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Bio js2 short_introduction

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LeylaJael Castro
LeylaJael Castro

This document provides an introduction to BioJS, an open source collection of JavaScript components for visually presenting biological data. It discusses the motivation and history of BioJS, including its evolution from version 1.0 to 2.0. Guidelines for developing BioJS components are presented, focusing on modularity, documentation, and sharing code. Community involvement and the role of Google Summer of Code are also summarized.

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Bi JS Introduction to BioJS Leyla Jael García Castro UniProt, EMBL-EBI 9th November 2014
Bi JS Components Application EMBL-EBI Motivation Discoverability, modularity and reuse Unify efforts, collaborate, avoid duplication
EMBL-EBI Bi JS BioJS at a glance A collection of JavaScript components following a common guideline to 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/biojs Learning: http://edu.biojs.net/ General information: http://biojs.net/ Where
EMBL-EBI From BioJS 1.0 to 2.0 Bi JS • 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
EMBL-EBI Bi JS Development Guidelines • 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
EMBL-EBI Bi JS Development Technology • Highly recommended • Module management • Module dependency • Dependency management  commonJS, require.js • Test suits  choose your preferred one and use it! • Either JavaScript or transpilers
EMBL-EBI Bi JS Development Community • Participate  biojs google groups • Share  submit your modules to BioJS registry
EMBL-EBI BioJS at GSoC Bi JS • 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
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
Thanks to: BioJS project members and collaborators EBI RDF Project

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Bio js2 short_introduction

  • 1. Bi JS Introduction to BioJS Leyla Jael García Castro UniProt, EMBL-EBI 9th November 2014
  • 2. Bi JS Components Application EMBL-EBI Motivation Discoverability, modularity and reuse Unify efforts, collaborate, avoid duplication
  • 3. EMBL-EBI Bi JS BioJS at a glance A collection of JavaScript components following a common guideline to 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/biojs Learning: http://edu.biojs.net/ General information: http://biojs.net/ Where
  • 4. EMBL-EBI From BioJS 1.0 to 2.0 Bi JS • 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
  • 5. EMBL-EBI Bi JS Development Guidelines • 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
  • 6. EMBL-EBI Bi JS Development Technology • Highly recommended • Module management • Module dependency • Dependency management  commonJS, require.js • Test suits  choose your preferred one and use it! • Either JavaScript or transpilers
  • 7. EMBL-EBI Bi JS Development Community • Participate  biojs google groups • Share  submit your modules to BioJS registry
  • 8. EMBL-EBI BioJS at GSoC Bi JS • 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
  • 9. 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
  • 10. Thanks to: BioJS project members and collaborators EBI RDF Project