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aquarium

The Aquarium Lab Operating System

https://github.com/aquariumbio/aquarium

Science Score: 26.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

biology lab lims molecular protocols
Last synced: 6 months ago · JSON representation

Repository

The Aquarium Lab Operating System

Basic Info
Statistics
  • Stars: 67
  • Watchers: 16
  • Forks: 15
  • Open Issues: 291
  • Releases: 31
Topics
biology lab lims molecular protocols
Created over 12 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Zenodo

README.md

AQUARIUM : The Laboratory Operating System

Aquarium allows a researcher to specify precisely how to perform an experimental protocol so that lab personnel will run the protocol the same way, every time.

Protocols, written in a Ruby DSL called Krill, encode how to manipulate Aquarium's inventory system (LIMS), compute formulae such as volumes, molarities, temperatures, and timing, as well as present lab technicians with images and detailed instructions. Protocols define formal unit operation types with typed inputs and outputs – allowing the researcher to construct a complex workflow by linking an output sample of one protocol to an input of another using the Aquarium graphical workflow designer.

Protocols and processes are scheduled and presented to technicians on touchscreen monitors placed throughout the lab. Every step is logged: who performed the step, which items were used, what data was gathered by which instruments, and how long it took -- data that can be used to debug and improve the experiment. More importantly, Aquarium provides a complete, executable description of the results obtained – one that could be used by another lab running Aquarium to reproduce the result.

Aquarium is the operating system of the UW BIOFAB, a service of the Klavins Lab at the University of Washington.

Users

Users should start at the "Getting Started" page of aquaverse

Developers

Developers should start with the developer documentation.

Owner

  • Name: Aquarium.bio
  • Login: aquariumbio
  • Kind: organization

Home of the Aquarium lab automation project

GitHub Events

Total
  • Watch event: 7
  • Push event: 16
  • Pull request event: 15
  • Create event: 16
Last Year
  • Watch event: 7
  • Push event: 16
  • Pull request event: 15
  • Create event: 16

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 11
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 11
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • 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
Pull Request Authors
  • bjkeller (20)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

components/aquadoc/lib/assets/bower.json bower
  • bootstrap latest
  • github-markdown-css latest
  • highlight latest
  • jquery latest
  • markdown-it latest
package.json npm
  • @bower_components/ace-builds ajaxorg/ace-builds#*
  • @bower_components/angular angular/bower-angular#1.7.7
  • @bower_components/angular-animate angular/bower-angular-animate#1.4 - 1.7.0 || ^1.7.2
  • @bower_components/angular-aria angular/bower-angular-aria#1.4 - 1.7.0 || ^1.7.2
  • @bower_components/angular-cookies angular/bower-angular-cookies#*
  • @bower_components/angular-material angular/bower-material#~1.1.3
  • @bower_components/angular-material-icons klarsys/angular-material-icons#*
  • @bower_components/angular-messages angular/bower-angular-messages#1.4 - 1.7.0 || ^1.7.2
  • @bower_components/angular-resource angular/bower-angular-resource#*
  • @bower_components/blueimp-canvas-to-blob blueimp/JavaScript-Canvas-to-Blob#>=2.1.1
  • @bower_components/blueimp-load-image blueimp/JavaScript-Load-Image#>=1.13.0
  • @bower_components/blueimp-tmpl blueimp/JavaScript-Templates#>=2.5.4
  • @bower_components/bootstrap-css jozefizso/bower-bootstrap-css#2.3.2
  • @bower_components/datatables.net DataTables/Dist-DataTables#*
  • @bower_components/github-markdown-css sindresorhus/github-markdown-css#*
  • @bower_components/jquery jquery/jquery-dist#>=1.6
  • @bower_components/jquery-autocomplete trendalytics/bower-jquery-autocomplete#*
  • @bower_components/jquery-cookie carhartl/jquery-cookie#*
  • @bower_components/jquery-file-upload blueimp/jQuery-File-Upload#*
  • @bower_components/jquery-ui components/jqueryui#*
  • @bower_components/jquery-ujs rails/jquery-ujs#*
  • @bower_components/lodash lodash/lodash#*
  • @bower_components/markdown-it markdown-it/markdown-it#*
  • @bower_components/should shouldjs/should.js#*
  • @bower_components/underscore jashkenas/underscore#*
ui/package.json npm
  • cypress ^3.1.0 development
yarn.lock npm
  • @bower_components/ace-builds 1.4.12
  • @bower_components/angular 1.7.7
  • @bower_components/angular-animate 1.8.2
  • @bower_components/angular-aria 1.8.2
  • @bower_components/angular-cookies 1.8.2
  • @bower_components/angular-material 1.1.26
  • @bower_components/angular-material-icons 0.7.1
  • @bower_components/angular-messages 1.8.2
  • @bower_components/angular-resource 1.8.2
  • @bower_components/blueimp-canvas-to-blob 3.28.0
  • @bower_components/blueimp-load-image 5.14.0
  • @bower_components/blueimp-tmpl 3.19.0
  • @bower_components/bootstrap-css 0.0.0
  • @bower_components/datatables.net 1.10.25
  • @bower_components/github-markdown-css 4.0.0
  • @bower_components/jquery 3.6.0
  • @bower_components/jquery-autocomplete 0.0.0
  • @bower_components/jquery-cookie 1.4.1
  • @bower_components/jquery-file-upload 10.31.0
  • @bower_components/jquery-ui 1.12.1
  • @bower_components/jquery-ujs 1.2.3
  • @bower_components/lodash 4.17.21
  • @bower_components/markdown-it 12.1.0
  • @bower_components/should 13.2.3
  • @bower_components/underscore 1.13.1
  • angular 1.8.2
  • argparse 2.0.1
  • blueimp-canvas-to-blob 3.28.0
  • blueimp-load-image 5.14.0
  • blueimp-tmpl 3.19.0
  • entities 2.1.0
  • jquery 3.6.0
  • linkify-it 3.0.2
  • mdurl 1.0.1
  • should-equal 2.0.0
  • should-format 3.0.3
  • should-type 1.4.0
  • should-type-adaptors 1.1.0
  • should-util 1.0.1
  • uc.micro 1.0.6
Gemfile rubygems
  • factory_bot_rails >= 5.2.0 development
  • ipaddress >= 0 development
  • rspec-rails >= 4.1.2 development
  • rspec-sorbet >= 0 development
  • rubocop >= 0 development
  • rubocop-rails >= 0 development
  • rubocop-sorbet >= 0 development
  • simplecov >= 0 development
  • sorbet >= 0 development
  • web-console ~> 3.3, >= 3.3.0 development
  • yard >= 0.9.20 development
  • yard-activerecord >= 0 development
  • activerecord-import >= 0
  • activerecord-nulldb-adapter >= 0
  • alphabetical_paginate >= 0
  • anemone >= 0
  • angular_rails_csrf = 2.1.1
  • aquadoc >= 0
  • aws-sdk >= 1.67.0, < 2.0
  • aws-sdk-s3 >= 0
  • aws-sdk-ses >= 0
  • bcrypt ~> 3.1
  • closure-compiler >= 0
  • mimemagic >= 0.3.10
  • mysql2 ~> 0.5.2
  • oj >= 0
  • paperclip ~> 6.1, >= 6.1.0
  • protected_attributes_continued >= 0
  • puma >= 0
  • rack-cors ~> 1.0.5
  • rails = 4.2.11.3
  • redcarpet >= 3.5.1
  • ruby-units >= 0
  • sassc-rails >= 2.1.2
  • sorbet-rails = 0.5.6
  • sorbet-runtime >= 0
  • tzinfo-data >= 0
  • where-or >= 0
  • will_paginate >= 0
Gemfile.lock rubygems
  • 123 dependencies
components/anemone/Gemfile rubygems
  • minitest >= 0
  • test-unit >= 0
components/anemone/anemone.gemspec rubygems
  • sqlite3 >= 0 development
  • rails = 4.2.11.3
components/aquadoc/aquadoc.gemspec rubygems
  • octokit ~> 4.15
  • yard ~> 0.9.20
Dockerfile docker
  • aquarium-development latest build
  • ruby ${RUBY_VERSION}-alpine${ALPINE_VERSION} build
components/aquadoc/env/Dockerfile docker
  • ubuntu 20 build
docker-compose.override.yml docker
  • aquarium-development latest
docker-compose.production.yml docker
  • aquariumbio/aquarium ${AQUARIUM_VERSION}
docker-compose.selenium.yml docker
  • selenium/standalone-chrome-debug latest
docker-compose.yml docker
  • minio/mc RELEASE.2020-11-25T23-04-07Z
  • minio/minio edge
  • mysql 5.7
  • nginx stable-alpine