TranSMART API & Plugin Development: A Case Study

TranSMART Community MeetingChilly-Mazarin, France

November 6, 2013

Requirements

• HTML5 Genome Browser (in-place in UI)• Drag-n-drop of High-Dimensional Data Nodes– Visualization of Genomic Variants– Visualization of Copy Number Variation Data

• Visualization of public data (gene annotations, SNP chip coverage, COSMIC annotations etc.)

• Switching between genome builds

Community Consultation• 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 Foundation

wiki with an inventory of pro’s and con’s of the various genome browsers available

Solution

• Dalliance genome browser chosen as frontend• MyDAS was chosen as backend• Both implemented as plugins• Core API had to be extended with a few VCF-

specific methods

Kees van Bochove - The Hyve

Emerging tranSMART Architecture

Extend the core API

Write some tests

Create some implementing plugins

• https://github.com/thehyve/transmart-mydas• https://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• Implementing VCF loading (and viewing) and

GWAS loading and viewing in tranSMART• VCF loader taken from GWAS Pfizer branch• Also, variant definitions (SNP loading) were

present in the J&J branch• It proved challenging to merge both

approaches, we but succeeded in the end• Generating more docs on the wiki!

2. Drag genomic node on genome browser

The end result