Load datasets
- Events in DataClass
Run Modules
- Gait sequence
- Initial contact detection

This reorganization would better reflect the content and provide clearer guidance for users.

Paper
The accompanying paper is very explicit, with numerous references that allow for further exploration in the field of actimetric evaluation. Here, even if i am not an expert of this domain, I use the term "actimetric" and wonder if this term should be integrated into the title to better delineate the library's scope. Indeed, the use of "Motion Data" is quite general and does not necessarily imply the use of IMUs in a mobility assessment context.

My major comment concerns the term "performance" as cited by the authors: "...a new dimension of measuring daily function, that is performance." Performance is implicitly related to the International Classification of Functioning, Disability and Health (ICF). I believe the authors should explicitly reference the ICF in the manuscript.

I also find no information in the "state of need" section regarding the four modules integrated into the library.

Minor Comments

Provide a reference to the Mobilise-D consortium.
Add The MathWorks, Inc. (2022) to the Matlab references.
Define FAIR.

Kevin-Mattheus-Moerman · 2024-08-09T06:48:44Z

@aaa34169 thanks for this detailed review!

JuliusWelzel · 2024-09-16T09:26:05Z

@Kevin-Mattheus-Moerman Thanks, we will address them ASAP!

JuliusWelzel · 2024-09-16T11:28:12Z

Double check authors and affiliations (including ORCIDs)

All correct

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.

We made the release 0.0.5 for the review of JOSS (also see PR102)

Archive the release on Zenodo/figshare/etc and post the DOI here.

Sourcecode has been archived on OSF with the following DOI: 10.17605/OSF.IO/8M2SP

Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

They match

Make sure that the license listed for the archive is the same as the software license.

It is the same LICENSE file

Let us know if there is anything we can help with :)

Kevin-Mattheus-Moerman · 2024-09-16T12:08:32Z

@editorialbot set version to v0.0.5

editorialbot · 2024-09-16T12:08:34Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman · 2024-09-16T12:08:49Z

@editorialbot set v0.0.5 as version

editorialbot · 2024-09-16T12:08:51Z

Done! version is now v0.0.5

Kevin-Mattheus-Moerman · 2024-09-16T12:09:42Z

@editorialbot set 10.17605/OSF.IO/8M2SP as archive

editorialbot · 2024-09-16T12:09:45Z

Done! archive is now 10.17605/OSF.IO/8M2SP

Kevin-Mattheus-Moerman · 2024-09-24T09:03:42Z

@JuliusWelzel sorry for the delay. I am just checking with some colleagues about the OSF archive. We usually handle ZENODO archives mostly, so I am just checking we are all happy with the OSF link. I'd say it should be fine but it doesn't render the things we usually look for in the same way.

JuliusWelzel · 2024-09-24T18:56:44Z

Hi @Kevin-Mattheus-Moerman,

no worries. If you need pointers where to find specific details, I am glad to help.

Best
Julius

Kevin-Mattheus-Moerman · 2024-09-25T17:02:19Z

@JuliusWelzel The OSF link can be acceptable. But can you ensure all authors are listed, trust the license matches your software license and that the version tag is mentioned? You may need to use the description field to mention the version tag.

JuliusWelzel · 2024-09-27T15:26:35Z

Hi @Kevin-Mattheus-Moerman, thanks for your feedback on the OSF archive.

The authors are listed in the projects wiki under authors at the end of the document. The wiki also references the version number. The version number also can be found in the projects metadata under description. The licence file is the same as on GH. I hope that resolves all issues.

JuliusWelzel · 2024-10-02T11:02:42Z

@Kevin-Mattheus-Moerman If there is anything else we can help move it over the finish line, please let us know. :)

Kevin-Mattheus-Moerman · 2024-10-02T11:21:55Z

@JuliusWelzel thanks for the judge. No I think we are all set. I'll try to wrap this up now.

Kevin-Mattheus-Moerman · 2024-10-02T11:22:04Z

@editorialbot recommend-accept

editorialbot · 2024-10-02T11:22:06Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-10-02T11:22:33Z

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

✅ OK DOIs

- 10.1038/s41746-023-00775-1 is OK
- 10.3390/brainsci9020034 is OK
- 10.1016/j.medengphy.2020.11.005 is OK
- 10.21105/joss.01778 is OK
- 10.1016/S1474-4422(20)30033-8 is OK
- 10.1038/sdata.2016.44 is OK
- 10.3233/JPD-181498 is OK
- 10.1038/s41597-024-03559-8 is OK
- 10.1038/s41467-020-17807-z is OK
- 10.1109/OJEMB.2024.3356791 is OK
- 10.1002/mds.28377 is OK
- 10.1371/journal.pone.0069627 is OK
- 10.1136/bmjopen-2021-050785 is OK
- 10.1186/s12984-023-01198-5 is OK
- 10.1186/s12984-019-0494-z is OK
- 10.1109/EMBC44109.2020.9176281 is OK
- 10.3389/fneur.2017.00135 is OK
- 10.3389/fneur.2018.00652 is OK
- 10.1080/0963828031000137063 is OK
- 10.1371/journal.pone.0061691 is OK
- 10.1016/S1474-4422(19)30397-7 is OK
- 10.1038/sdata.2016.18 is OK
- 10.5281/zenodo.7903963 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: International classification of functioning, disab...
- No DOI given, and none found for title: Estimate Gait Quality Composite
- No DOI given, and none found for title: mobile-gaitlab
- No DOI given, and none found for title: Mobilise-D consortium
- No DOI given, and none found for title: Mobilise-D Technical Validation Study Recommended ...
- No DOI given, and none found for title: MATLAB version: 9.13.0 (R2022b)

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-02T11:23:34Z

👋 @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#5952, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-10-02T11:26:55Z

Kevin-Mattheus-Moerman · 2024-10-02T11:27:13Z

@editorialbot accept

editorialbot · 2024-10-02T11:27:15Z

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

editorialbot · 2024-10-02T11:34:41Z

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: Abedinifar
  given-names: Masoud
  orcid: "https://orcid.org/0000-0002-4050-9835"
- family-names: Welzel
  given-names: Julius
  orcid: "https://orcid.org/0000-0001-8958-0934"
- family-names: Hansen
  given-names: Clint
  orcid: "https://orcid.org/0000-0003-4813-3868"
- family-names: Maetzler
  given-names: Walter
  orcid: "https://orcid.org/0000-0002-5945-4694"
- family-names: Romijnders
  given-names: Robbin
  orcid: "https://orcid.org/0000-0002-2507-0924"
contact:
- family-names: Romijnders
  given-names: Robbin
  orcid: "https://orcid.org/0000-0002-2507-0924"
doi: 10.17605/OSF.IO/8M2SP
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Abedinifar
    given-names: Masoud
    orcid: "https://orcid.org/0000-0002-4050-9835"
  - family-names: Welzel
    given-names: Julius
    orcid: "https://orcid.org/0000-0001-8958-0934"
  - family-names: Hansen
    given-names: Clint
    orcid: "https://orcid.org/0000-0003-4813-3868"
  - family-names: Maetzler
    given-names: Walter
    orcid: "https://orcid.org/0000-0002-5945-4694"
  - family-names: Romijnders
    given-names: Robbin
    orcid: "https://orcid.org/0000-0002-2507-0924"
  date-published: 2024-10-02
  doi: 10.21105/joss.06842
  issn: 2475-9066
  issue: 102
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6842
  title: "KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python
    Toolbox for Analyzing Neurological Motion Data from Various
    Recording Modalities"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06842"
  volume: 9
title: "KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python
  Toolbox for Analyzing Neurological Motion Data from Various Recording
  Modalities"

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.

editorialbot · 2024-10-02T11:34:46Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-10-02T11:34:47Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06842 joss-papers#5953
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06842
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-10-20T11:40:15Z

@JuliusWelzel once again congratulations on this publication!

I'd like to send a special thank you to the reviewers: @aaa34169, @davidpagnon !!

editorialbot · 2024-10-20T11:40:17Z

🎉🎉🎉 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.06842/status.svg)](https://doi.org/10.21105/joss.06842)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06842">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06842/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06842/status.svg
   :target: https://doi.org/10.21105/joss.06842

This is how it will look in your documentation:

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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editorialbot added review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 5, 2024

editorialbot assigned Kevin-Mattheus-Moerman Jun 5, 2024

editorialbot mentioned this issue Jun 5, 2024

[PRE REVIEW]: NGMT: NeuroGeriatric Motion Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities #6627

Closed

JuliusWelzel mentioned this issue Jul 19, 2024

Merge changes for JOSS review into main neurogeriatricskiel/KielMAT#102

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 2, 2024

editorialbot added accepted published Papers published in JOSS labels Oct 2, 2024

Kevin-Mattheus-Moerman closed this as completed Oct 20, 2024

[REVIEW]: KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities #6842

[REVIEW]: KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities #6842

Comments

editorialbot commented Jun 5, 2024 • edited Loading

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Kevin-Mattheus-Moerman commented Jun 5, 2024

aaa34169 commented Jun 5, 2024 • edited Loading

Review checklist for @aaa34169

Conflict of interest

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Software paper

davidpagnon commented Jun 5, 2024 • edited Loading

Review checklist for @davidpagnon

Conflict of interest

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General checks

Functionality

Documentation

Software paper

JuliusWelzel commented Jun 12, 2024

davidpagnon commented Jun 12, 2024

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General checks

Functionality

Documentation

Software paper

Kevin-Mattheus-Moerman commented Jul 16, 2024

Kevin-Mattheus-Moerman commented Jul 16, 2024

JuliusWelzel commented Jul 23, 2024

Software paper

JuliusWelzel commented Jul 23, 2024

davidpagnon commented Jul 24, 2024

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Checks on repository

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