Presentation about the use of open source software in pharmaceutical companies at Global Discovery & Development Innovation Summit (GDDIS) in Princeton, NY, fall 2013.
TranSMART: How open source software revolutionizes drug discovery through cross-pharma collaboration
1. TranSMART:
how
open
source
so3ware
revolu6onizes
drug
discovery
through
cross-‐pharma
collabora6on
Kees
van
Bochove,
CEO
The
Hyve
October
23,
2013,
Princeton
2. The
Open
Source
Defini6on
1.
Free
Redistribu6on
2.
Availability
of
Source
Code
3.
Allow
Derived
Works
4.
Integrity
of
The
Author's
Source
Code
5.
No
Discrimina6on
Against
Persons
or
Groups
6.
No
Discrimina6on
Against
Fields
of
Endeavor
7.
Redistribu6on
of
License
8.
License
Must
Not
Be
Specific
to
a
Product
9.
License
Must
Not
Restrict
Other
So3ware
10.
License
Must
Be
Technology-‐Neutral
3. Open
Source
• Source
code
for
so3ware
is
openly
accessible
and
reusable
for
everyone
• Contrasts
with
tradi6onal
IT
business
model:
selling
so3ware
‘in
a
shrink-‐wrapped
box’
• For
IT
vendors,
revenue
is
earned
with
services
rather
than
with
products
• Example
of
well-‐known
open
source
products:
Linux
(e.g.
RedHat,
Ubuntu,
Android),
Firefox,
WordPress,
OpenOffice,
VLC,
OpenStack
7. Yet
Another
‘New’
Web-‐based
Solu6on
for
the
Management
of
Microarray
Data
?!
8. Not
Invented
Here
Syndrome
Image
from
Rob
Hoo3,
CTO
Netherlands
Bioinforma6cs
Centre
hfp://nothinkingbeyondthispoint.blogspot.nl/2011/11/decision-‐tree-‐for-‐scien6fic.html
9. Different
Non-‐Func6onal
Requirements
• Bioinforma6cian
in
academics:
solve
a
novel
problem
or
at
least
create
a
novel
solu6on
that
has
publica6on
value
– So3ware
should
demonstrate
working
principle
• Bioinforma6cian
/
IT
Services
in
pharma/clinic:
– So3ware
should
allow
tes6ng
of
hypotheses,
and
should
be
well
tested,
maintainable,
extensible,
scalable
etc.
14. February
2012
Janssen
makes
a
bold
move.
is
now
Open
Source!
No-‐brainer,
zero
cost!
Ehm..
wait
a
minute…
15. TranSMART
Open
Source
History
• February
2012:
J&J
releases
tranSMART
as
open
source
on
GitHub
under
GPL
v3
• December
2012:
CTMM
TraIT
project
decides
to
use
tranSMART
as
core
infrastructure
component
• January
2013:
IMI
eTRIKS
starts,
uses
tranSMART
as
core
infrastructure
component
• February
2013:
kickoff
of
tranSMART
Founda6on,
U.
Michigan
publishes
PostgreSQL
port
• March
2013:
IMI
EMIF
kickoff,
tranSMART
is
used
as
data
integra6on
component
16. Amsterdam,
June
2013:
tranSMART
Workshop
Afendees
from
10
Pharma
companies,
11
University
Medical
Centers
and
12
IT
companies
Recombinant
/ Deloitte
CDISC
Thomson
Reuters
Pfizer
Astra
Zeneca
VUmc
The Hyve
Sanofi
Johnson &
Johnson
Philips
University
of Michigan
hfp://lanyrd.com/2013/transmart
University of
Luxembourgh
17. TranSMART
in
a
nutshell
• Datawarehouse
bringing
together
scien6sts
from
clinical
sciences,
preclinical
research
and
discovery
–
around
the
data
• Combina6on
of
internal
datasets
and
documents
with
public
datasets
and
knowledge
• Tailored
to
both
biologists/clinicians
and
bioinforma6cians
• Dual
nature:
in
use
for
transla6onal
research
in
both
pharma
and
hospitals/clinic
19. tranSMART
Founda6on
Board
Brian
Athey,
PhD,
University
of
Michigan
Michael
Braxenthaler,
PhD,
Roche,
Pistoia
Alliance
Kevin
Smith,
MSIS,
University
of
Michigan
Ashley
George,
PhD,
GlaxoSmithKline,
Pistoia
Alliance
Keith
Elliston,
PhD,
Seneca
Creek
Research
Yike
Guo,
PhD,
Imperial
College
London
20. Center for Translational Molecular Medicine
(CTMM)
• Public-private consortium
• Dedicated to the development of Molecular Diagnostics and
Molecular Imaging technologies
• Focusing
on
the
transla6onal
aspects
of
molecular
medicine.
• 120
partners
– universi6es,
academic
medical
centers,
medical
technology
enterprises
and
chemical
and
pharmaceu6cal
companies.
• Budget
300
M€
• 22
projects
/
research
consor6a
• TraIT is the Translational Research IT project supporting these
projects with a joint IT infrastructure
21. TraIT February 2013: 26 partners
EUR
16
million
/
4
years
Growing
TraIT
project
team
22. CTMM
TraIT
Goal
• To
build
an
IT
infrastructure
for
transla6onal
research
for
all
20
CTMM
disease
projects
and
other
major
Dutch
ini6a6ves
and
ins6tu6ons,
such
as
all
UMC’s,
NKI,
De
Maastricht
Studie
etc.
• Data
integra6on
and
viewing
is
done
with
a.o.
tranSMART.
• Approach:
Think
big,
start
small,
act
now
24. TraIT
tools
&
applica6ons:
the
landscape
Hospital
(IT)
Transla6onal
Research
(IT)
data
domains
HIS
PACS
LIS
Samples
(IT)
BIMS
Public
Data
P
s
e
u
d
o
n
y
m
i
z
a
t
i
o
n
clinical
data
integrated
data
OpenClinica
transla<onal
analy<cs
workbench
imaging
data
tranSMART/
cohort
explorer
NBIA
+
AIM
biobanking
CBM-‐NL
tranSMART/i2b2
datware
house
R
experimental
data
e.g.
PhenotypeDB,
e.g.
Annai
Systems
Galaxy,
Chipster
Galaxy
30. Source
code
of
major
projects
is
readily
available
on
GitHub
31. That’s
great!
But…
I’m
afraid
it’s
s6ll
up
to
you
and
me
to
put
the
pieces
together.
32. Phenotype
Database
Wrifen
in
Grails,
supports
several
types
of
omics
data,
provides
data
integra6on
and
visualiza6on,
has
R,
Groovy
and
PHP
API’s.
Very
similar
to
tranSMART
hfp://phenotypefounda6on.org
36. Governance
of
R
community
Brian
Ripley:
“ The
R
Project
is
governed
by
a
self-‐perpetua6ng
oligarchy,
a
group
with
a
lot
of
power.
R
was
principally
developed
for
the
benefit
of
the
core
team.”
As
cited
on
hfp://blog.revolu6onanaly6cs.com/2011/08/brian-‐ripley-‐on-‐
the-‐r-‐development-‐process.html
38. Galaxy
is
the
most
widely
used
open
source
bioinforma6cs
web
interface
AFAIK.
Probably
in
no
small
amount
thanks
to
their
con6nuous
dedica6on
to
improving
the
UI.
But
there’s
something
else.
40. I2B2
(from
Harvard)
is
deployed
in
~100
medical
centers
across
U.S.
I2B2
is
clinical
and
genomics
data
repository
and
an
important
cornerstone
of
tranSMART.
41. Apps
in
a
hospital:
SMART
• SMART
=
Subs6tutable
Medical
Apps
Reusable
Technologies
• Write
app
once,
and
run
it
on
any
SMART-‐supported
EHR
system!
•
Interfaces
with
major
EHR
vendors
to
get
a
common
Applica6on
Programming
Interface
(API)
h?p://smartplaAorms.org
hfps://www.|ordnet.com/
workdetail/harvard-‐medical-‐school
44. • An
open
source
CMS
(Content
Management
System)
wrifen
in
Python,
nowadays
backing
thousands
of
produc6on
grade
websites
• Started
by
2
developers
in
2000,
now
an
ac6ve
open
source
project
with
hundreds
of
ac6ve
developers
• In
2004,
the
Plone
Founda6on
was
formed
to
formalize
IP
and
secure
the
future
of
Plone
• Plone
Collec6ve
has
hundreds
of
plugins
45.
46. What
do
all
these
success
stories
have
in
common?
Bioconductor
Packages
Galaxy
Toolshed
Plone
Collec6ve
Drupal
Modules
SMART
Apps
47. Success
factors
Lessons
learned
about
open
source
projects
Solve
an
unmet
business
need
Strong,
ac6ve
community
Engage
mul6ple
vendors
Enable
real
6me
collabora6on
Modular
architecture:
‘app
store’,
data
marketplace
etc.
• Sustainable
funding
/
business
model
• And
some
good
luck!
•
•
•
•
•
