Joss-reviews: [REVIEW]: BioSigKit: A Matlab Toolbox and Interface for Analysis of BioSignals

Created on 11 Apr 2018 · 81Comments · Source: openjournals/joss-reviews

Submitting author: @hooman650 (Hooman Sedghamiz)
Repository: https://github.com/hooman650/BioSigKit
Version: V1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @marianux, @fernandoandreotti, @bzenger
Archive: 10.5281/zenodo.1464968

Status

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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) 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

REVIEWER 1

@marianux, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @marianux

Conflict of interest

[ ] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Version: Does the release version given match the GitHub release (V1.0.0)?
[ ] Authorship: Has the submitting author (@hooman650) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

[ ] Authors: Does the paper.md file include a list of authors with their affiliations?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

REVIEWER 2

@fernandoandreotti, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @fernandoandreotti

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Version: Does the release version given match the GitHub release (V1.0.0)?
[x] Authorship: Has the submitting author (@hooman650) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] 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?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] 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 function 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

REVIEWER 3

@Kevin-Mattheus-Moerman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @Kevin-Mattheus-Moerman

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (V1.0.0)?
[x] Authorship: Has the submitting author (@hooman650) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

REVIEWER 4

@bzenger, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @bzenger

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (V1.0.0)?
[x] Authorship: Has the submitting author (@hooman650) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

accepted published recommend-accept review

Source

whedon

Most helpful comment

@Kevin-Mattheus-Moerman I have completed the review. I am waiting for one response from the author about community involvement and users seeking support. I tested the system with data from our own laboratory experiments and the system performed as described. Documentation and statements of need were adequate.

EDIT: Review is complete

bzenger on 17 Oct 2018

👍2

All 81 comments

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @marianux it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

whedon on 11 Apr 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 11 Apr 2018

--> Check article proof :page_facing_up: <--

whedon on 11 Apr 2018

@hooman650 this is where the review takes place. @marianux thanks for agreeing to review this work. :tada:
Let me know if you have any questions. Reviewers can leave comments here and are also encouraged to open issues on the project repository and refer to them here. Thanks.

Kevin-Mattheus-Moerman on 11 Apr 2018

@cMadan @germangh let me know if you are able to assist in the review of this submission. Thanks! :rabbit:

Kevin-Mattheus-Moerman on 11 Apr 2018

@marianux you asked about a deadline. Typical review times range from days or weeks to months for larger projects with many issues. There is no official deadline but we obviously encourage a smooth and reasonably fast review process.

Kevin-Mattheus-Moerman on 11 Apr 2018

@Kevin-Mattheus-Moerman I have been away from the field for a few years already so I am not a good reviewer for this work anymore. Hope you find someone else!

germangh on 11 Apr 2018

@germangh ok thanks for your reply

Kevin-Mattheus-Moerman on 11 Apr 2018

@Kevin-Mattheus-Moerman, I don't think I'll have time to review this submission, but it definitely looks like an asset to the field! :)

cMadan on 12 Apr 2018

@whedon generate pdf

Kevin-Mattheus-Moerman on 12 Apr 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 12 Apr 2018

Okay no worries @cMadan

Kevin-Mattheus-Moerman on 12 Apr 2018

--> Check article proof :page_facing_up: <--

whedon on 12 Apr 2018

@hooman650 would you be able to suggest any more reviewers from your field?

Kevin-Mattheus-Moerman on 12 Apr 2018

@Kevin-Mattheus-Moerman, within the list of JOSS reviewers, @jordigh , @nicoguaro, @sealhuang @mosteo, @nirum ; and out of that list I can think of @fernandoandreotti , also @marianux has done his PhD on ECG analysis and has also made a very nice toolbox so he might be able to suggest someone else from his circle?

hooman650 on 12 Apr 2018

Interesting platform you have here. I have just applied to become a reviewer for JOSS and could do it.

fernandoandreotti on 13 Apr 2018

@fernandoandreotti thank you!

hooman650 on 13 Apr 2018

@whedon add @fernandoandreotti as reviewer

Kevin-Mattheus-Moerman on 13 Apr 2018

OK, @fernandoandreotti is now a reviewer

whedon on 13 Apr 2018

Thanks @marianux @fernandoandreotti for agreeing to review this submission.

Review is centered largely on the software and the below paper. You use the above tick boxes to guide the review process. You can comment and provide feedback in this review issue. You are also encouraged to open issues on the project repository and link to them here.

Here are the reviewer guidelines. Let me know if you have any questions.

Let the reviewing begin! :rocket: :robot:

--> Check article proof :page_facing_up: <--

Kevin-Mattheus-Moerman on 13 Apr 2018

Hi @marianux and @fernandoandreotti , I wanted to thank you for your time and agreeing to review this submission and kindly follow up and see whether there is something I could do in the meantime to improve the submission....
Thanks again,
Hooman

hooman650 on 27 Apr 2018

Dear Hooman,

first of all great work implementing all these 6 QRS detectors in an object oriented way and including a GUI. The examples ran smoothly.

My concern regarding the toolbox is the fact that despite as it being advertised a toolbox for biosignals, the only implemented routines are QRS detectors. Rather than creating a new toolbox from scratch, I wonder why not add those to other toolboxes such as WFDB or the ecg-kit?

Best regards,

Fernando

fernandoandreotti on 1 May 2018

Thank you @fernandoandreotti and @marianux for taking the time and going over the BioSigKit.

Your comments are very accurate. I understand that currently only documented functions in BioKitSig are offering QRS detectors with the exception of the last algorithm which is a general peak detector. And this might seem like reinventing the wheel beside that a few algorithms are new.

Please note that the goal of BioKitSig is to be a general biosignal processing toolbox. There are at least 5 other subroutines for processing Accelerometer signals, Fetal ECG extraction with projection methods, nonlinear projection filtering for ECG processing and ECG derived respiration computation and activity detection in EMG that are implemented but since they still do not have documentation are not included in the current version. If it is okay I will update the BioSigKit repository today adding these subroutines with documentation that would make this submission distinct from WFDB and ecg-kit.

Warm regards,
Hooman

hooman650 on 2 May 2018

@marianux and @fernandoandreotti how are you getting on with the review process? Let me know if you have any questions.

Kevin-Mattheus-Moerman on 21 May 2018

Dear @marianux and @fernandoandreotti , in regards to your comments and our last correspondence, I have already added 10 subroutines to BioSigKit where these are detailed in the homepage repository of the BioSigKit. These subroutines help perform several different tasks such as: ECG-derived respiration, alarm detection in EMG signals and audio signals, Foetal ecg extraction from maternal ECG, artifact removal from ECG recordings and many more. Please also refer to the cheat-sheet.pdf in the repository for further details and the codemap on the bottom of the repository.

Thank you
Hooman

hooman650 on 21 May 2018

@fernandoandreotti can you review @hooman650 's reply to the issues you raised?

Kevin-Mattheus-Moerman on 31 May 2018

@marianux can you given an indication as to when you are able to work on this review? thanks :rocket:

Kevin-Mattheus-Moerman on 31 May 2018

Hi @fernandoandreotti and @marianux , hope the day is treating you well! I know you are very busy and I do not mean to rush you. I have been receiving a couple of emails from some users that were asking me how they can cite the work... the subroutines of the Biosigkit are pretty popular, for example the Pan-tompkin subroutine has been downloaded more than 13,000 times (https://www.mathworks.com/matlabcentral/fileexchange/45840-complete-pan-tompkins-implementation-ecg-qrs-detector) ... or this one (https://www.mathworks.com/matlabcentral/fileexchange/45404-ecg-q-r-s-wave-online-detector ) that has more than 6000 downloads... These are indications that the tool can be very beneficial for different aspects of research...there are many more subroutines that I have included in the tool that can be helpful for the research community... I really appreciate your feedback on this so we can make it available for the research community...
Cheers
Hooman

hooman650 on 6 Jun 2018

Dear @hooman650, thank you for including more routines to the BioSigKit. Despite me believing that routines are relevant (as the download numbers say), I still believe that the BioSigKit as a standalone toolbox is lacking. This because rather than tackling a single problem, it now presents a bundle of unrelated signal processing routines. For this reason, I would strongly recommend that they are contributed to other toolboxes. For instance the WFDB-App and EDR, QRS detectors and the FECGSYN already has a handful fetal ECG extraction algorithms. I believe contributing to other toolboxes would make these algorithms more visible and guarantee their long term support. Nonetheless, the final decision is yours.
I have reviewed the form above and checked what I believe is present in the toolbox. I think that showing the performance of the proposed algorithms, as well as clarifying the general scope of the toolbox is still necessary.
Best regards, Fernando

fernandoandreotti on 6 Jun 2018

@fernandoandreotti thank you for your feedback and taking the time to review this...I would be happy to also contribute the subroutines to other tools such as WFDB-App and FECGSYN, the aim of BioSigKit is not to introduce new algorithms that have not been exactly examined but rather gather the popular ones that have been published separately under one roof (BioSigKit)... otherwise it should have been submitted to a more specialized bioemdical signal processing journal (e.g. IEEE transactions) and not JOSS. As I already mentioned a few links in my previous message, a lot of subroutines are already being extensively employed in research and downloaded (e.g. pan-tompkins implementation). I would like to thank you again for taking the time and reviewing this...

hooman650 on 25 Jun 2018

Dear @Kevin-Mattheus-Moerman could you please provide a path forward in regards to this paper? :) It has been almost 3 month that this thread has been opened .... thanks in advance

hooman650 on 28 Jun 2018

@hooman650 apologies for the delays encountered with this submission. I'm going to ask for help with this submission from a fellow editor @cMadan as I am in the middle of moving from the USA to Europe with my family. I'll provide an update here shortly to give you some guidance on next steps.

Kevin-Mattheus-Moerman on 24 Jul 2018

@hooman650 as you are aware you have received comments from the reviewers in this issue and also here. Please try to respond to the reviewers as best you can.

@fernandoandreotti and @marianux, I aimed to summarize your points below. Please correct me and/or statements as you see fit.

:memo: Comments by @fernandoandreotti
[ ] "I think that showing the performance of the proposed algorithms, as well as clarifying the general scope of the toolbox is still necessary."
:memo: Comments by @marianux mentions:
(For some of these you've responded here, however have the changes in relation to describing the difference with respect to other packages, and why your toolbox should be an independent package been added to the paper/documentation?)
[ ] The main concern would be that there are several toolboxes that pursues the same goal. I think that the author would emphasize which are the differences with other existing approaches, or which advantages would this toolbox have.
[ ] Work needed on documentation, installation instructions, and API documentation
:memo: Comments by me
[ ] Both reviewers mention something like "Maybe you should reconsider not reinventing the wheel, and collaborating with other open-source projects." To address these types of statements I feel you can work on pointing out the difference/overlap in the nature of your toolbox and the other works. Also clearly state the value of your collected/novel works. For JOSS it is not a requirement that the work is 100% novel/different. Novel collections of tools and novel implementations in different languages can be acceptable also. So please address the reviewers comments as best you can in the paper and documentation.

Kevin-Mattheus-Moerman on 24 Jul 2018

@cMadan would you be able to assist with the editing of this one? I will be extremely busy for the next two weeks and it would be great to help move the review of this submission along.

Kevin-Mattheus-Moerman on 24 Jul 2018

@Kevin-Mattheus-Moerman, sure I can assist with editing this submission

cMadan on 30 Jul 2018

@hooman650 can you provide an update as to how you are getting on? Are you able to formulate a reply to my summary of the reviewers comments?

Kevin-Mattheus-Moerman on 17 Aug 2018

@Kevin-Mattheus-Moerman I am sorry for the tardy reply, I am still working on your previous comments and soon (latest Monday) will update the repository :) thank you again

hooman650 on 17 Aug 2018

@Kevin-Mattheus-Moerman , I have update the paper.bib file and explained the differences between the BioSigKit toolbox and other toolboxes such as ecg-kit. The respository is updated as detailed below:

CheatSheet.pdf added that details all subroutines of the toolbox
Demo.m that runs a demo and example of all subroutines
paper.bib is updated with the details of the toolkit.
A Codemap is used in the repository that details all the subroutines for future collaboration.
The readme.md is also updated that details the use of the toolbox.

Hope that I have addressed the comments properly.

Have a good weekend,
Hooman

hooman650 on 20 Aug 2018

@fernandoandreotti @marianux could you please weigh in on @hooman650 's revisions? Thanks.

Kevin-Mattheus-Moerman on 20 Aug 2018

@Kevin-Mattheus-Moerman with your permission, I ask whedon to rebuild the paper...

hooman650 on 21 Aug 2018

@whedon commands

hooman650 on 21 Aug 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

whedon on 21 Aug 2018

@whedon generate pdf

hooman650 on 21 Aug 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 21 Aug 2018

--> Check article proof :page_facing_up: <--

whedon on 21 Aug 2018

@fernandoandreotti @marianux thanks again for your initial review. Could you please provide feedback on how the author has now dealt with your suggestions?

Kevin-Mattheus-Moerman on 27 Aug 2018

Hi all, my suggestion was to collaborate with another open-source project
that already did the same. IMHO the work was important, but not enough
different from others already published.

Best,
M.

El lun., 27 de ago. de 2018 a la(s) 04:23, Kevin Mattheus Moerman (
[email protected]) escribió:

@fernandoandreotti https://github.com/fernandoandreotti @marianux
https://github.com/marianux thanks again for your initial review. Could
you please provide feedback on how the author has now dealt with your
suggestions?

—
You are receiving this because you were mentioned.
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https://github.com/openjournals/joss-reviews/issues/671#issuecomment-416138693,
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marianux on 27 Aug 2018

Thank you, just felt like to leave a short note in regards to the research importance of BioSigKit. Please see below 35 "peer-reviewed" citations in regards to only "three" subroutines of BioSigKit:

I have created BioSigKit based on numerous requests from fellow researchers that were simply asking me to put all of my highly cited work together in a single toolbox. Since many subroutines such as for instance "Activity detection with Hilbert Transform"(which happens to be the pick of the week by mathworks), "Activity detection based on processing 3 channel Accelerometer processing" and many more cannot simply be contributed to other existing projects, I hope that you agree that BioSigKit can be a helpful general purpose signal processing toolbox like OSET since it offers many novel and useful implementation of signal processing algorithms.

Thank you again,
Best
Hooman

hooman650 on 27 Aug 2018

👍1

@fernandoandreotti thanks again for your initial review. Could you please provide feedback on how the author has now dealt with your suggestions?

Kevin-Mattheus-Moerman on 10 Sep 2018

@marianux thanks for your reply and for your review work. I understand your concern in relation to this package being similar to previously published works. After considering your feedback I feel this work is sufficiently original and independent enough to warrant being a potential publication in JOSS. Given this, would you be able to provide feedback (and tick boxes at the top of this issue where appropriate) in relation to the other aspects of this work? Thanks.

Kevin-Mattheus-Moerman on 10 Sep 2018

👍1

I agree with @marianux view.

fernandoandreotti on 13 Sep 2018

@hooman650 I've just posted an issue on your repository. Can you have a look?

Please also work on community guidelines (see https://github.com/hooman650/BioSigKit/issues/4)