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https://github.com/alleninstitute/allensdk

code for reading and processing Allen Institute for Brain Science data

https://github.com/alleninstitute/allensdk

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    35 of 77 committers (45.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.9%) to scientific vocabulary

Keywords

bioinformatics scientific

Keywords from Contributors

neuroscience electrophysiology open-science notebooks nwb neuron distributed cryptocurrencies data-engineering experiment
Last synced: 9 months ago · JSON representation

Repository

code for reading and processing Allen Institute for Brain Science data

Basic Info
Statistics
  • Stars: 358
  • Watchers: 32
  • Forks: 153
  • Open Issues: 381
  • Releases: 54
Topics
bioinformatics scientific
Created about 11 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Codeowners

README.md

The Allen SDK

Join the chat at https://gitter.im/AllenInstitute/AllenSDK Documentation Status Actions Status

This repository contains code for processing and analyzing data in the Allen Brain Atlas.

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

We welcome contributions! See the contribution guide here. See here for the list of authors.

If you have more general questions or comments about the AllenSDK please post them to the Allen Brain Map Community Forum.

Owner

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

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

GitHub Events

Total
  • Issues event: 13
  • Watch event: 22
  • Issue comment event: 16
  • Pull request event: 1
  • Fork event: 7
Last Year
  • Issues event: 13
  • Watch event: 22
  • Issue comment event: 16
  • Pull request event: 1
  • Fork event: 7

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 5,503
  • Total Committers: 77
  • Avg Commits per committer: 71.468
  • Development Distribution Score (DDS): 0.846
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
David Feng d****f@a****g 849
Adam Amster a****r@a****g 757
nilegraddis n****s@g****m 700
danielsf s****l@a****g 519
Tim Fliss t****f@a****g 475
Nicholas Mei n****i@a****g 287
nicholasc n****e@g****m 239
nileg n****g@a****g 222
Dan d****k@a****g 212
Keith Godfrey k****g@a****g 131
Josh Siegle j****s@a****g 116
Jed Perkins p****d@g****m 113
Christopher Morrison c****n@a****g 107
Kat Schelonka k****n@g****m 98
Nick Ponvert n****t@g****m 67
Mike Huang h****e@g****m 66
kaeldai k****i@g****m 62
Corinne Teeter c****t@a****g 51
isaak.willett@alleninstitute.org i****t@a****g 49
matchings m****g@a****g 45
Doug Ollerenshaw d****w@g****m 41
matyasz t****z@g****m 33
Ani Nandi a****8@g****m 29
Sergey Gratiy s****g@a****g 27
Doug Ollerenshaw d****o@a****g 23
Tim Fliss t****f@a****g 18
Wesley Jones w****s@u****m 14
Nathan Gouwens n****g@a****g 14
David Feng d****f 13
Corbett Bennett c****b@a****g 10
and 47 more...
Committer Domains (Top 20 + Academic)
alleninstitute.org: 29 kitware.com: 1 gerkin.org: 1 gitter.im: 1 89eb27801839.(none): 1 unibas.ch: 1 stud.uni-goettingen.de: 1 onerussian.com: 1 uw.edu: 1 ibs-nathans-ux1.corp.alleninstitute.org: 1 axon.corp.alleninstitute.org: 1 mail.huji.ac.il: 1 fake.email: 1 upgradeya.com: 1 alleninst.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 108
  • Total pull requests: 80
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 56
  • Total pull request authors: 15
  • Average comments per issue: 2.44
  • Average comments per pull request: 1.29
  • Merged pull requests: 60
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 12
  • Pull requests: 2
  • Average time to close issues: 4 days
  • Average time to close pull requests: N/A
  • Issue authors: 9
  • Pull request authors: 2
  • Average comments per issue: 0.58
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • morriscb (10)
  • aamster (9)
  • corbennett (9)
  • AngCamp (8)
  • matchings (5)
  • mariakesa (4)
  • alih100011 (4)
  • vigji (2)
  • mohamadamin-fjz (2)
  • DowntonCrabby (2)
  • danielsf (2)
  • jkbhagatio (2)
  • slcalgin (2)
  • kdharris101 (2)
  • RobertoDF (2)
Pull Request Authors
  • morriscb (35)
  • mikejhuang (14)
  • aamster (11)
  • corbennett (3)
  • chaseking (2)
  • Ahad-Allen (2)
  • RobertoDF (2)
  • matchings (1)
  • nataliaorlova (1)
  • omidzobeiri (1)
  • anirban6908 (1)
  • mabuice (1)
  • ivanmilevtues (1)
  • dependabot[bot] (1)
  • brendanjohnharris (1)
Top Labels
Issue Labels
bug (43) enhancement (21) question (21) vbn (10) vbo (8) behavior (6) notebook (6) NWB file (2) braintv (2) vcn (2) requires data release (2) Epic (2) external (1) noprogram (1) ophys (1) documentation (1) works internally (1) blocked - waiting on NWB file release (1)
Pull Request Labels
behavior (1) braintv (1) celltypes (1) dependency (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 6,149 last-month
  • Total docker downloads: 10
  • Total dependent packages: 21
    (may contain duplicates)
  • Total dependent repositories: 40
    (may contain duplicates)
  • Total versions: 81
  • Total maintainers: 1
pypi.org: allensdk

core libraries for the allensdk.

  • Versions: 80
  • Dependent Packages: 21
  • Dependent Repositories: 40
  • Downloads: 6,149 Last month
  • Docker Downloads: 10
Rankings
Dependent packages count: 0.6%
Dependent repos count: 2.3%
Average: 3.2%
Stargazers count: 3.6%
Docker downloads count: 3.6%
Forks count: 4.1%
Downloads: 5.2%
Maintainers (1)
alleninstitute
Last synced: 9 months ago
conda-forge.org: allensdk

The Allen Software Development Kit houses source code for reading and processing Allen Brain Atlas data. The Allen SDK focuses on the Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 14.1%
Stargazers count: 20.9%
Average: 30.0%
Dependent repos count: 34.0%
Dependent packages count: 51.2%
Last synced: 10 months ago

Dependencies

doc_requirements.txt pypi
  • aiohttp ==3.7.4
  • argschema >=3.0.1,<4.0.0
  • docutils <0.18
  • flake8 >=1.5.0,<4.0.0
  • future >=0.14.3,<1.0.0
  • glymur ==0.8.19
  • h5py >=2.8,<3.0.0
  • hdmf ==1.0.2
  • jinja2 >=2.7.3,<2.12.0
  • jupyter >=1.0.0,<2.0.0
  • markupsafe ==2.0.1
  • matplotlib >=1.4.3,<4.0.0
  • nest_asyncio ==1.2.0
  • numpy >=1.15.4,<1.19.0
  • numpydoc >=0.6.0,<1.0.0
  • pandas >=0.25.1,<=0.25.3
  • pep8 ==1.7.0,<2.0.0
  • psycopg2-binary >=2.7,<3.0.0
  • pylint >=1.5.4,<3.0.0
  • pynrrd >=0.2.1,<1.0.0
  • pynwb ==1.0.2
  • requests <3.0.0
  • requests-toolbelt <1.0.0
  • scikit-build <1.0.0
  • scikit-image >=0.14.0,<0.17.0
  • scipy >=0.15.1,<2.0.0
  • seaborn <1.0.0
  • simpleitk >=2.0.2,<3.0.0
  • simplejson >=3.10.0,<4.0.0
  • six >=1.9.0,<2.0.0
  • statsmodels ==0.9.0
  • xarray <0.16.0
requirements.txt pypi
  • aiohttp ==3.7.4
  • argschema >=3.0.1,<4.0.0
  • boto3 ==1.17.21
  • cachetools >=4.2.1,<5.0.0
  • future >=0.14.3,<1.0.0
  • glymur ==0.8.19
  • h5py *
  • hdmf >=2.5.8
  • jinja2 >=2.7.3,<2.12.0
  • matplotlib >=1.4.3,<3.4.3
  • ndx-events <=0.2.0
  • nest_asyncio *
  • numpy *
  • pandas >=1.1.5
  • psycopg2-binary >=2.7,<3.0.0
  • pynrrd >=0.2.1,<1.0.0
  • pynwb *
  • requests <3.0.0
  • requests-toolbelt <1.0.0
  • scikit-build <1.0.0
  • scikit-image >=0.14.0,<0.17.0
  • scipy >=1.4.0,<2.0.0
  • seaborn <1.0.0
  • semver *
  • simpleitk >=2.0.2,<3.0.0
  • simplejson >=3.10.0,<4.0.0
  • six >=1.9.0,<2.0.0
  • sqlalchemy *
  • statsmodels <=0.13.0
  • tables >=3.6.0,<3.7.0
  • tqdm >=4.27
  • xarray <0.16.0
test_requirements.txt pypi
  • coverage >=3.7.1,<6.0.0
  • flake8 >=1.5.0,<4.0.0
  • jinja2 >=2.7.3,<2.12.0
  • jupyter >=1.0.0,<2.0.0
  • mock >=1.0.1,<5.0.0
  • moto ==2.0.1
  • numpydoc >=0.6.0,<1.0.0
  • pep8 ==1.7.0,<2.0.0
  • pylint >=1.5.4,<3.0.0
  • pytest >=4.4.0,<6.0.0
  • pytest-cov >=2.6.1,<3.0.0
  • pytest-cover >=3.0.0,<4.0.0
  • pytest-mock >=1.5.0,<3.0.0
  • pytest-pep8 >=1.0.6,<2.0.0
  • pytest-xdist >=1.14,<2.0.0
  • scikit-learn <1.0.0
.github/workflows/github-actions-ci.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/nightly.yml actions
  • actions/checkout v2 composite
.github/workflows/notebook_runner.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • stefanzweifel/git-auto-commit-action v4 composite
allensdk/brain_observatory/eye_tracking/stage_1/Dockerfile docker
  • tensorflow/tensorflow 1.13.2-gpu build
allensdk/brain_observatory/eye_tracking/stage_2/Dockerfile docker
  • tensorflow/tensorflow 1.13.2-gpu build
allensdk/brain_observatory/eye_tracking/stage_3/Dockerfile docker
  • tensorflow/tensorflow 1.13.2-gpu build
allensdk/brain_observatory/eye_tracking/stage_4/Dockerfile docker
  • tensorflow/tensorflow 1.13.2-gpu build
docker/allensdk/Dockerfile docker
  • continuumio/anaconda3 latest build
docker/anaconda/Dockerfile docker
  • alleninstitute/allensdk anaconda_neuron_1370 build
docker/anaconda3/Dockerfile docker
  • continuumio/miniconda3 4.8.2 build
docker/anaconda3_neuron_1370/Dockerfile docker
  • continuumio/anaconda3 latest build
docker/anaconda_neuron_1370/Dockerfile docker
  • continuumio/anaconda 4.1.1 build
docker/aws_jupyterhub/Dockerfile docker
  • alleninstitute/allensdk anaconda3_neuron_1370 build
docker/aws_swarm/docker-compose.yml docker
  • alleninstitute/anaconda3_neuron_1370 latest
docker/fhl2017_gpu/Dockerfile docker
  • gw000/debian-cuda latest build
docker/gpu/Dockerfile docker
  • alleninstitute/anaconda3_neuron_1370 latest build
docker/ubuntu/Dockerfile docker
  • ubuntu trusty build
dev_requirements.txt pypi
  • ipykernel * development
  • ipython * development
  • nbconvert * development
  • papermill * development
  • traitlets * development
notebook_requirements.txt pypi
  • scikit-learn *
setup.py pypi
docker/anaconda3_neuron_1370/shared/environment.yml conda
  • _license 1.1
  • abstract-rendering 0.5.1
  • argcomplete 0.8.1
  • astropy 0.4.2
  • atom 0.3.9
  • beautiful-soup 4.3.2
  • binstar 0.7.1
  • bitarray 0.8.1
  • blaze 0.6.3
  • blz 0.6.2
  • bokeh 0.6.1
  • boto 2.32.1
  • cairo 1.12.2
  • casuarius 1.1
  • cdecimal 2.3
  • cffi 0.8.6
  • chaco 4.4.1
  • colorama 0.3.1
  • configobj 5.0.6
  • cryptography 0.5.4
  • curl 7.38.0
  • cython 0.21
  • cytoolz 0.7.0
  • datashape 0.3.0
  • dateutil 2.1
  • decorator 3.4.0
  • docutils 0.12
  • dynd-python 0.6.5
  • enable 4.3.0
  • enaml 0.9.8
  • flask 0.10.1
  • freetype 2.4.10
  • future 0.13.1
  • futures 2.1.6
  • gevent 1.0.1
  • gevent-websocket 0.9.3
  • greenlet 0.4.4
  • grin 1.2.1
  • h5py 2.3.1
  • hdf5 1.8.13
  • ipython 2.2.0
  • ipython-notebook 2.2.0
  • ipython-qtconsole 2.2.0
  • itsdangerous 0.24
  • jdcal 1.0
  • jinja2 2.7.3
  • jpeg 8d
  • kiwisolver 0.1.3
  • lcms 1.19
  • libdynd 0.6.5
  • libffi 3.0.13
  • libpng 1.5.13
  • libsodium 0.4.5
  • libtiff 4.0.2
  • libxml2 2.9.0
  • libxslt 1.1.28
  • llvm 3.3
  • llvmpy 0.12.7
  • lxml 3.4.0
  • markupsafe 0.23
  • matplotlib 1.4.0
  • mock 1.0.1
  • mpi4py 1.3
  • mpich2 1.4.1p1
  • multipledispatch 0.4.7
  • networkx 1.9.1
  • nltk 3.0.0
  • nose 1.3.4
  • numba 0.14.0
  • numexpr 2.3.1
  • numpy 1.9.0
  • numpy 1.9.2
  • openpyxl 1.8.5
  • openssl 1.0.1h
  • openssl 1.0.1k
  • pandas 0.14.1
  • patsy 0.3.0
  • pep8 1.5.7
  • pil 1.1.7
  • pip 1.5.6
  • pixman 0.26.2
  • ply 3.4
  • psutil 2.1.1
  • py 1.4.25
  • py2cairo 1.10.0
  • pycosat 0.6.1
  • pycparser 2.10
  • pycrypto 2.6.1
  • pycurl 7.19.5
  • pyface 4.4.0
  • pyflakes 0.8.1
  • pygments 1.6
  • pyopenssl 0.14
  • pyparsing 2.0.1
  • pyqt 4.10.4
  • pytables 3.1.1
  • pytest 2.6.3
  • python 2.7.8
  • python 2.7.9
  • pytz 2014.7
  • pyyaml 3.11
  • pyzmq 14.3.1
  • qt 4.8.5
  • readline 6.2
  • redis 2.6.9
  • redis-py 2.9.1
  • requests 2.4.1
  • requests 2.6.0
  • rope 0.9.4
  • runipy 0.1.1
  • scikit-image 0.10.1
  • scikit-learn 0.16.0
  • scipy 0.14.0
  • scipy 0.15.1
  • setuptools 5.8
  • sip 4.15.5
  • six 1.8.0
  • sockjs-tornado 1.0.1
  • sphinx 1.2.3
  • spyder 2.3.1
  • spyder-app 2.3.1
  • sqlalchemy 0.9.7
  • sqlite 3.8.4.1
  • ssl_match_hostname 3.4.0.2
  • statsmodels 0.5.0
  • sympy 0.7.5
  • system 5.8
  • theano 0.6.0
  • tk 8.5.15
  • tk 8.5.18
  • toolz 0.7.0
  • tornado 4.0.2
  • traits 4.4.0
  • traitsui 4.4.0
  • ujson 1.33
  • unicodecsv 0.9.4
  • util-linux 2.21
  • werkzeug 0.9.6
  • xlrd 0.9.3
  • xlsxwriter 0.5.7
  • xlwt 0.7.5
  • yaml 0.1.4
  • zeromq 4.0.4
  • zlib 1.2.7
  • zlib 1.2.8
docker/fhl2017_gpu/shared/environment.yml conda
  • _license 1.1
  • abstract-rendering 0.5.1
  • argcomplete 0.8.1
  • astropy 0.4.2
  • atom 0.3.9
  • beautiful-soup 4.3.2
  • binstar 0.7.1
  • bitarray 0.8.1
  • blaze 0.6.3
  • blz 0.6.2
  • bokeh 0.6.1
  • boto 2.32.1
  • cairo 1.12.2
  • casuarius 1.1
  • cdecimal 2.3
  • cffi 0.8.6
  • chaco 4.4.1
  • colorama 0.3.1
  • configobj 5.0.6
  • cryptography 0.5.4
  • curl 7.38.0
  • cython 0.21
  • cytoolz 0.7.0
  • datashape 0.3.0
  • dateutil 2.1
  • decorator 3.4.0
  • docutils 0.12
  • dynd-python 0.6.5
  • enable 4.3.0
  • enaml 0.9.8
  • flask 0.10.1
  • freetype 2.4.10
  • future 0.13.1
  • futures 2.1.6
  • gevent 1.0.1
  • gevent-websocket 0.9.3
  • greenlet 0.4.4
  • grin 1.2.1
  • h5py 2.3.1
  • hdf5 1.8.13
  • ipython 2.2.0
  • ipython-notebook 2.2.0
  • ipython-qtconsole 2.2.0
  • itsdangerous 0.24
  • jdcal 1.0
  • jinja2 2.7.3
  • jpeg 8d
  • kiwisolver 0.1.3
  • lcms 1.19
  • libdynd 0.6.5
  • libffi 3.0.13
  • libpng 1.5.13
  • libsodium 0.4.5
  • libtiff 4.0.2
  • libxml2 2.9.0
  • libxslt 1.1.28
  • llvm 3.3
  • llvmpy 0.12.7
  • lxml 3.4.0
  • markupsafe 0.23
  • matplotlib 1.4.0
  • mock 1.0.1
  • mpi4py 1.3
  • mpich2 1.4.1p1
  • multipledispatch 0.4.7
  • networkx 1.9.1
  • nltk 3.0.0
  • nose 1.3.4
  • numba 0.14.0
  • numexpr 2.3.1
  • numpy 1.9.0
  • numpy 1.9.2
  • openpyxl 1.8.5
  • openssl 1.0.1h
  • openssl 1.0.1k
  • pandas 0.14.1
  • patsy 0.3.0
  • pep8 1.5.7
  • pil 1.1.7
  • pip 1.5.6
  • pixman 0.26.2
  • ply 3.4
  • psutil 2.1.1
  • py 1.4.25
  • py2cairo 1.10.0
  • pycosat 0.6.1
  • pycparser 2.10
  • pycrypto 2.6.1
  • pycurl 7.19.5
  • pyface 4.4.0
  • pyflakes 0.8.1
  • pygments 1.6
  • pyopenssl 0.14
  • pyparsing 2.0.1
  • pyqt 4.10.4
  • pytables 3.1.1
  • pytest 2.6.3
  • python 2.7.8
  • python 2.7.9
  • pytz 2014.7
  • pyyaml 3.11
  • pyzmq 14.3.1
  • qt 4.8.5
  • readline 6.2
  • redis 2.6.9
  • redis-py 2.9.1
  • requests 2.4.1
  • requests 2.6.0
  • rope 0.9.4
  • runipy 0.1.1
  • scikit-image 0.10.1
  • scikit-learn 0.16.0
  • scipy 0.14.0
  • scipy 0.15.1
  • setuptools 5.8
  • sip 4.15.5
  • six 1.8.0
  • sockjs-tornado 1.0.1
  • sphinx 1.2.3
  • spyder 2.3.1
  • spyder-app 2.3.1
  • sqlalchemy 0.9.7
  • sqlite 3.8.4.1
  • ssl_match_hostname 3.4.0.2
  • statsmodels 0.5.0
  • sympy 0.7.5
  • system 5.8
  • theano 0.6.0
  • tk 8.5.15
  • tk 8.5.18
  • toolz 0.7.0
  • tornado 4.0.2
  • traits 4.4.0
  • traitsui 4.4.0
  • ujson 1.33
  • unicodecsv 0.9.4
  • util-linux 2.21
  • werkzeug 0.9.6
  • xlrd 0.9.3
  • xlsxwriter 0.5.7
  • xlwt 0.7.5
  • yaml 0.1.4
  • zeromq 4.0.4
  • zlib 1.2.7
  • zlib 1.2.8