[REVIEW]: BCImat: a Matlab-based framework for Intracortical Brain-Computer Interfaces and their simulation with an artificial spiking neural network

[whedon]

Submitting author: @eferrea (Enrico Ferrea)
Repository: https://github.com/eferrea/BCI-Master
Branch with paper.md (empty if default branch):
Version: v.1.0.0
Editor: @oliviaguest
Reviewers: @mstimberg, @puolival
Archive: 10.5281/zenodo.6759182

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Review checklist for @mstimberg

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Conflict of interest

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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?
• Contribution and authorship: Has the submitting author (@eferrea) 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

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?
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• 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?

Review checklist for @puolival

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@eferrea) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mstimberg, @puolival it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1175

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (332.1 files/s, 36526.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          16            371            342           1071
C++                              4            216            121            488
XML                              3              0              0            176
TeX                              1             13              0            173
Markdown                         2             53              0             95
C/C++ Header                     1              9             10             20
YAML                             1              1              4             18
DOS Batch                        1              0              0              9
-------------------------------------------------------------------------------
SUM:                            29            663            477           2050
-------------------------------------------------------------------------------


Statistical information for the repository '72453a089fb461b9e3bf5986' was
gathered on 2021/11/29.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
nerofumo82                      10           918             54          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
nerofumo82                  864           94.1          0.1               15.39

[whedon]

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

OK DOIs

- 10.1126/science.aaa5417 is OK
- 10.1016/S0140-6736(17)30601-3 is OK
- 10.1016/S0140-6736(12)61816-9 is OK
- 10.1038/nn.3265 is OK
- 10.1038/nature11076 is OK
- 10.1073/pnas.0808113105 is OK
- 10.1038/nature10845 is OK
- 10.1038/nature13665 is OK
- 10.1016/j.neuron.2014.08.038 is OK

MISSING DOIs

- 10.1101/2021.02.16.431440 may be a valid DOI for title: Statistical determinants of visuomotor adaptation in a virtual reality three-dimensional environment
- 10.1523/jneurosci.02-11-01527.1982 may be a valid DOI for title: On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex
- 10.1109/thms.2020.2968411 may be a valid DOI for title: Brain–computer interface software: A review and discussion

INVALID DOIs

- None

[whedon]

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

[eferrea]

Hi @oliviaguest, I am here in the new page. Thanks @puolival for reviewing the paper.

[oliviaguest]

Hi all! 👋 Thank you so much @mstimberg, @puolival for accepting to review this. Please read the instructions above. Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them. 🌸

For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[mstimberg]

Review @mstimberg

As mentioned earlier, I am neither a MATLAB-expert, nor do I know much about BCI – so please read my review with this in mind.

I was able to install and compile all dependencies, as well the TrackM software and the mex files for the Matlab GUI presented in this paper (under Ubuntu Linux 20.04). I was able to run both pieces of software and test its basic functionality, and did not encounter any major problem. I do not have access to Blackrock neural interface, so I obviously could not test the package in a real BCI application.
I have opened a number of issues on the main repository (eferrea/BCI-Master#2, eferrea/BCI-Master#3, eferrea/BCI-Master#4, eferrea/BCI-Master#5, eferrea/BCI-Master#6), with suggestions for improvements to documentation, usability and testing. I fear that in its current state, the package will be difficult to use for new users, and some parts of it look like code that is rather aimed for internal than for general use (e.g. hardcoded private IP addresses). Everything looks to be fixable, though, I did not encounter any major blocking issues.
Regarding the Software paper, I do not have much to criticize. As friendly whedon noted earlier, three papers are missing DOIs and one of them is also missing the year (leading to a "n.d." in the citation).

[eferrea]

Hi @mstimberg, many thanks for the constructive review. I will address all of your concerns as soon as possible.

[whedon]

👋 @mstimberg, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @puolival, please update us on how your review is going (this is an automated reminder).

[eferrea]

Hi @mstimberg and hi @oliviaguest , I implemented all suggestions to improve documentation and code usability. You can check my answers directly on the open issues. I also updated the missing DOI and the missing year. Thanks.

[mstimberg]

@eferrea thanks for the substantial changes, all of my concerns have been addressed (except for the few minor issues I commented in eferrea/BCI-Master#2, eferrea/BCI-Master#3, eferrea/BCI-Master#4). Before the formal acceptance from my side, there's only one more thing that I unfortunately forgot to mention earlier: it would be good to make an official release on github (or just a tag) and give the software a version number. This will make it much clearer which version of the code was described by the JOSS paper, and will allow you to easily communicate changes with respect to this version in the future. But it might make sense to wait with this until the end of the reviewing process, of course.

[mstimberg]

@whedon generate pdf

[whedon]

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

[eferrea]

@mstimberg , thanks for your comments. I answered your questions (eferrea/BCI-Master#2, eferrea/BCI-Master#3, eferrea/BCI-Master#4).
In addition, I have to mention that I just added in the paper.md a small paragraph of our funding sources.
As you suggested, I will then wait until the end of the review process to make an official release.

[mstimberg]

@whedon generate pdf

[whedon]

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

[oliviaguest]

@eferrea is the version right?

[editorialbot]

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

[oliviaguest]

Also, please review and merge eferrea/BCI-Master#7, @eferrea — just some typos.

[mstimberg]

I certainly don't intend to complicate things and to draw out the publishing process further, but I wonder: other journals I've reviewed for that mention the reviewer names in the paper state something along the lines of "reviewers endorsed the manuscript in its current form", although I'm not sure if that's the case for JOSS? I'm saying this since I'm not 100% sure that @puolival would subscribe to that statement and might not be happy to be listed on the paper.

[eferrea]

Hi @oliviaguest, thanks for your edits. I merged them and then I corrected affiliation number 4 since it has recently changed. I also agree with @mstimberg that @puolival should not be listed as reviewer of the paper.

[oliviaguest]

@eferrea sorry, but why? Didn't their contribution get used? This is a strange request unless you think their labour was worth nothing to you.

[eferrea]

@oliviaguest for me it is completely fine if the JOSS regulations are fine with that. Thanks.

[mstimberg]

@oliviaguest (sorry, forgot to tag you earlier): to avoid misunderstandings, @eferrea's comment was related to my earlier comment:

I certainly don't intend to complicate things and to draw out the publishing process further, but I wonder: other journals I've reviewed for that mention the reviewer names in the paper state something along the lines of "reviewers endorsed the manuscript in its current form", although I'm not sure if that's the case for JOSS? I'm saying this since I'm not 100% sure that @puolival would subscribe to that statement and might not be happy to be listed on the paper.

I am completely convinced that @puolival deserves to be listed to be a reviewer, I am just not 100% sure that they want to be listed as a reviewer.

[eferrea]

@oliviaguest , sorry I also did not notice you were not tagged.

[oliviaguest]

I appreciate you raising this, but I don't appreciate being told, even if indirectly, how to manage this. I'll happily give @puolival time to reply, but I'm wondering if maybe an @openjournals/joss-eics should take over completely from here. I'm happy to back off, especially if my job is almost completely done anyway.

[danielskatz]

Given that the entire review history is public, I don't think that we need additional statements from reviewers. This hasn't been the practice of JOSS in the past.

[mstimberg]

I appreciate you raising this, but I don't appreciate being told, even if indirectly, how to manage this.

I hear what you are saying, apologies for that – I'll try to be more careful in the future.

[oliviaguest]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1126/science.aaa5417 is OK
- 10.1016/S0140-6736(17)30601-3 is OK
- 10.1016/S0140-6736(12)61816-9 is OK
- 10.1038/s41598-022-13866-y is OK
- 10.1523/JNEUROSCI.02-11-01527.1982 is OK
- 10.1038/nn.3265 is OK
- 10.1038/nature11076 is OK
- 10.1073/pnas.0808113105 is OK
- 10.1038/nature10845 is OK
- 10.1038/nature13665 is OK
- 10.1016/j.neuron.2014.08.038 is OK
- 10.1109/THMS.2020.2968411 is OK
- 10.1145/505008.505019 is OK
- 10.1162/089976606774841585 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3336, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@eferrea - please update the zenodo metadata (title, authors) to match the paper.

[eferrea]

@danielskatz and @oliviaguest I updated the author list and title.

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03956 joss-papers#3346
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03956
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[eferrea]

Great! @danielskatz @oliviaguest @mstimberg @puolival , many thanks for your contribution in this reviewing process.

[danielskatz]

The DOI doesn't yet resolve for me, so I'll keep this open until it does.

[danielskatz]

Congratulations to @eferrea (Enrico Ferrea) and co-authors!!

And thanks to @mstimberg and @puolival for reviewing, and @oliviaguest for editing!
We couldn't do this without you

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.03956/status.svg)](https://doi.org/10.21105/joss.03956)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03956/status.svg" alt="DOI badge" >
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reStructuredText:
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   :target: https://doi.org/10.21105/joss.03956

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