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Introduction to BioJSLeyla Jael García Castro
UniProt, EMBL-EBI
9th November 2014
Bi JS
EMBL-EBI
Components Application
MotivationDiscoverability, modularity and reuse
Unify efforts, collaborate, avoid duplication
Bi JS
EMBL-EBI
BioJS at a glanceBi JS
A collection of JavaScript componentsfollowing a common guidelineto visually present biological
What
When• Jan 2014 – F1000 collection• May/Aug 2014 – Google Summer of Code• July 2014 – BioJS 2.0 release
• Aug 2011 – Student project• Dec 2012 – BioJS 1.0 at EBI• Feb 2013 – AppNote in Bioinformatics
Community of developers and collaborators
Who
Development: https://github.com/biojs/biojsLearning: http://edu.biojs.net/
General information: http://biojs.net/Where
EMBL-EBI
From BioJS 1.0 to 2.0• BioJS 1.0
– Fixed core Inheritance and event model– Built process with jsdoc + maven not working for everybody– Not compatible with common module and dependency management
tools
• BioJS 2.0– No core but guidelines + event module– Better support for module and dependency management– Developers are free to use their preferred technologies
Bi JS
EMBL-EBI
• Make it simple one thing at a time
• Use modules separate retrieval, process, visualization
• Document code and examples
• Make it open GitHub
• Share publish your modules as a Node Packaged Module
Guidelines
Bi JS Development
EMBL-EBI
Bi JS
• Highly recommended
• Module management
• Module dependency
• Dependency management commonJS, require.js
• Test suits choose your preferred one and use it!
• Either JavaScript or transpilers
DevelopmentTechnology
EMBL-EBI
Bi JS Development
• Participate biojs google groups
• Share submit your modules to BioJS registry
Community
EMBL-EBI
BioJS at GSoC
• GSoC is a program designed to – Encourage students participation in open source software
development. – Inspire young developers to begin participating in open source
development– Get more open source code created and released for the benefit of all
• What does it mean for BioJS?– Ideal way to explore potential new ideas or bring ideas into production– Getting more people involved– First participation 2014
• 5 successful projects Genetic variations, proteome taxonomy, BAM file, MSA, phylogenetic tree
• BioJS 2.0 initiative
8
Bi JS
EMBL-EBI
• Links across datasets VoID linksets– Gray A., Jupp S., Malone J. Competency driven linksets of
convenience– From an ENSEMBL protein, which entities in other datasets
can I reach?
• Path finder across multiple datasets– Improve idea– Path finder algorithm– Visualization draft
BioJS project members and collaborators
EBI RDF Project
Thanks to: