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Open Source Science

https://github.com/alleninstitute/bmtk

Brain Modeling Toolkit

https://github.com/alleninstitute/bmtk

Science Score: 67.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: plos.org
  • ✓
    Committers with academic emails
    8 of 26 committers (30.8%) from academic institutions
  • ✓
    Institutional organization owner
    Organization alleninstitute has institutional domain (alleninstitute.org)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary

Keywords

modeling neural-networks neuroinformatics neuron neuroscience python simulation
Last synced: 5 months ago · JSON representation

Repository

Brain Modeling Toolkit

Basic Info
Statistics
  • Stars: 297
  • Watchers: 24
  • Forks: 94
  • Open Issues: 71
  • Releases: 17
Topics
modeling neural-networks neuroinformatics neuron neuroscience python simulation
Created over 8 years ago · Last pushed 5 months ago
Metadata Files
Readme Contributing License

README.md

The Brain Modeling Toolkit

A software development package for building, simulating, and analyzing large-scale networks of different levels of resolution.

Please give feedback via our brief user survey, which will inform future development, fixes, and documentation.

Registering allows us to communicate with BMTK users and is encouraged, but not required: registration link.

See the paper about BMTK: link.

Please cite BMTK as follows:

Dai et al. Brain Modeling Toolkit: An open-source software suite for multiscale modeling of brain circuits. PLoS Comput Biol 16(11): e1008386. https://doi.org/10.1371/journal.pcbi.1008386

Level of Support

We are releasing this code to the public as a tool we expect others to use. Questions concerning bugs and related issues are welcomed. We expect to address them promptly and pull requests will be vetted by our staff before inclusion.

Quickstart

bmtk requires Python 2.7 or 3.5+, plus additional python dependicies. To install with base requirements from a command-line:

bash $ git clone https://github.com/AllenInstitute/bmtk.git $ cd bmtk $ python setup.py install

There are examples of building models and running simulations located in docs/examples/. Some of the simulation engines may require additional requirements to run.

Tests

There are a collection of unit tests in bmtk.tests which can be run using pytest

bash $ cd bmtk $ py.test

Documentation

User Guide

Copyright 2017 Allen Institute

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Create event: 7
  • Release event: 1
  • Issues event: 13
  • Watch event: 25
  • Delete event: 1
  • Issue comment event: 26
  • Push event: 98
  • Pull request review comment event: 5
  • Pull request review event: 3
  • Gollum event: 3
  • Pull request event: 65
  • Fork event: 10
Last Year
  • Create event: 7
  • Release event: 1
  • Issues event: 13
  • Watch event: 25
  • Delete event: 1
  • Issue comment event: 26
  • Push event: 98
  • Pull request review comment event: 5
  • Pull request review event: 3
  • Gollum event: 3
  • Pull request event: 65
  • Fork event: 10

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 796
  • Total Committers: 26
  • Avg Commits per committer: 30.615
  • Development Distribution Score (DDS): 0.343
Past Year
  • Commits: 107
  • Committers: 8
  • Avg Commits per committer: 13.375
  • Development Distribution Score (DDS): 0.411
Top Committers
Name Email Commits
kaeldai k****i@g****m 523
Xiao-Ping Liu x****6@g****m 71
Sergey Gratiy s****g@a****g 30
kael y****u@e****m 28
shinya.ito s****o@a****g 28
Padraig Gleeson p****n@g****m 20
Riuqlav v****s@g****m 13
Mizzou Neuro l****b@m****u 12
Laura Green l****n@g****m 11
Beatriz Herrera b****f@g****m 10
ewesteinde e****e@a****g 8
nilsvanrompaey n****y@s****e 8
Tyler Banks t****r@t****t 7
ZIAO CHEN c****3@g****m 6
CellAssembly y****l@g****m 5
Tyler Banks t****8@m****u 3
Mizzou Neuro a****h@g****m 3
Aaron D. Milstein n****s@g****m 2
AlexStasik 3****k 1
Andreas Tille t****e@d****g 1
Dictus Hugo h****s@e****h 1
Kyle Chen k****3@o****m 1
Werner Van Geit w****t@e****h 1
betsyi 3****i 1
Ben Latimer l****b@c****u 1
gregglickert g****9@g****m 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 3 epfl.ch: 2 comet-ln3.sdsc.edu: 1 debian.org: 1 mizzou.edu: 1 tylerbanks.net: 1 student.kuleuven.be: 1 missouri.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 59
  • Total pull requests: 204
  • Average time to close issues: 6 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 35
  • Total pull request authors: 15
  • Average comments per issue: 2.39
  • Average comments per pull request: 0.16
  • Merged pull requests: 189
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 63
  • Average time to close issues: 9 days
  • Average time to close pull requests: 7 days
  • Issue authors: 8
  • Pull request authors: 8
  • Average comments per issue: 1.9
  • Average comments per pull request: 0.29
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nicolomeneghetti (6)
  • MargauxCalice (5)
  • Jballbe (5)
  • Helveg (4)
  • GregGlickert (3)
  • CloudyDory (3)
  • yeraonjin06 (2)
  • tjbanks (2)
  • LHGreen (2)
  • mitometa (2)
  • moravveji (2)
  • shixnya (2)
  • latimerb (1)
  • mariakesa (1)
  • CatarinaM17 (1)
Pull Request Authors
  • kaeldai (127)
  • xpliu16 (45)
  • shixnya (23)
  • LHGreen (8)
  • mr-c (4)
  • nilsvanrompaey (4)
  • ewesteinde (4)
  • chenziao (4)
  • emollier (2)
  • beaherrera (2)
  • clinssen (2)
  • CloudyDory (1)
  • HDictus (1)
  • Riuqlav (1)
  • tjbanks (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 574 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 7
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 2
pypi.org: bmtk

Brain Modeling Toolkit

  • Versions: 17
  • Dependent Packages: 2
  • Dependent Repositories: 7
  • Downloads: 574 Last month
Rankings
Dependent packages count: 3.2%
Stargazers count: 4.2%
Forks count: 4.9%
Dependent repos count: 5.5%
Average: 6.6%
Downloads: 15.1%
Maintainers (1)
kaeldai
Last synced: 5 months ago
spack.io: py-bmtk

The Brain Modeling Toolkit

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Forks count: 12.7%
Stargazers count: 14.4%
Average: 21.1%
Dependent packages count: 57.3%
Maintainers (1)
adamjstewart
Last synced: 5 months ago

Dependencies

setup.py pypi
  • enum *
  • h5py *
  • jsonschema *
  • matplotlib *
  • numpy *
  • pandas *
  • scikit-image *
  • scipy *
  • six *
  • sympy *
test_requirements.txt pypi
  • flake8 * test
  • pytest * test
  • pytest-cov * test
.github/workflows/validate-pull-request.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v4 composite
  • andstor/file-existence-action v1 composite
docker/Dockerfile docker
  • continuumio/miniconda3 latest build
requirements.txt pypi
docker/environment.yml pypi
  • allensdk ==2.15.1
  • h5py ==3.8.0
  • imageio ==2.26.0
  • jsonschema ==4.17.3
  • lazy-loader ==0.1
  • mpmath ==1.3.0
  • networkx ==3.0
  • neuron ==8.0.0
  • packaging ==23.0
  • pywavelets ==1.4.1
  • scikit-image ==0.20.0
  • sympy ==1.12rc1