HNN-core

HNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEG - Published in JOSS (2023)

https://github.com/jonescompneurolab/hnn-core

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 8 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
5 of 31 committers (16.1%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

computational-modeling eeg meg neuron-simulator

Keywords from Contributors

neuroscience ecog electrocorticography electroencephalography magnetoencephalography neuroimaging

Scientific Fields

Engineering Computer Science - 36% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Simulation and optimization of neural circuits for MEG/EEG source estimates

Basic Info

Host: GitHub
Owner: jonescompneurolab
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://jonescompneurolab.github.io/hnn-core/
Size: 172 MB

Statistics

Stars: 62
Watchers: 11
Forks: 68
Open Issues: 141
Releases: 8

Topics

computational-modeling eeg meg neuron-simulator

Created almost 7 years ago · Last pushed 5 months ago

Metadata Files

Readme License Code of conduct Citation

hnn-core

HNN-GUI

About

This is a leaner and cleaner version of the code based off the HNN repository.

The Human Neocortical Neurosolver (HNN) is an open-source neural modeling tool designed to help researchers/clinicians interpret human brain imaging data. Based off the original HNN repository, HNN-core provides a convenient way to run simulations of an anatomically and biophysically detailed dynamical system model of human thalamocortical brain circuits with only a few lines of code. Given its modular, object-oriented design, HNN-core makes it easy to generate and evaluate hypotheses on the mechanistic origin of signals measured with magnetoencephalography (MEG), electroencephalography (EEG), or intracranial electrocorticography (ECoG). A unique feature of the HNN model is that it accounts for the biophysics generating the primary electric currents underlying such data, so simulation results are directly comparable to source localized data (current dipoles in units of nano-Ampere-meters); this enables precise tuning of model parameters to match characteristics of recorded signals. Multimodal neurophysiology data such as local field potential (LFP), current-source density (CSD), and spiking dynamics can also be simulated simultaneously with current dipoles.

While the HNN-core API is designed to be flexible and serve users with varying levels of coding expertise, the HNN-core GUI is designed to be useful to researchers with no formal computational neural modeling or coding experience.

For more information visit https://hnn.brown.edu. There, we describe the use of HNN in studying the circuit-level origin of some of the most commonly measured MEG/EEG and ECoG signals: event related potentials (ERPs) and low frequency rhythms (alpha/beta/gamma).

Contributors are very welcome! Please read our Contributing Guide if you are interested.

Please consider supporting HNN development efforts by voluntarily providing your demographic information here! Note that any demographic information we collect is anonymized and aggregated for reporting on the grants that fund the continued development of HNN. All questions are voluntary.

Installation

See Installation Guide. To install hnn-core with the minimum dependencies on Mac or Linux, simply do:

$ pip install hnn_core

hnn-core currently supports Python 3.9 through 3.13, inclusively.

If you want to track the latest developments of hnn-core, you can install the current version of the code (nightly) with:

$ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master

If you are interested in features like GUI, Optimization, or Parallel support, or are on Windows, then please see our Installation Guide.

Documentation and examples

Once you have installed hnn_core and the dependencies for the features you want, we recommend downloading and executing the example scripts provided on the documentation pages (as well as in the GitHub repository).

Note that python plots are by default non-interactive (blocking): each plot must thus be closed before the code execution continues. We recommend using and 'interactive' python interpreter such as ipython:

$ ipython --matplotlib

and executing the scripts using the %run-magic:

%run plot_simulate_evoked.py

When executed in this manner, the scripts will execute entirely, after which all plots will be shown. For an even more interactive experience, in which you execute code and interrogate plots in sequential blocks, we recommend editors such as VS Code and Spyder.

Bug reports

Use the GitHub Issues tracker to report bugs. For user questions and scientific discussions, please see our GitHub Discussions page.

Interested in Contributing?

Please read our Contributing Guide and make sure to abide by our Code of Conduct.

Governance Structure

Our governance structure can be found here.

Citing

If you use HNN-core in your work, please cite our publication in JOSS:

Jas et al., (2023). HNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEG. Journal of Open Source Software, 8(92), 5848, https://doi.org/10.21105/joss.05848

Owner

Name: jonescompneurolab
Login: jonescompneurolab
Kind: organization

Repositories: 6
Profile: https://github.com/jonescompneurolab

JOSS Publication

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

Published

December 15, 2023

DOI

10.21105/joss.05848

Volume 8, Issue 92, Page 5848

Authors

Mainak Jas

Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA

Ryan Thorpe

Department of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Nicholas Tolley

Department of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Christopher Bailey

Department of Clinical Medicine, Aarhus University, Aarhus, Denmark

Steven Brandt
Department of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Blake Caldwell

Bassett Medical Center, Cooperstown, NY, USA

Huzi Cheng
Department of Psychological and Brain Sciences, Indiana University Bloomington, Bloomington, IN, USA

Dylan Daniels

Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Carolina Fernandez Pujol

Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA

Mostafa Khalil
Department of Psychiatry and Behavioral Health, Penn State Milton S. Hershey Medical Center, Penn State College of Medicine, Hershey, PA, USA

Samika Kanekar

Warren Alpert Medical, Brown University, Providence, RI

Carmen Kohl

Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Orsolya Kolozsvári

Department of Psychology, University of Jyväskylä, Jyväskylä, Finland, Jyväskylä Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland

Kaisu Lankinen

Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA, Department of Radiology, Harvard Medical School, Boston, MA, USA

Kenneth Loi
Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Department of Molecular and Cell Biology; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA

Sam Neymotin

Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA

Rajat Partani

Department of Computer Science and Engineering, National Institute of Technology Karnataka, Karnataka, India

Mattan Pelah
Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Florida State University, Tallahassee, FL, USA

Alex Rockhill

Department of Human Physiology, University of Oregon, Eugene, OR, USA

Mohamed Sherif

Department of Psychiatry and Human Behavior, Brown University, Providence, RI, USA, Rhode Island Hospital, Providence, RI, USA

Matti Hamalainen

Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland

Stephanie Jones

Department of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

Editor

Brian McFee

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Jas
  given-names: Mainak
  orcid: "https://orcid.org/0000-0002-3199-9027"
- family-names: Thorpe
  given-names: Ryan
  orcid: "https://orcid.org/0000-0003-2491-8599"
- family-names: Tolley
  given-names: Nicholas
  orcid: "https://orcid.org/0000-0003-0358-0074"
- family-names: Bailey
  given-names: Christopher
  orcid: "https://orcid.org/0000-0003-3318-3344"
- family-names: Brandt
  given-names: Steven
- family-names: Caldwell
  given-names: Blake
  orcid: "https://orcid.org/0000-0002-6882-6998"
- family-names: Cheng
  given-names: Huzi
- family-names: Daniels
  given-names: Dylan
  orcid: "https://orcid.org/0009-0008-1958-353X"
- family-names: Pujol
  given-names: Carolina Fernandez
  orcid: "https://orcid.org/0009-0003-0611-1270"
- family-names: Khalil
  given-names: Mostafa
- family-names: Kanekar
  given-names: Samika
  orcid: "https://orcid.org/0000-0002-6111-4461"
- family-names: Kohl
  given-names: Carmen
  orcid: "https://orcid.org/0000-0001-7585-595X"
- family-names: Kolozsvári
  given-names: Orsolya
  orcid: "https://orcid.org/0000-0002-1619-6314"
- family-names: Lankinen
  given-names: Kaisu
  orcid: "https://orcid.org/0000-0003-2210-2385"
- family-names: Loi
  given-names: Kenneth
- family-names: Neymotin
  given-names: Sam
  orcid: "https://orcid.org/0000-0003-3646-5195"
- family-names: Partani
  given-names: Rajat
  orcid: "https://orcid.org/0000-0002-6863-7046"
- family-names: Pelah
  given-names: Mattan
- family-names: Rockhill
  given-names: Alex
  orcid: "https://orcid.org/0000-0003-3868-7453"
- family-names: Sherif
  given-names: Mohamed
  orcid: "https://orcid.org/0000-0002-8951-1645"
- family-names: Hamalainen
  given-names: Matti
  orcid: "https://orcid.org/0000-0001-6841-112X"
- family-names: Jones
  given-names: Stephanie
  orcid: "https://orcid.org/0000-0001-6760-5301"
contact:
- family-names: Jones
  given-names: Stephanie
  orcid: "https://orcid.org/0000-0001-6760-5301"
doi: 10.5281/zenodo.10289164
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jas
    given-names: Mainak
    orcid: "https://orcid.org/0000-0002-3199-9027"
  - family-names: Thorpe
    given-names: Ryan
    orcid: "https://orcid.org/0000-0003-2491-8599"
  - family-names: Tolley
    given-names: Nicholas
    orcid: "https://orcid.org/0000-0003-0358-0074"
  - family-names: Bailey
    given-names: Christopher
    orcid: "https://orcid.org/0000-0003-3318-3344"
  - family-names: Brandt
    given-names: Steven
  - family-names: Caldwell
    given-names: Blake
    orcid: "https://orcid.org/0000-0002-6882-6998"
  - family-names: Cheng
    given-names: Huzi
  - family-names: Daniels
    given-names: Dylan
    orcid: "https://orcid.org/0009-0008-1958-353X"
  - family-names: Pujol
    given-names: Carolina Fernandez
    orcid: "https://orcid.org/0009-0003-0611-1270"
  - family-names: Khalil
    given-names: Mostafa
  - family-names: Kanekar
    given-names: Samika
    orcid: "https://orcid.org/0000-0002-6111-4461"
  - family-names: Kohl
    given-names: Carmen
    orcid: "https://orcid.org/0000-0001-7585-595X"
  - family-names: Kolozsvári
    given-names: Orsolya
    orcid: "https://orcid.org/0000-0002-1619-6314"
  - family-names: Lankinen
    given-names: Kaisu
    orcid: "https://orcid.org/0000-0003-2210-2385"
  - family-names: Loi
    given-names: Kenneth
  - family-names: Neymotin
    given-names: Sam
    orcid: "https://orcid.org/0000-0003-3646-5195"
  - family-names: Partani
    given-names: Rajat
    orcid: "https://orcid.org/0000-0002-6863-7046"
  - family-names: Pelah
    given-names: Mattan
  - family-names: Rockhill
    given-names: Alex
    orcid: "https://orcid.org/0000-0003-3868-7453"
  - family-names: Sherif
    given-names: Mohamed
    orcid: "https://orcid.org/0000-0002-8951-1645"
  - family-names: Hamalainen
    given-names: Matti
    orcid: "https://orcid.org/0000-0001-6841-112X"
  - family-names: Jones
    given-names: Stephanie
    orcid: "https://orcid.org/0000-0001-6760-5301"
  date-published: 2023-12-15
  doi: 10.21105/joss.05848
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5848
  title: "HNN-core: A Python software for cellular and circuit-level
    interpretation of human MEG/EEG"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05848"
  volume: 8
title: "HNN-core: A Python software for cellular and circuit-level
  interpretation of human MEG/EEG"

GitHub Events

Total

Fork event: 15
Create event: 16
Release event: 1
Issues event: 95
Watch event: 6
Delete event: 8
Member event: 1
Issue comment event: 388
Push event: 166
Gollum event: 25
Pull request review comment event: 255
Pull request review event: 264
Pull request event: 176

Last Year

Fork event: 15
Create event: 16
Release event: 1
Issues event: 95
Watch event: 6
Delete event: 8
Member event: 1
Issue comment event: 388
Push event: 166
Gollum event: 25
Pull request review comment event: 255
Pull request review event: 264
Pull request event: 176

Committers

Last synced: 5 months ago

All Time

Total Commits: 2,923
Total Committers: 31
Avg Commits per committer: 94.29
Development Distribution Score (DDS): 0.776

Past Year

Commits: 240
Committers: 11
Avg Commits per committer: 21.818
Development Distribution Score (DDS): 0.471

Top Committers

Name	Email	Commits
Mainak Jas	m**s@g**m	656
Nick Tolley	n**y@g**m	565
George Dang	5****g	350
Ryan Thorpe	r**e@b**u	343
Huzi Cheng	t**s@i**m	212
Christopher J. Bailey	b**j@g**m	202
Blake Caldwell	2**l@g**m	139
Camilo Diaz	k**9@g**m	93
Carolina Fernandez	c**8@m**u	80
Austin E. Soplata	a****a	63
katduecker	k**r@g**m	32
samadpls	a**1@g**m	32
raj1701	r**i@g**m	32
dylansdaniels	d**s@g**m	21
kenloi	k**i@b**u	19
Carmen	k**1@g**m	15
mohdsherif	m**b@g**m	14
spbrandt	1****t	10
Orsolya Beatrix Kolozsvari	o**i@g**m	7
Kaisu Lankinen	k**n@m**u	6
Samika Kanekar	s**n@g**m	6
Stephanie R. Jones	S**s@B**u	5
Alex	a**l@m**g	5
Yaroslav Halchenko	d**n@o**m	5
Maira Usman	m**3@g**m	3
Tianqi Cheng	t**g@T**l	3
Dikshant jha	1****4	1
Pynmash	1****h	1
Shehroz Kashif	1****f	1
mjpelah	9****h	1
and 1 more...

Committer Domains (Top 20 + Academic)

brown.edu: 3 onerussian.com: 1 mailbox.org: 1 mgh.harvard.edu: 1 miami.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 154
Total pull requests: 336
Average time to close issues: 9 months
Average time to close pull requests: 25 days
Total issue authors: 15
Total pull request authors: 24
Average comments per issue: 1.61
Average comments per pull request: 2.34
Merged pull requests: 218
Bot issues: 9
Bot pull requests: 2

Past Year

Issues: 83
Pull requests: 208
Average time to close issues: 25 days
Average time to close pull requests: 13 days
Issue authors: 8
Pull request authors: 16
Average comments per issue: 0.7
Average comments per pull request: 1.86
Merged pull requests: 128
Bot issues: 9
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

asoplata (51)
gtdang (34)
jasmainak (17)
github-actions[bot] (9)
ntolley (9)
kmilo9999 (7)
dylansdaniels (6)
rythorpe (5)
darcywaller (4)
blakecaldwell (4)
katduecker (3)
samadpls (2)
chenghuzi (1)
kenneth59715 (1)
hanbuck30 (1)

Pull Request Authors

asoplata (120)
gtdang (67)
dylansdaniels (26)
kmilo9999 (21)
ntolley (18)
samadpls (14)
dikshant182004 (10)
katduecker (9)
jasmainak (9)
Myrausman (6)
Chetank99 (5)
carolinafernandezp (5)
Freedisch (4)
pynmash (4)
Shehrozkashif (4)

Top Labels

Issue Labels

hnn-gui-integration (26) hnn-gui (17) bug (16) enhancement (15) good first issue (11) maint (10) docs (10) testing (9) refactor (8) parallelization (3) optimization (3) visualization (3) installation (2) science (2) distribution-packaging (2) default-model-update (2) moderate difficulty (2) blocked/cannot proceed (1) question (1) low-priority (1) website (1) file-formats (1) IO (1)

Pull Request Labels

docs (17) bug (13) hnn-gui (11) website (10) testing (8) installation (6) enhancement (5) parallelization (2) maint (2) default-model-update (2) distribution-packaging (2) high difficulty (1) optimization (1) refactor (1) hnn-gui-integration (1)

Packages

Total packages: 1
Total downloads:
- pypi 87 last-month

Total dependent packages: 0
Total dependent repositories: 3
Total versions: 11
Total maintainers: 3

pypi.org: hnn-core

Code for biophysical simulation of a cortical column using Neuron

Documentation: https://hnn-core.readthedocs.io/
License: BSD (3-clause)
Latest release: 0.4.2
published 7 months ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 3
Downloads: 87 Last month

Rankings

Dependent repos count: 9.0%

Dependent packages count: 10.1%

Average: 12.9%

Downloads: 19.8%

Maintainers (3)

mainakjas ntolley rythorpe

Last synced: 4 months ago

Dependencies

.github/workflows/linkcheck.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/unit_tests.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/windows_unit_tests.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

doc/Dockerfile docker

jupyter/minimal-notebook 65761486d5d3 build

binder/requirements.txt pypi

NEURON *
ipywidgets *
matplotlib *
scipy *
voila *

pyproject.toml pypi

setup.py pypi

NEURON *
h5io *
matplotlib >=3.5.3
numpy *
scipy *

HNN-core

Science Score: 100.0%

Keywords

Keywords from Contributors

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Basic Info

Statistics

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Metadata Files

README.md

hnn-core

About

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Interested in Contributing?

Governance Structure

Citing

Owner

JOSS Publication

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

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

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All Time

Past Year

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pypi.org: hnn-core

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Maintainers (3)

Dependencies