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seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

https://github.com/seek4science/seek

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
    Links to: science.org, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary

Keywords

biohackcovid20 data datamanagement fair isa opendata publication science semantic-web synthetic-biology systems-biology
Last synced: 6 months ago · JSON representation

Repository

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

Basic Info
  • Host: GitHub
  • Owner: seek4science
  • License: bsd-3-clause
  • Language: Ruby
  • Default Branch: main
  • Homepage: http://www.seek4science.org
  • Size: 434 MB
Statistics
  • Stars: 89
  • Watchers: 22
  • Forks: 55
  • Open Issues: 423
  • Releases: 55
Topics
biohackcovid20 data datamanagement fair isa opendata publication science semantic-web synthetic-biology systems-biology
Created over 11 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing Citation

README.md

Build Status DOI

FAIRDOM-SEEK

License

Copyright 2009-2023, University of Manchester and HITS gGmbH

BSD 3-clause

About FAIRDOM-SEEK

The FAIRDOM-SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets,models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology.

FAIRDOM-SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users.

For an example of FAIRDOM-SEEK please visit our Demo.

To see FAIRDOM-SEEK being used for real science, as part of FAIRDOM please visit FAIRDOMHub

For more information please visit: SEEK for Science

FAIRDOM

FAIRDOM-SEEK is being developed and funded as part of the FAIRDOM initiative. For more information please visit: FAIRDOM.

Installation

We recommend installing FAIRDOM-SEEK on Debian or Ubuntu.

To install the latest release please visit: SEEK install guide

For details about other distributions and installing on macOS please visit: Other distributions guide

The documentation is available in its own repository: seek-documentation.

Contacting Us

For details about how to contact us, to raise bugs or offer suggestion, please visit Contacting Us

Contributing to FAIRDOM-SEEK

In general :

  1. Fork it ( https://github.com/seek4science/seek/fork )
  2. Create your feature branch (git checkout -b my-new-feature)
  3. Commit your changes (git commit -am 'Add some feature')
  4. Push to the branch (git push origin my-new-feature)
  5. Create a new Pull Request

For more details on how and what you can contribute to SEEK please visit Contributing

Owner

  • Name: FAIRDOM-SEEK
  • Login: seek4science
  • Kind: organization

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 274
  • Total pull requests: 296
  • Average time to close issues: 6 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 38
  • Total pull request authors: 15
  • Average comments per issue: 0.59
  • Average comments per pull request: 0.15
  • Merged pull requests: 213
  • Bot issues: 0
  • Bot pull requests: 36
Past Year
  • Issues: 110
  • Pull requests: 146
  • Average time to close issues: 16 days
  • Average time to close pull requests: 5 days
  • Issue authors: 20
  • Pull request authors: 10
  • Average comments per issue: 0.32
  • Average comments per pull request: 0.1
  • Merged pull requests: 98
  • Bot issues: 0
  • Bot pull requests: 22
View more stats
Top Authors
Issue Authors
  • stuzart (98)
  • kdp-cloud (36)
  • fbacall (32)
  • floradanna (23)
  • whomingbird (17)
  • OlgaKrebs (7)
  • AndrewWood94 (7)
  • NielsGeudens (6)
  • fmeineke (6)
  • anneelinh (4)
  • rabuono (4)
  • somathias (3)
  • jjkoehorst (3)
  • hexylena (2)
  • Linus4 (2)
Pull Request Authors
  • stuzart (101)
  • kdp-cloud (63)
  • fbacall (56)
  • dependabot[bot] (36)
  • whomingbird (25)
  • AndrewWood94 (5)
  • somathias (2)
  • elichad (1)
  • davidcalfran8 (1)
  • jjkoehorst (1)
  • fherreazcue (1)
  • hexylena (1)
  • floradanna (1)
  • Menjabin (1)
  • PhilReedData (1)
Top Labels
Issue Labels
bug (66) datahub (39) bioindustry (21) enhancement (20) workflowhub (16) samples (11) api (6) extended metadata (4) documentation (4) publication (3) UX (3) cv-ontology (2) custom metadata (2) search (2) investigate (1)
Pull Request Labels
dependencies (35) ruby (35) bug (33) datahub (15) enhancement (5) bioindustry (5) documentation (4) workflowhub (3)

Dependencies

.github/workflows/ansible-install.yml actions
  • actions/checkout v3 composite
  • technote-space/workflow-conclusion-action v3.0.3 composite
  • mysql 8.0.21 docker
.github/workflows/docker-image.yml actions
  • actions/checkout v2 composite
.github/workflows/tests.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
  • actions/setup-python v4 composite
  • ruby/setup-ruby v1 composite
  • mysql 5.7 docker
  • postgres 11 docker
  • tenforce/virtuoso * docker
Dockerfile docker
  • ruby 2.7-buster build
docker-compose-relative-root.yml docker
  • fairdom/seek 1.13
  • fairdom/seek-solr 8.11
  • mysql 5.7
docker-compose-virtuoso.yml docker
  • fairdom/seek 1.13
  • fairdom/seek-solr 8.11
  • mysql 5.7
  • tenforce/virtuoso latest
docker-compose-with-email.yml docker
  • eeacms/postfix latest
  • fairdom/seek 1.13
  • fairdom/seek-solr 8.11
  • mysql 5.7
docker-compose.yml docker
  • fairdom/seek 1.13
  • fairdom/seek-solr 8.11
  • mysql 5.7
Gemfile rubygems
  • better_errors >= 0 development
  • binding_of_caller >= 0 development
  • database_cleaner ~> 1.7.0 development
  • gem-licenses >= 0 development
  • listen ~> 3.3 development
  • magic_lamp >= 0 development
  • minitest ~> 5.14 development
  • minitest-reporters >= 0 development
  • pry >= 0 development
  • pry-doc >= 0 development
  • pry-remote >= 0 development
  • rack-mini-profiler ~> 2.0 development
  • rails-controller-testing >= 0 development
  • rails-perftest >= 0 development
  • rails_best_practices >= 0 development
  • request-log-analyzer >= 0 development
  • rubocop >= 0 development
  • ruby-prof >= 0 development
  • simplecov >= 0 development
  • sunspot_matchers >= 0 development
  • teaspoon >= 0 development
  • teaspoon-mocha >= 0 development
  • test-prof >= 0 development
  • vcr ~> 2.9 development
  • web-console >= 4.1.0 development
  • webdrivers >= 0 development
  • webmock >= 0 development
  • whenever-test >= 0 development
  • RedCloth >= 4.3.0
  • active_model_serializers ~> 0.10.13
  • activerecord-import >= 0
  • activerecord-session_store >= 0
  • acts-as-taggable-on >= 0
  • acts_as_list >= 0
  • acts_as_tree >= 0
  • addressable >= 0
  • api_smith >= 0
  • attr_encrypted ~> 3.0.0
  • auto_strip_attributes >= 0
  • bibtex-ruby ~> 5.1.0
  • bio ~> 1.5.1
  • bioportal >= 3.0
  • bives ~> 2.0
  • bootsnap >= 1.4.4
  • bootstrap-sass >= 3.4.1
  • bundler >= 1.8.4
  • cff ~> 0.9.0
  • citeproc-ruby ~> 2.0.0
  • coffee-rails ~> 4.2
  • commonmarker >= 0
  • country_select >= 0
  • csl-styles ~> 2.0.0
  • daemons = 1.1.9
  • delayed_job_active_record >= 0
  • docsplit >= 0
  • doi_query_tool >= 0
  • doorkeeper >= 5.2.5
  • dotenv-rails ~> 2.7.6
  • equivalent-xml >= 0
  • exception_notification >= 0
  • factory_girl = 2.6.4
  • feedjira ~> 1
  • fleximage >= 0
  • fssm >= 0
  • gitlab_omniauth-ldap ~> 2.2.0
  • google-analytics-rails >= 0
  • handlebars_assets >= 0
  • hpricot ~> 0.8.2
  • i18n-js >= 0
  • indefinite_article >= 0
  • jbuilder ~> 2.7
  • jbuilder-json_api >= 0
  • jquery-rails ~> 4.2.2
  • jquery-ui-rails >= 0
  • json-schema >= 0
  • libreconv >= 0
  • libxml-ruby ~> 2.9.0
  • linkeddata ~> 3.2.0
  • lograge >= 0
  • loofah >= 0
  • mechanize >= 0
  • metainspector >= 0
  • mimemagic ~> 0.3.7
  • my_responds_to_parent >= 0
  • mysql2 >= 0
  • nokogiri ~> 1.13.10
  • omniauth ~> 2.1.0
  • omniauth-github >= 0
  • omniauth-rails_csrf_protection >= 0
  • omniauth_openid_connect >= 0
  • open4 >= 0
  • openid_connect = 1.3.0
  • openseek-api >= 0
  • passenger >= 0
  • pg >= 0
  • pothoven-attachment_fu >= 0
  • private_address_check >= 0
  • progress_bar >= 0
  • psych >= 0
  • puma ~> 5.6
  • rack-attack ~> 6.6.0
  • rack-cors >= 0
  • rails ~> 6.1.7
  • rails-html-sanitizer >= 0
  • rails-observers >= 0
  • rails-static-router >= 0
  • rails_autolink >= 0
  • ransack >= 0
  • rdf-virtuoso >= 0.2.0
  • rdoc >= 0
  • recaptcha ~> 4.1.0
  • remotipart ~> 1.4.4
  • request_store >= 0
  • responders >= 0
  • rest-client ~> 2.0
  • rfc-822 >= 0
  • rmagick = 2.15.2
  • ro-bundle ~> 0.3.0
  • ro-crate ~> 0.5.1
  • rspec-rails ~> 5.1
  • rubyzip >= 0
  • rugged >= 0
  • sample-template-generator ~> 0.5
  • sass-rails >= 6
  • savon = 1.1.0
  • seedbank >= 0
  • simple-spreadsheet-extractor ~> 0.17.0
  • sprockets-rails >= 0
  • sqlite3 ~> 1.4
  • stringio = 0.1.0
  • sunspot_rails >= 0
  • terrapin >= 0
  • terser ~> 1.1, >= 1.1.1
  • unicorn-rails >= 0
  • uuid ~> 2.3
  • validate_url >= 0
  • whenever ~> 1.0.0
  • will_paginate ~> 3.1
  • yaml_db >= 0
  • zenodo-client >= 0
Gemfile.lock rubygems
  • 345 dependencies
docker-compose.build.yml docker
requirements.txt pypi
  • cwltool ==3.1.20230601100705
  • galaxy2cwl ==0.1.4
  • gxformat2 ==0.15.0
  • html5lib ==1.0.1
  • ipython ==8.10.0
  • nbconvert ==7.4.0
  • psutil ==5.9.3
test/fixtures/git/blank-repository/_git/description cran
test/fixtures/git/fixture-workflow/_git/description cran
test/fixtures/git/galaxy-sort-change-case/_git/description cran
test/fixtures/git/galaxy-sort-change-case-remote/_git/description cran
test/fixtures/git/local-fixture-workflow/_git/description cran
test/fixtures/git/nf-core-rnaseq/_git/description cran
test/fixtures/files/workflows/rp2/tools/RetroPath2-cwl/Dockerfile docker
  • ibisba/knime-workflow-base 3.6.2-1 build
test/fixtures/files/workflows/rp2/tools/rp2paths-cwl/Dockerfile docker
  • conda/miniconda3 latest build
  • scratch latest build