TranSMART API &Plugin
Development: A Case Study
TranSMART Community Meeting
Chilly-Mazarin, France
November 6, 2013
Requirements
• HTML5 Genome Browser (in-place in UI)
• Drag-n-drop of High-Dimensional Data Nodes
– Visualization of Genom...
CommunityConsultation
• Asktransmart-discuss mailing list whatpeople are
using / planning to use as genome browser
• Ask t...
Solution
•
•
•
•

Dalliance genome browser chosen as frontend
MyDAS was chosen as backend
Both implemented as plugins
Core...
EmergingtranSMARTArchitecture

Kees van Bochove - The Hyve
Extend the core API
Writesome tests
Createsomeimplementingplugins
• https://github.com/thehyve/transmart-mydas
• https://github.com/thehyve/dalliance-plugin
M...
Addthem to transmartApp

but don’tforceituponothers
Leverageother branches
• Implementing VCF loading (and viewing) and
GWAS loading and viewing in tranSMART
• VCF loader tak...
The end result
2. Drag genomic node on genome browser
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tranSMART Community Meeting 5-7 Nov 13 - Session 3: Modularization (Plug‐Ins, APIs)

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tranSMART Community Meeting 5-7 Nov 13 - Session 3: Modularization (Plug‐Ins, APIs)
Kees van Bochove, The Hyve

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

  1. 1. TranSMART API &Plugin Development: A Case Study TranSMART Community Meeting Chilly-Mazarin, France November 6, 2013
  2. 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. 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. 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. 5. EmergingtranSMARTArchitecture Kees van Bochove - The Hyve
  6. 6. Extend the core API
  7. 7. Writesome tests
  8. 8. Createsomeimplementingplugins • https://github.com/thehyve/transmart-mydas • https://github.com/thehyve/dalliance-plugin MyDAS Backend Plugin TranSMART Core API DB DallianceFrontendPlugin
  9. 9. Addthem to transmartApp but don’tforceituponothers
  10. 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. 11. The end result 2. Drag genomic node on genome browser

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