TranSMART	
  API	
  &	
  Plugin	
  
Development:	
  A	
  Case	
  Study	
  
Kees	
  van	
  Bochove,	
  The	
  Hyve	
  
Tran...
Requirements	
  
•  HTML5	
  Genome	
  Browser	
  (in-­‐place	
  in	
  UI)	
  
•  Drag-­‐n-­‐drop	
  of	
  High-­‐Dimensio...
Community	
  ConsultaCon	
  
•  Ask	
  transmart-­‐discuss	
  mailing	
  list	
  what	
  people	
  
are	
  using	
  /	
  p...
SoluCon	
  
•  Dalliance	
  genome	
  browser	
  chosen	
  as	
  frontend	
  
•  MyDAS	
  was	
  chosen	
  as	
  backend	
...
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/thehy...
Add	
  them	
  to	
  transmartApp	
  
but	
  don’t	
  force	
  it	
  upon	
  others	
  
Leverage	
  other	
  branches	
  
•  ImplemenCng	
  VCF	
  loading	
  (and	
  viewing)	
  and	
  
GWAS	
  loading	
  and	
...
2.	
  Drag	
  genomic	
  node	
  on	
  genome	
  browser	
  
The	
  end	
  result	
  
Upcoming SlideShare
Loading in …5
×

TranSMART API Plugin Case Study: Genome Browser

1,005 views

Published on

TranSMART API case study at the tranSMART Community meeting at Sanofi in Chilly-Mazarin, November 2013.

Published in: Software, Technology, Art & Photos
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
1,005
On SlideShare
0
From Embeds
0
Number of Embeds
24
Actions
Shares
0
Downloads
12
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

TranSMART API Plugin Case Study: Genome Browser

  1. 1. TranSMART  API  &  Plugin   Development:  A  Case  Study   Kees  van  Bochove,  The  Hyve   TranSMART  Community  MeeCng   Chilly-­‐Mazarin,  France   November  6,  2013  
  2. 2. 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  
  3. 3. 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  
  4. 4. 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  
  5. 5. Emerging  tranSMART  Architecture   Kees  van  Bochove  -­‐  The  Hyve  
  6. 6. Extend  the  core  API  
  7. 7. Write  some  tests  
  8. 8. 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  
  9. 9. Add  them  to  transmartApp   but  don’t  force  it  upon  others  
  10. 10. 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!  
  11. 11. 2.  Drag  genomic  node  on  genome  browser   The  end  result  

×