tranSMART Community Meeting 5-7 Nov 13 - Session 3: Modularization (Plug‐Ins, APIs)
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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.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: Modularization (Plug‐Ins, APIs)
- 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
- 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