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[PRE REVIEW]: NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data #7465

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editorialbot opened this issue Nov 12, 2024 · 42 comments
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[PRE REVIEW]: NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data #7465

editorialbot opened this issue Nov 12, 2024 · 42 comments
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@ferchaure @Kevin-Mattheus-Moerman @kinleyid @TheCedarPrince
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pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Nov 12, 2024 •
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Submitting author: @AdamWysokinski (Adam Wysokiński)
Repository: https://github.com/JuliaHealth/NeuroAnalyzer.jl
Branch with paper.md (empty if default branch):
Version: v0.24.11
Editor: @Kevin-Mattheus-Moerman
Reviewers: @kinleyid, @ferchaure, @TheCedarPrince
Managing EiC: Arfon Smith

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cefb2c86708619ddd786b49ce47c98df"><img src="https://joss.theoj.org/papers/cefb2c86708619ddd786b49ce47c98df/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cefb2c86708619ddd786b49ce47c98df/status.svg)](https://joss.theoj.org/papers/cefb2c86708619ddd786b49ce47c98df)

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Thanks for submitting your paper to JOSS @AdamWysokinski. Currently, there isn't a JOSS editor assigned to your paper.

@AdamWysokinski if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Nov 12, 2024
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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.39 s (759.7 files/s, 162461.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          277          11873          12415          36385
Markdown                         4            108              0            831
CSV                              1              0              0            307
GLSL                             1              0              0            167
TOML                             2              5              0            143
TeX                              1              6              0             93
Bourne Shell                     2              1              0             88
Arduino Sketch                   2             20             24             87
YAML                             2              6              4             68
Dockerfile                       1              9              2             15
-------------------------------------------------------------------------------
SUM:                           293          12028          12445          38184
-------------------------------------------------------------------------------

Commit count by author:

  1433	Adam Wysokiński
   316	Adam Wysokinski
    34	Adam
    27	CI Builder
    10	michalrzak
     1	Jacob S. Zelko

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

✅ OK DOIs

- 10.1137/141000671 is OK
- 10.1145/3276490 is OK
- 10.1155/2011/130714 is OK
- 10.1155/2011/156869 is OK
- 10.3389/fnins.2013.00267 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Meet Julia: The Future of Data Science

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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Paper file info:

📄 Wordcount for paper.md is 1334

✅ The paper includes a Statement of need section

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License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

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arfon commented Nov 12, 2024

@AdamWysokinski - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

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

@arfon arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Nov 12, 2024
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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Five most similar historical JOSS papers:

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7374

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.7157

Pycrostates: a Python library to study EEG microstates
Submitting author: @vferat
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @AJQuinn, @vahid-sb, @tuliofalmeida, @anshu-97
Similarity score: 0.7018

pyomeca: An Open-Source Framework for Biomechanical Analysis
Submitting author: @romainmartinez
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @BKillen05, @mitkof6
Similarity score: 0.7001

PyView: A general purpose tool for analyzing calcium imaging data
Submitting author: @ajkswamy
Handling editor: @csoneson (Active)
Reviewers: @adamltyson, @Yannan-Chen
Similarity score: 0.6986

⚠️ 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.

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

@arfon Thank you for letting me know. No problem, I'm not in a hurry. Just tell me if there is anything more that I should do now, since I'm new to the JOSS reviewing process.

@Kevin-Mattheus-Moerman
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@AdamWysokinski 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:

  • 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/).

@Kevin-Mattheus-Moerman
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@editorialbot assign me as editor

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Assigned! @Kevin-Mattheus-Moerman is now the editor

@Kevin-Mattheus-Moerman
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@AdamWysokinski I'll also handle this work as editor. I'll soon start looking for reviewers. If you would like to suggest any reviewers please do so. You can mention their GitHub handles here but please leave out the @ symbol so they are not tagged. Thanks.

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 10, 2025
@AdamWysokinski
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@AdamWysokinski 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:

Dear Editor, thank you. Your are right, I have added appropriate section in the README.md file in the project repository, I do hope it now fulfill the requirements.

@AdamWysokinski
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@AdamWysokinski I'll also handle this work as editor. I'll soon start looking for reviewers. If you would like to suggest any reviewers please do so. You can mention their GitHub handles here but please leave out the @ symbol so they are not tagged. Thanks.

I would like to suggest TheCedarPrince, vladdez, ferchaure and behinger.

@Kevin-Mattheus-Moerman
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@TheCedarPrince, @vladdez, @ferchaure, @behinger, @AJQuinn, @azraq27, @rob-luke, @kinleyid, @paulmthompson, @alexmorley would you be interested in reviewing this submission for JOSS (the Journal of Open Source Software? The work is titled NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data and features the use of the Julia programming language for "importing, editing, processing, visualizing, and analyzing EEG, MEP and EDA data".

JOSS reviews take place on GitHub and focus on the software 💾 as well as a short paper 📜 . We typically aim for a 2-3 week review but we can be more flexible if needed. You can find more about our review process in our review guidelines. Here is an example of an ongoing review if you want to see what it is like: #7564.

If you are interested you can let me know by responding here.

Thanks!

@TheCedarPrince I see you are also a contributor on the project, please do confirm if you have a conflict of interest or not. Thanks.

@AdamWysokinski
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AdamWysokinski commented Jan 11, 2025 •
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There is a minor typo in line 133 (missing space) of the paper -- may I correct it now?

@Kevin-Mattheus-Moerman
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@AdamWysokinski yes, you can continuously make changes.

@kinleyid
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@Kevin-Mattheus-Moerman Yes, happy to review!

@AdamWysokinski
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Hello @AdamWysokinski, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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

@AdamWysokinski
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@editorialbot generate pdf

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Five most similar historical JOSS papers:

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7410

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.7173

Pycrostates: a Python library to study EEG microstates
Submitting author: @vferat
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @AJQuinn, @vahid-sb, @tuliofalmeida, @anshu-97
Similarity score: 0.7046

pyomeca: An Open-Source Framework for Biomechanical Analysis
Submitting author: @romainmartinez
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @BKillen05, @mitkof6
Similarity score: 0.7017

PyView: A general purpose tool for analyzing calcium imaging data
Submitting author: @ajkswamy
Handling editor: @csoneson (Active)
Reviewers: @adamltyson, @Yannan-Chen
Similarity score: 0.7006

⚠️ 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.

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

@editorialbot
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Five most similar historical JOSS papers:

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7410

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.7174

Pycrostates: a Python library to study EEG microstates
Submitting author: @vferat
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @AJQuinn, @vahid-sb, @tuliofalmeida, @anshu-97
Similarity score: 0.7050

pyomeca: An Open-Source Framework for Biomechanical Analysis
Submitting author: @romainmartinez
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @BKillen05, @mitkof6
Similarity score: 0.7011

PyView: A general purpose tool for analyzing calcium imaging data
Submitting author: @ajkswamy
Handling editor: @csoneson (Active)
Reviewers: @adamltyson, @Yannan-Chen
Similarity score: 0.7007

⚠️ 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.

@AdamWysokinski
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7408

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.7169

Pycrostates: a Python library to study EEG microstates
Submitting author: @vferat
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @AJQuinn, @vahid-sb, @tuliofalmeida, @anshu-97
Similarity score: 0.7046

pyomeca: An Open-Source Framework for Biomechanical Analysis
Submitting author: @romainmartinez
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @BKillen05, @mitkof6
Similarity score: 0.7013

PyView: A general purpose tool for analyzing calcium imaging data
Submitting author: @ajkswamy
Handling editor: @csoneson (Active)
Reviewers: @adamltyson, @Yannan-Chen
Similarity score: 0.7004

⚠️ 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.

@ferchaure
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@Kevin-Mattheus-Moerman yes, happy to help

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@editorialbot add @kinleyid as reviewer

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@kinleyid added to the reviewers list!

@Kevin-Mattheus-Moerman
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@editorialbot add @ferchaure as reviewer

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@ferchaure added to the reviewers list!

@AdamWysokinski
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@Kevin-Mattheus-Moerman Dear Editor, I think everything has been set up, should I do something to proceed?

@TheCedarPrince
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@Kevin-Mattheus-Moerman :

@TheCedarPrince I see you are also a contributor on the project, please do confirm if you have a conflict of interest or not. Thanks.

To disclose, I am the leader of the JuliaHealth organization which @AdamWysokinski is a member of. I have used NeuroAnalyzer.jl before for some of my own work which resulted in the following publication: https://www.frontiersin.org/journals/network-physiology/articles/10.3389/fnetp.2024.1478280/full . In the course of this, I contributed a small bug fix in the process of using the tool.

If that surmounts to a sufficient conflict of interest, then please let me know and I will withdraw my name as reviewer. Otherwise, happy to be a reviewer here as well. :-)

Cheers,

~ tcp 🌳

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@TheCedarPrince thanks for clarifying that. I think that does not constitute a conflict of interest so I'll add you as reviewer now.

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@editorialbot add @TheCedarPrince as reviewer

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@TheCedarPrince added to the reviewers list!

@Kevin-Mattheus-Moerman
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@AdamWysokinski apologies for the delay in getting started. I will now trigger the review to start.

@Kevin-Mattheus-Moerman
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@editorialbot start review

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OK, I've started the review over in #7734.

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