[PRE REVIEW]: concore for Simulating Closed-Loop Peripheral Neuromodulation Control Systems

[editorialbot]

Submitting author: @pradeeban (Pradeeban Kathiravelu) Repository: https://github.com/ControlCore-Project/concore/ Branch with paper.md (empty if default branch): Version: 2.0.1 Editor: Pending Reviewers: Pending Managing EiC: Daniel S. Katz

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Software report:

github.com/AlDanial/cloc v 1.88  T=2.52 s (402.7 files/s, 148001.4 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
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SWIG                                 3          66734            763         103365
C/C++ Header                       261          12751          16085          51555
C++                                 97           6812           6188          32858
MATLAB                             497           1910          32160          22032
XML                                 57              0             22          11136
Verilog-SystemVerilog               20            276            583           3070
Python                              42            428            403           2455
CMake                               14             98            110            442
Bourne Shell                         9             15             47            235
Markdown                             4             82              0            175
Bourne Again Shell                   4              1              0            113
TeX                                  1              0              0             40
DOS Batch                            4              3              0             23
YAML                                 1              1              4             18
MUMPS                                1              0              0              3
-----------------------------------------------------------------------------------
SUM:                              1015          89111          56365         227520
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1007

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1109/access.2022.3161471 may be a valid DOI for title: CONTROL-CORE: A Framework for Simulation and Design of Closed-Loop Peripheral Neuromodulation Control Systems
- 10.1109/tbme.2017.2759667 may be a valid DOI for title: Closed-loop vagus nerve stimulation based on state transition models
- 10.1145/3154979.3154984 may be a valid DOI for title: Generation and proliferation of random directed acyclic graphs for workflow scheduling problem

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[pradeeban]

Thanks, @editorialbot. The suggested DOIs are correct. I have added the DOIs to the paper now and committed to GitHub.

[pradeeban]

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[pradeeban]

@editorialbot generate pdf

[danielskatz]

@editorialbot check references

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

OK DOIs

- 10.1109/access.2022.3161471 is OK
- 10.1109/tbme.2017.2759667 is OK
- 10.1145/3154979.3154984 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[danielskatz]

@pradeeban - I see your submission note to the editor

The CONTROL-CORE framework, which concore is part of, is published in IEEE Access - https://doi.org/10.1109/ACCESS.2022.3161471. That paper is cited in this JOSS paper. [...] The project's early development happened in a private repository. We made the source code public in the concore-2.0.0 version. The main branch is the stable one, with the dev branch with commits of experimental nature that need additional testing before the merge.

Can you explain how this submission is different than the IEEE Access publication?

[pradeeban]

Hi @danielskatz, A few points:

• The IEEE Access paper is about the broad CONTROL-CORE framework/umbrella and significantly focuses on neuroscience. This paper focuses on the concore open source project in a more simplistic, less overwhelming manner.

• At the time of the IEEE Access paper submission, the CONTROL-CORE framework was merely an open-source project. We quickly opened the source code (which was initially developed in a private git repository) before publication through bulk "Initial commits."

• Since the IEEE Access paper, concore has evolved as a truly open-source project, welcoming open-source contributions (merged in the dev branch). concore Editor is a new addition, adopting the DHGWorkflow for concore.

All the above points make the papers different as in concore open-source project vs. CONTROL-CORE umbrella/framework for neuromodulation control systems.

At the Department of Biomedical Informatics, Emory University, we try to strengthen ourselves as an open-source framework. Many of our projects are open source, and we have been a mentoring organization for Google Summer of Code (GSoC) since 2012 (https://github.com/NISYSLAB/Emory-BMI-GSoC). concore is a new addition to our open source efforts. We hope JOSS will give us more scrutiny and visibility on the open source angle. Although we include the link to the source code in our previous papers, the code repositories are never reviewed, unlike JOSS. We like JOSS for this initiative, highlighting our software efforts alongside the research rather than leaving the source code as a mere footnote.

I hope I have clarified it. Please let me know if you have more questions/comments.

Thank you. Regards, Pradeeban.

[danielskatz]

Thanks - I think the next step should be for editors to look at this and make sure we think there is enough difference from the previous publication before we start a review. This should take a week or two.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[arfon]

@pradeeban, thanks for your submission to JOSS. I've given your earlier paper from March this year (CONTROL-CORE: A Framework for Simulation and Design of Closed-Loop Peripheral Neuromodulation Control Systems) a quick review and it looks like this submission here would be about broadly speaking the same work (i.e., not allowed as a dual publication).

Could you help me understand exactly what the code changes are to your framework since the publication in March this year? Linking to diffs on GitHub will help me make a good decision here.

[pradeeban]

Thanks, @arfon, for your consideration and pointers. After discussing with the co-authors, we have decided to withdraw the paper at this time.

[arfon]

@editorialbot withdraw

[editorialbot]

Paper withdrawn.