[PRE REVIEW]: AnalyZe: A MATLAB Application GUI for Visualizing and Analyzing Electrical Impedance Spectroscopy data in Biological Applications

[editorialbot]

Submitting author: @Doug-vN (Douglas van Niekerk)
Repository: https://github.com/bestgroup-Camb/AnalyZe
Branch with paper.md (empty if default branch): JOSS-Submission
Version: v5.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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Author instructions

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

@Doug-vN 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.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (113.7 files/s, 155382.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                           5           2626           1152           9477
TeX                              1             12              3            160
Markdown                         2             57              0            141
YAML                             1              1              4             18
HTML                             1              2              0             14
-------------------------------------------------------------------------------
SUM:                            10           2698           1159           9810
-------------------------------------------------------------------------------

Commit count by author:

   112	Doug-vN
     2	bestgroup-Camb

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1941

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

⚠️ An error happened when generating the pdf.

[Doug-vN]

@editorialbot commands

[editorialbot]

Hello @Doug-vN, here are the things you can ask me to do:

# List all available commands
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# 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

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@editorialbot generate preprint

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[Doug-vN]

Hello, here are my suggestions for potential reviewers:

1. Julie-Fabre
2. alberto-battistel
3. larsenkg

[Doug-vN]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[Doug-vN]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

impedance.py: A Python package for electrochemical impedance analysis
Submitting author: @mdmurbach
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Reviewers: @ma-sadeghi, @EricaEgg
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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- No DOI given, and none found for title: Electrochemical methods: fundamentals and applicat...
- No DOI given, and none found for title: Electrochemical impedance spectroscopy
- Entry without DOI or title found
- No DOI given, and none found for title: ZView® For Windows — scribner.com
- No DOI given, and none found for title: NOVA — metrohm.com
- No DOI given, and none found for title: PSTrace - PalmSens — palmsens.com
- 10.21105/joss.02349 may be a valid DOI for title: impedance. py: A Python package for electrochemica...
- No DOI given, and none found for title: ZFit
- 10.1186/2045-8118-10-5 may be a valid DOI for title: Impedance-based cell monitoring: barrier propertie...
- 10.1016/0167-2738(86)90031-7 may be a valid DOI for title: A nonlinear least squares fit procedure for analys...
- No DOI given, and none found for title: Global Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Linear systems and signals
- No DOI given, and none found for title: Electrochemical impedance spectroscopy─ a tutorial
- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

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

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• The above code report shows 9477 lines of MATLAB code. In the case of GUIs or APPs it is often the case that significant portions of the code are "auto-generated" e.g. using "MATLABs App Designer utility". Therefore, could you please clarify what portion (or what files if you can link to them) where your own contribution? Usually this is the code responsible for functional analysis only, rather than the GUI handling.
• In your paper affiliations, please spell out UK as United Kingdom.
• I recommend adding a .gitignore file to your main repository folder and to add the following lines to help git ignore MATLAB's temporary backup files (.asv files).

# Ignore MATLAB temporary files
*.asv

[Doug-vN]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "-" (NAME) [#<BibTeX::Bibliography data=[1]>, "@", #<BibTeX::Entry >, {:title=>["Electrochemical impedance spectroscopy"], :author=>["Wang, Shangshang and Zhang, Jianbo and Gharbi, Ouma{\\\"\\i}ma and Vivier, Vincent and Gao, Ming and Orazem, Mark E"], :journal=>["Nature Reviews Methods Primers"], :volume=>["1"], :number=>["1"], :pages=>["41"], :year=>["2021"], :publisher=>["Nature Publishing Group UK London"]}, ",", "doi"]

[Doug-vN]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "doi" (NAME) [#<BibTeX::Bibliography data=[8]>, "@", #<BibTeX::Entry >, {:title=>["Impedance-based cell monitoring: barrier properties and beyond"], :author=>["Benson, Kathrin and Cramer, Sandra and Galla, Hans-Joachim"], :journal=>["Fluids and Barriers of the CNS"], :volume=>["10"], :pages=>["1--11"], :year=>["2013"], :publisher=>["Springer"]}]

[Doug-vN]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s43586-021-00039-w is OK
- 10.21105/joss.02349 is OK
- 10.1186/2045-8118-10-5 is OK
- 10.1016/0167-2738(86)90031-7 is OK
- 10.1021/acsmeasuresciau.2c00070 is OK

MISSING DOIs

- No DOI given, and none found for title: Electrochemical methods: fundamentals and applicat...
- Entry without DOI or title found
- No DOI given, and none found for title: ZView® For Windows — scribner.com
- No DOI given, and none found for title: NOVA — metrohm.com
- No DOI given, and none found for title: PSTrace - PalmSens — palmsens.com
- No DOI given, and none found for title: ZFit
- No DOI given, and none found for title: Global Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Linear systems and signals

INVALID DOIs

- None

[Doug-vN]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "author" (NAME) [#<BibTeX::Bibliography data=[2]>, "@", #<BibTeX::Entry >, {:title=>["EC-Lab --- biologic.com"]}]

[Doug-vN]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s43586-021-00039-w is OK
- 10.21105/joss.02349 is OK
- 10.1186/2045-8118-10-5 is OK
- 10.1016/0167-2738(86)90031-7 is OK
- 10.1021/acsmeasuresciau.2c00070 is OK

MISSING DOIs

- No DOI given, and none found for title: Electrochemical methods: fundamentals and applicat...
- No DOI given, and none found for title: EC-Lab — biologic.com
- No DOI given, and none found for title: ZView® For Windows — scribner.com
- No DOI given, and none found for title: NOVA — metrohm.com
- No DOI given, and none found for title: PSTrace - PalmSens — palmsens.com
- No DOI given, and none found for title: ZFit
- No DOI given, and none found for title: Global Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Optimization Toolbox — uk.mathworks.com
- No DOI given, and none found for title: Linear systems and signals

INVALID DOIs

- None

[Doug-vN]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

impedance.py: A Python package for electrochemical impedance analysis
Submitting author: @mdmurbach
Handling editor: @mbobra (Active)
Reviewers: @ma-sadeghi, @EricaEgg
Similarity score: 0.7168

fuelcell: A Python package and graphical user interface for electrochemical data analysis
Submitting author: @samaygarg
Handling editor: @jgostick (Active)
Reviewers: @jlopata21, @shimpalee
Similarity score: 0.6721

Viime: Visualization and Integration of Metabolomics Experiments
Submitting author: @waxlamp
Handling editor: @lpantano (Active)
Reviewers: @joannawolthuis, @rowlandm, @jkanche
Similarity score: 0.6668

RHEOS.jl -- A Julia Package for Rheology Data Analysis
Submitting author: @akabla
Handling editor: @jedbrown (Active)
Reviewers: @adambeall, @gbruer15, @HaoZeke
Similarity score: 0.6603

OT_Analysis: a software for rich analysis of force curves when probing living cells with optical tweezers
Submitting author: @phpuech
Handling editor: @prashjha (Active)
Reviewers: @ryEllison, @florian-huber
Similarity score: 0.6593

⚠️ 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.

[Doug-vN]

Hi @Kevin-Mattheus-Moerman thanks so much for your comment!

I've now:

• included all doi's where available.
• updated paper affiliations text.
• included a .gitignore file

My code contribution (barring tests) is contained in the file AnalyZe.m.
The autogenerated code produced by the MATLAB App designer consists of lines:

• 1-558
• 9170-12212 (end)

My code responsible for functional analysis is included in lines: 559-2037.
The remainder of the code (lines: 2038-9169) was written by me but primarily consists (with a few exceptions) of the On-Event callback functions used by the application to handle user input, data, visualizations and other GUI functionality.

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@Doug-vN thanks for the detailed response, and for making those changes. I've just added the query-scope label which will trigger a scope review by the editorial board. The objective of the scope review is to determine if the functionality offered by the work is substantial enough, is research software, and conforms to our substantial scholarly effort criteria. This is normal for projects that are on the small side, or which appear to focus on visualization, or which are mostly an GUI/App. The scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

Note to editors, executing cloc on lines 559-2037 in Analyze.m returns:

-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                           1            371            103           1005
-------------------------------------------------------------------------------

[Doug-vN]

Sounds good, thanks @Kevin-Mattheus-Moerman!

[Doug-vN]

Hi @Kevin-Mattheus-Moerman, just checking in! Was there anything more that you needed from me at this time?

[Doug-vN]

Hi @Kevin-Mattheus-Moerman, any word on the scope review?

[Kevin-Mattheus-Moerman]

@Doug-vN apologies for the slower than usual scope review. Unfortunately, after review by the JOSS editorial team we've determined that this work is not in scope for JOSS.

The scope decision was based largely on the relatively small size of the core code developed (see also our substantial scholarly effort criteria), and also the project organisation (core functionality is capture by a single MATLAB file featuring both original and autogenerated code).

We will next proceed to reject this submission.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.