TranSMART API & Plugin Development: A case study. Presentation at the tranSMART community meeting in Chilly-Mazarin at Sanofi R&D in November 2013.

1. TranSMART
API
&
Plugin
Development:
A
Case
Study
Kees
van
Bochove,
The
Hyve
TranSMART
Community
MeeCng
Chilly-­‐Mazarin,
France
November
6,
2013

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. 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. 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. Emerging
tranSMART
Architecture
Kees
van
Bochove
-­‐
The
Hyve

6. Extend
the
core
API

7. Write
some
tests

8. Create
some
implemenCng
plugins
• h`ps://github.com/thehyve/transmart-­‐mydas
• h`ps://github.com/thehyve/dalliance-­‐plugin
MyDAS
Backend
Plugin
TranSMART
Core
API
DB
Dalliance
Frontend
Plugin

9. Add
them
to
transmartApp
but
don’t
force
it
upon
others

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