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Open Source Science

https://github.com/openneuroorg/openneuro

A free and open platform for analyzing and sharing neuroimaging data

https://github.com/openneuroorg/openneuro

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    6 of 37 committers (16.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary

Keywords

bids datasets graphql neuroimaging neuroscience react

Keywords from Contributors

data-standards neuroimaging-data standards fmri brain-imaging mri brainweb quality-control singularity-containers eeg
Last synced: 6 months ago · JSON representation

Repository

A free and open platform for analyzing and sharing neuroimaging data

Basic Info
  • Host: GitHub
  • Owner: OpenNeuroOrg
  • License: mit
  • Language: TypeScript
  • Default Branch: master
  • Homepage: https://openneuro.org/
  • Size: 81.2 MB
Statistics
  • Stars: 129
  • Watchers: 8
  • Forks: 42
  • Open Issues: 173
  • Releases: 214
Topics
bids datasets graphql neuroimaging neuroscience react
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

OpenNeuro

CodeCov Coverage Status styled with prettier

About

OpenNeuro is a free and open platform for analyzing and sharing neuroimaging data. It is based around the Brain Imaging Data Structure specification.

Development setup

This project is managed with Lerna and Yarn. To get started, install Yarn and bootstrap the repo.

shell yarn install

You can run tests with yarn test at the top level of the project. For each package, yarn test --watch will interactively run the tests for changes since the last commit.

Before starting up the services, you will need to copy the example .env.example file to .env and config.env.example to config.env. Many of the values are optional, and most that aren't have default values included in their .example file. Required values below:

  • JWT_SECRET in config.env must be set to a large random string.
  • PERSISTENT_DIR in .env is an absolute path to a directory that will be used to store datasets. This should be a git-annex compatible filesystem and large enough to store some test datasets.

To setup Google as an authentication provider, register a new client app and set the following variables. For development use, you will create a new Google project with oauth credentials for a JavaScript client side app. "Authorized JavaScript Origins" is set to http://localhost:9876 and "Authorized Redirect URIs" is set to http://localhost:9876/crn/auth/google/callback for a site accessible at http://localhost:9876.

```

Ending in .apps.googleusercontent.com

GOOGLECLIENTID=

24 character secret string

GOOGLECLIENTSECRET= ```

podman-compose is used to run a local copy of all required services together.

macOS Development Setup

If you're working on macOS and encounter issues with file watching in Vite, use the following environment variables (in config.env):

CHOKIDAR_USEPOLLING=true

If you're working on macOS and encounter issues with elastic search, use the following environment variables (in config.env):

ES_JAVA_OPTS: -XX:UseSVE=0 CLI_JAVA_OPTS: -XX:UseSVE=0

```shell

This will run podman-compose in the background (-d flag is --detach)

podman-compose up -d ```

For example, you can restart the server container with podman-compose restart server or view logs with podman-compose logs -f --tail=10 server.

Major Components

JavaScript packages are published in the @openneuro npm namespace.

OpenNeuro Command-line utility tool

OpenNeuro supports a CLI tool based on nodejs for uploading and downloading OpenNeuro datasets.

Owner

  • Name: OpenNeuroOrg
  • Login: OpenNeuroOrg
  • Kind: organization

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 10,268
  • Total Committers: 37
  • Avg Commits per committer: 277.514
  • Development Distribution Score (DDS): 0.519
Past Year
  • Commits: 760
  • Committers: 6
  • Avg Commits per committer: 126.667
  • Development Distribution Score (DDS): 0.349
Top Committers
Name Email Commits
Nell Hardcastle n****l@s****m 4,941
Zack Michael z****k@s****m 1,185
Gregory Noack g****k@t****m 1,113
Teal Hobson-Lowther t****l@s****m 756
David Nishikawa d****d@s****m 627
Zack Michael z****k@s****m 472
Xia Amendolara x****a@s****m 263
James Stiehl j****s@s****m 239
Matthew Zito m****o@g****m 132
dependabot[bot] 4****] 113
Christopher J. Markiewicz m****z@s****u 79
Tommy Tran t****y@s****m 62
Ross Blair r****2@s****u 50
constellates c****s 49
Chris Gorgolewski k****i@g****m 38
Matthew m****w@s****m 29
Kate Rountree k****e@s****m 24
Franklin Feingold 3****d 22
Yaroslav Halchenko d****n@o****m 18
anibalsolon a****n@g****m 14
root r****t@d****u 12
zacksqm z****m@d****u 7
Sebastian Urchs s****s@g****m 4
James Stiehl j****s@S****l 3
Adina Wagner a****r@t****e 2
James Stiehl j****l@g****m 2
Tommaso Di Noto t****o@h****t 2
mathiasg m****g@s****u 1
Taylor Hanayik h****k@g****m 1
Stefan Appelhoff s****f@m****g 1
and 7 more...
Committer Domains (Top 20 + Academic)
squishymedia.com: 9 stanford.edu: 3 dev-openfmri.tacc.utexas.edu: 2 nevada.unr.edu: 1 squishymedia.compwd: 1 mailbox.org: 1 hotmail.it: 1 t-online.de: 1 onerussian.com: 1 squishmedia.com: 1 thinknoack.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 362
  • Total pull requests: 849
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 12 days
  • Total issue authors: 70
  • Total pull request authors: 10
  • Average comments per issue: 1.74
  • Average comments per pull request: 1.05
  • Merged pull requests: 665
  • Bot issues: 2
  • Bot pull requests: 210
Past Year
  • Issues: 142
  • Pull requests: 481
  • Average time to close issues: 10 days
  • Average time to close pull requests: 4 days
  • Issue authors: 30
  • Pull request authors: 7
  • Average comments per issue: 0.61
  • Average comments per pull request: 1.06
  • Merged pull requests: 375
  • Bot issues: 0
  • Bot pull requests: 89
View more stats
Top Authors
Issue Authors
  • effigies (117)
  • nellh (64)
  • yarikoptic (33)
  • thinknoack (17)
  • franklin-feingold (14)
  • ckrountree (13)
  • tsalo (8)
  • jbwexler (7)
  • alexrockhill (5)
  • bpinsard (4)
  • ericearl (4)
  • larsoner (3)
  • jcohenadad (3)
  • Arshitha (3)
  • jpeelle (2)
Pull Request Authors
  • nellh (464)
  • dependabot[bot] (210)
  • thinknoack (98)
  • effigies (53)
  • yarikoptic (12)
  • hanayik (4)
  • mgxd (3)
  • magland (2)
  • surchs (2)
  • ehavener (1)
Top Labels
Issue Labels
bug (185) Tracking (18) feature (15) UI/UX (7) documentation (4) enhancement (4) Maintenance (2) idea (2) performance (1) reported by external user (1) mobile (1) Search (1) Paused (1) dependencies (1) python (1)
Pull Request Labels
dependencies (208) javascript (108) python (86) github_actions (14)

Packages

  • Total packages: 12
  • Total downloads:
    • npm 5,412 last-month
  • Total dependent packages: 24
    (may contain duplicates)
  • Total dependent repositories: 25
    (may contain duplicates)
  • Total versions: 2,791
  • Total maintainers: 4
npmjs.org: @openneuro/client

OpenNeuro shared client library.

  • Versions: 254
  • Dependent Packages: 4
  • Dependent Repositories: 3
  • Downloads: 693 Last month
Rankings
Downloads: 3.4%
Dependent packages count: 4.5%
Forks count: 4.6%
Average: 4.8%
Stargazers count: 5.2%
Dependent repos count: 6.4%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: @openneuro/search

OpenNeuro search client functions.

  • Versions: 190
  • Dependent Packages: 3
  • Dependent Repositories: 3
  • Downloads: 832 Last month
Rankings
Downloads: 3.9%
Forks count: 4.6%
Stargazers count: 5.2%
Average: 5.2%
Dependent packages count: 5.9%
Dependent repos count: 6.4%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: @openneuro/components

OpenNeuro component library and Storybook configuration

  • Versions: 264
  • Dependent Packages: 2
  • Dependent Repositories: 3
  • Downloads: 600 Last month
Rankings
Downloads: 3.5%
Forks count: 4.6%
Stargazers count: 5.2%
Average: 5.7%
Dependent repos count: 6.4%
Dependent packages count: 8.8%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: @openneuro/server

Core service for the OpenNeuro platform.

  • Versions: 287
  • Dependent Packages: 2
  • Dependent Repositories: 3
  • Downloads: 879 Last month
Rankings
Downloads: 3.5%
Forks count: 4.6%
Stargazers count: 5.2%
Average: 5.7%
Dependent repos count: 6.4%
Dependent packages count: 8.8%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: @openneuro/cli

OpenNeuro command line uploader / editor.

  • Versions: 255
  • Dependent Packages: 2
  • Dependent Repositories: 3
  • Downloads: 302 Last month
Rankings
Downloads: 3.6%
Forks count: 4.6%
Stargazers count: 5.2%
Average: 5.7%
Dependent repos count: 6.4%
Dependent packages count: 8.8%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: openneuro-client

OpenNeuro shared client library.

  • Versions: 176
  • Dependent Packages: 4
  • Dependent Repositories: 1
  • Downloads: 176 Last month
Rankings
Dependent packages count: 4.5%
Forks count: 4.6%
Stargazers count: 5.2%
Average: 6.3%
Downloads: 7.0%
Dependent repos count: 10.3%
Maintainers (3)
chrisfilo nellh danish808
Last synced: 6 months ago
npmjs.org: openneuro-cli

OpenNeuro command line uploader / editor.

  • Versions: 191
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 167 Last month
Rankings
Forks count: 4.6%
Stargazers count: 5.2%
Average: 7.7%
Dependent packages count: 8.9%
Downloads: 9.3%
Dependent repos count: 10.3%
Maintainers (3)
chrisfilo nellh danish808
Last synced: 6 months ago
npmjs.org: @openneuro/app

React JS web frontend for the OpenNeuro platform.

  • Versions: 287
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 806 Last month
Rankings
Downloads: 3.7%
Forks count: 4.6%
Stargazers count: 5.2%
Dependent repos count: 6.4%
Average: 8.2%
Dependent packages count: 20.9%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: @openneuro/indexer

OpenNeuro elastic search indexing tool

  • Versions: 287
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 943 Last month
Rankings
Downloads: 3.7%
Forks count: 4.6%
Stargazers count: 5.2%
Dependent repos count: 6.4%
Average: 8.2%
Dependent packages count: 20.9%
Maintainers (2)
nellh rblair
Last synced: 6 months ago
npmjs.org: openneuro-server

Core service for the OpenNeuro platform.

  • Versions: 229
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Forks count: 4.6%
Stargazers count: 5.2%
Downloads: 6.2%
Average: 9.5%
Dependent repos count: 10.3%
Dependent packages count: 21.0%
Maintainers (3)
chrisfilo nellh danish808
Last synced: 6 months ago
npmjs.org: openneuro-app

React JS web frontend for the OpenNeuro platform.

  • Versions: 236
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 1 Last month
Rankings
Forks count: 4.6%
Stargazers count: 5.2%
Downloads: 8.5%
Average: 9.9%
Dependent repos count: 10.3%
Dependent packages count: 21.0%
Maintainers (3)
chrisfilo nellh danish808
Last synced: 6 months ago
npmjs.org: openneuro-indexer

OpenNeuro elastic search indexing tool

  • Versions: 135
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 6 Last month
Rankings
Forks count: 5.7%
Stargazers count: 7.5%
Downloads: 9.8%
Average: 12.9%
Dependent packages count: 16.2%
Dependent repos count: 25.3%
Maintainers (1)
nellh
Last synced: 6 months ago

Dependencies

package.json npm
  • @babel/core ^7.13.15 development
  • @babel/plugin-proposal-class-properties ^7.13.0 development
  • @babel/plugin-proposal-object-rest-spread ^7.13.8 development
  • @babel/plugin-proposal-optional-chaining ^7.13.12 development
  • @babel/plugin-syntax-dynamic-import ^7.8.3 development
  • @babel/plugin-transform-runtime ^7.13.15 development
  • @babel/preset-env ^7.13.15 development
  • @babel/preset-react ^7.13.13 development
  • @babel/preset-typescript ^7.13.0 development
  • @babel/runtime-corejs3 ^7.13.10 development
  • @loadable/babel-plugin ^5.13.2 development
  • @sentry/cli 1.37.4 development
  • @testing-library/jest-dom ^5.14.1 development
  • @types/babel__core ^7 development
  • @types/babel__plugin-transform-runtime ^7 development
  • @types/babel__preset-env ^7 development
  • @types/jest ^26.0.23 development
  • @types/testing-library__jest-dom ^5 development
  • @typescript-eslint/eslint-plugin ^4.19.0 development
  • @typescript-eslint/parser ^4.19.0 development
  • @yarnpkg/pnpify ^3.1.1-rc.8 development
  • babel-eslint 10.0.3 development
  • codecov 3.8.3 development
  • core-js ^3.3.2 development
  • eslint 7.23.0 development
  • eslint-config-prettier ^8.1.0 development
  • eslint-plugin-import ^2.22.1 development
  • eslint-plugin-prettier ^3.3.1 development
  • eslint-plugin-react ^7.23.1 development
  • eslint-plugin-react-hooks ^4.2.0 development
  • graphql 14.7.0 development
  • history 5.2.0 development
  • husky 5.1.1 development
  • jest 27.5.1 development
  • lerna 3.20.2 development
  • lint-staged ^10.5.4 development
  • pinst ^2.1.6 development
  • prettier ^2.2.1 development
  • react 17.0.2 development
  • ts-jest 27.1.4 development
  • tsc-watch ^4.2.9 development
  • typescript 4.5.4 development
  • @elastic/apm-rum-react ^1.4.0
packages/openneuro-app/package.json npm
  • @babel/core ^7.6.4 development
  • @babel/plugin-proposal-class-properties ^7.5.5 development
  • @babel/plugin-proposal-object-rest-spread ^7.6.2 development
  • @babel/plugin-proposal-optional-chaining ^7.6.0 development
  • @babel/plugin-syntax-dynamic-import ^7.2.0 development
  • @babel/plugin-transform-runtime ^7.6.2 development
  • @babel/preset-env ^7.6.3 development
  • @babel/preset-react ^7.6.3 development
  • @babel/preset-typescript ^7.7.4 development
  • @babel/runtime ^7.6.3 development
  • @babel/runtime-corejs3 ^7.13.10 development
  • @jest/globals ^26.6.2 development
  • @loadable/babel-plugin ^5.10.3 development
  • @testing-library/jest-dom ^5.11.4 development
  • @testing-library/react ^11.1.0 development
  • @types/jest ^26.0.22 development
  • @types/jsdom ^16 development
  • @types/node 16.11.13 development
  • @types/react ^17.0.8 development
  • @types/react-dom ^17.0.5 development
  • @types/react-router-dom 5.1.8 development
  • @types/testing-library__jest-dom ^5.14.0 development
  • @types/uuid ^8 development
  • babel-core ^7.0.0-bridge.0 development
  • babel-jest ^24.9.0 development
  • esbuild-plugin-globals ^0.1.1 development
  • jest 27.5.1 development
  • jest-fetch-mock ^1.4.1 development
  • jsdom ^16.5.3 development
  • object.fromentries ^2.0.0 development
  • rollup-plugin-polyfill-node ^0.9.0 development
  • sass ^1.32.8 development
  • stream-browserify ^3.0.0 development
  • typescript 4.5.4 development
  • vite 2.9.7 development
  • @apollo/client 3.4.17
  • @artsy/fresnel ^1.3.1
  • @elastic/apm-rum 5.11.0
  • @emotion/react 11.6.0
  • @emotion/styled 11.6.0
  • @niivue/niivue 0.23.1
  • @openneuro/client ^4.9.2
  • @openneuro/components ^4.9.2
  • babel-runtime ^6.26.0
  • bids-validator 1.9.3
  • bytes ^3.0.0
  • comlink ^4.0.5
  • core-js ^3.3.2
  • cross-fetch ^3.1.4
  • date-fns ^2.16.1
  • draft-js ^0.11.7
  • email-validator ^2.0.4
  • express ^4.17.1
  • graphql 14.7.0
  • history 5.2.0
  • jwt-decode ^2.2.0
  • markdown-to-jsx ^7.1.2
  • nifti-reader-js ^0.5.4
  • os-browserify ^0.3.0
  • pluralize 8.0.0
  • prop-types ^15.6.0
  • react ^17.0.1
  • react-cookie 4.0.3
  • react-copy-to-clipboard ^5.0.1
  • react-dom ^17.0.1
  • react-helmet 6.1.0
  • react-multi-carousel ^2.6.3
  • react-router 5.2.0
  • react-router-dom 5.2.0
  • react-spring ^8.0.27
  • react-toastify 6.0.9
  • react-usestateref ^1.0.5
  • react-virtualized remorses/react-virtualized-fixed-import.git#9.22.3
  • resize-observer-polyfill ^1.5.1
  • semver ^5.5.0
  • subscriptions-transport-ws ^0.9.9
  • universal-cookie ^4.0.4
  • universal-cookie-express ^4.0.3
  • uuid ^8.3.2
  • xmldoc ^1.1.0
.github/workflows/docs.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • peaceiris/actions-gh-pages v3 composite
Dockerfile docker
  • node 18.17.1-bullseye build
docker-compose.yml docker
  • docker.elastic.co/elasticsearch/elasticsearch 7.16.1
  • mongo 5.0
  • nginx 1.16.1
  • node 18.17.1-bullseye
  • redis alpine
packages/openneuro-app/Dockerfile docker
  • nginx alpine build
  • openneuro/node latest build
.yarn/sdks/eslint/package.json npm
.yarn/sdks/prettier/package.json npm
.yarn/sdks/typescript/package.json npm
docs/requirements.txt pypi
  • furo >=2022.9.15
  • myst-parser >=0.18.1
  • pygments-graphql-lexer >=0.1.0
  • sphinx >=5.2.2
  • sphinx-copybutton >=0.5.0
  • sphinxext-rediraffe >=0.2.7