The document discusses the development of new plugins for the TranSMART platform to add genomic visualization capabilities. It describes requirements like adding an HTML5 genome browser and supporting visualization of genomic variants and copy number variation data. It then details the process of consulting the community to choose the Dalliance genome browser and MyDAS backend, and extending the core API to support these plugins. The plugins were implemented and added to TranSMART to provide the new genomic visualization features.

1. TranSMART API &Plugin
Development: A Case Study
TranSMART Community Meeting
Chilly-Mazarin, France
November 6, 2013

2. Requirements
• HTML5 Genome Browser (in-place in UI)
• Drag-n-drop of High-Dimensional Data Nodes
– Visualization of GenomicVariants
– Visualization of CopyNumberVariation Data
• Visualization of public data (gene
annotations, SNP chip coverage, COSMIC
annotationsetc.)
• Switchingbetween genome builds

3. CommunityConsultation
• Asktransmart-discuss mailing list whatpeople are
using / planning to use as genome browser
• Ask the sameon the LinkedIngroup
• Start a wiki topic on the tranSMART Foundation
wikiwithaninventory of pro’s and con’s of the
various genome browsersavailable

4. Solution
•
•
•
•
Dalliance genome browser chosen as frontend
MyDAS was chosen as backend
Both implemented as plugins
Core API had to beextendedwith a few VCFspecificmethods

5. EmergingtranSMARTArchitecture
Kees van Bochove - The Hyve

6. Extend the core API

7. Writesome tests

8. Createsomeimplementingplugins
• https://github.com/thehyve/transmart-mydas
• https://github.com/thehyve/dalliance-plugin
MyDAS Backend Plugin
TranSMART Core API
DB
DallianceFrontendPlugin

9. Addthem to transmartApp
but don’tforceituponothers

10. Leverageother 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
• Itprovedchallenging to
mergebothapproaches, we butsucceeded in
the end
• Generating more docson the wiki!

11. The end result
2. Drag genomic node on genome browser