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TranSMART API & Plugin Development: A case study. Presentation at the tranSMART community meeting in Chilly-Mazarin at Sanofi R&D in November 2013.
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TranSMART API & Plugin Development: A Case Study
Kees van Bochove, The Hyve TranSMART Community MeeCng
Chilly-‐Mazarin, France
November 6, 2013
Requirements
• HTML5 Genome Browser (in-‐place in UI) • Drag-‐n-‐drop of High-‐Dimensional Data Nodes – VisualizaCon of Genomic Variants
– VisualizaCon of Copy Number VariaCon Data
• VisualizaCon of public data (gene annotaCons, SNP chip coverage, COSMIC annotaCons etc.)
• Switching between genome builds
Community ConsultaCon • Ask transmart-‐discuss mailing list what people are using / planning to use as genome browser
• Ask the same on the LinkedIn group
• Start a wiki topic on the tranSMART FoundaCon wiki with an inventory of pro’s and con’s of the various genome browsers available
SoluCon
• Dalliance genome browser chosen as frontend • MyDAS was chosen as backend
• Both implemented as plugins
• Core API had to be extended with methods for retrieving genomic variant data
Emerging tranSMART Architecture
Kees van Bochove -‐ The Hyve
Extend the core API
Write some tests
Create some implemenCng plugins
• h`ps://github.com/thehyve/transmart-‐mydas • h`ps://github.com/thehyve/dalliance-‐plugin
DB
MyDAS Backend Plugin Dalliance Frontend Plugin
TranSMART Core API
Add them to transmartApp
but don’t force it upon others
Leverage other branches • ImplemenCng VCF loading (and viewing) and GWAS loading and viewing in tranSMART
• VCF loader scripts requested by email and ported to Postgres
• Also, conflicCng variant definiCons (SNP loading) were present in the J&J branch
• It proved challenging to merge both approaches, but we succeeded in the end
• GeneraCng more docs on the wiki!
2. Drag genomic node on genome browser
The end result