TranSMART API case study at the tranSMART Community meeting at Sanofi in Chilly-Mazarin, 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
DB
MyDAS
Backend
Plugin
Dalliance
Frontend
Plugin
TranSMART
Core
API

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