[PRE REVIEW]: HNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEG

[editorialbot]

Submitting author: @ntolley (Nicholas Tolley)
Repository: https://github.com/jonescompneurolab/hnn-core
Branch with paper.md (empty if default branch): joss_paper
Version: 0.3
Editor: @bmcfee
Reviewers: @isdanni, @neurofractal
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c"><img src="https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c/status.svg)](https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c)

Author instructions

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

@ntolley 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:

@editorialbot commands

[editorialbot]

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

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.31 s (273.7 files/s, 72891.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          51           2742           5392          10508
reStructuredText                11            402            169            821
JSON                             3              0              0            663
YAML                             6             36              7            276
TeX                              1             26              0            247
Markdown                         2             60              0            212
HTML                             3             10              0             94
Jupyter Notebook                 3              0            733             66
make                             2             19              9             61
Dockerfile                       1             19              2             58
INI                              1              0              0              3
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            85           3314           6312          13012
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2215

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.21105/joss.02505 is OK
- 10.1101/2023.06.16.545371 is OK

MISSING DOIs

- 10.1152/jn.00535.2009 may be a valid DOI for title: Quantitative analysis and biophysically realistic neural modeling of the MEG mu rhythm: rhythmogenesis and modulation of sensory-evoked responses
- 10.1007/s10548-021-00838-0 may be a valid DOI for title: Neural mechanisms underlying human auditory evoked responses revealed by human neocortical neurosolver
- 10.1101/2021.04.16.440210 may be a valid DOI for title: Thalamocortical mechanisms regulating the relationship between transient beta events and human tactile perception
- 10.3389/fpsyg.2018.02117 may be a valid DOI for title: A prospective study of the impact of transcranial alternating current stimulation on EEG correlates of somatosensory perception
- 10.1016/j.neuroimage.2021.118479 may be a valid DOI for title: Laminar dynamics of high amplitude beta bursts in human motor cortex
- 10.1101/2020.05.08.084947 may be a valid DOI for title: Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
- 10.1101/2023.03.06.531459 may be a valid DOI for title: Laminar Specificity of the Auditory Perceptual Awareness Negativity: A Biophysical Modeling Study
- 10.1016/b978-012264841-0/50054-8 may be a valid DOI for title: Dynamic causal modelling
- 10.3389/fnins.2013.00267 may be a valid DOI for title: MEG and EEG data analysis with MNE-Python
- 10.3389/fninf.2013.00041 may be a valid DOI for title: LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons
- 10.3389/fninf.2013.00010 may be a valid DOI for title: The Virtual Brain: a simulator of primate brain network dynamics
- 10.1101/2022.12.13.520225 may be a valid DOI for title: Diverse beta burst waveform motifs characterize movement-related cortical dynamics
- 10.1101/2021.10.11.463545 may be a valid DOI for title: Distinct neocortical mechanisms underlie human SI responses to median nerve and laser evoked peripheral activation
- 10.1101/2023.04.17.537118 may be a valid DOI for title: Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
- 10.1103/revmodphys.65.413 may be a valid DOI for title: Magnetoencephalography—theory, instrumentation, and applications to noninvasive studies of the working human brain
- 10.1109/mcse.2007.55 may be a valid DOI for title: Matplotlib: A 2D graphics environment

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@ntolley thanks for this submission. I am the AEiC on this track and here to help with the initial steps. I will be looking for a handling editor. For the moment can you check those potentially missing DOIs? ☝️ You can amend your .bib file and rerun (in a clean comment here):
@editorialbot generate pdf

Followed by:
@editorialbot check references

Thanks.

[Kevin-Mattheus-Moerman]

@editorialbot invite @bmcfee as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@bmcfee do you think you can handle this submission? There are very few editors available in this domain at the moment, but I thought your signal processing background might make you a good fit too.

[bmcfee]

Sure - it's a little outside my wheelhouse, but I can probably stir up some neuro-flavored reviewers.

[bmcfee]

@editorialbot assign @bmcfee as editor

[editorialbot]

Assigned! @bmcfee is now the editor

[ntolley]

@editorialbot generate pdf

[ntolley]

@editorialbot check references

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.7554/eLife.51214 is OK
- 10.1152/jn.00535.2009 is OK
- 10.1007/s10548-021-00838-0 is OK
- 10.1093/cercor/bhab221 is OK
- 10.3389/fpsyg.2018.02117 is OK
- 10.1016/j.neuroimage.2021.118479 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1371/journal.pcbi.1008386 is OK
- 10.7554/eLife.44494 is OK
- 10.1371/journal.pcbi.1011003 is OK
- 10.1016/b978-012264841-0/50054-8 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1155/2011/852961 is OK
- 10.3389/fninf.2013.00041 is OK
- 10.3389/fninf.2013.00010 is OK
- 10.1016/j.pneurobio.2023.102490 is OK
- 10.1101/2021.10.11.463545 is OK
- 10.1101/2023.04.17.537118 is OK
- 10.1103/RevModPhys.65.413 is OK
- 10.21105/joss.02505 is OK
- 10.1101/2023.06.16.545371 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1162/neco.1997.9.6.1179 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ntolley]

Thanks @Kevin-Mattheus-Moerman and @bmcfee!

Just updated the DOI's and seems like everything is passing.

[isdanni]

Hey @bmcfee If reviewers haven't been decided I'm happy to review this one.

[bmcfee]

Thanks @isdanni ! I'm still working through my list of invites, but happy to add you on here.

[bmcfee]

@editorialbot add @isdanni as reviewer

[editorialbot]

@isdanni added to the reviewers list!

[bmcfee]

@editorialbot add @neurofractal as reviewer

[editorialbot]

@neurofractal added to the reviewers list!

[bmcfee]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5848.