TranSMART:	
  
how	
  open	
  source	
  so3ware	
  
revolu6onizes	
  drug	
  discovery	
  
through	
  cross-­‐pharma	
  co...
The	
  Open	
  Source	
  Defini6on	
  
1.	
  Free	
  Redistribu6on	
  
2.	
  Availability	
  of	
  Source	
  Code	
  
3.	
 ...
Open	
  Source	
  
•  Source	
  code	
  for	
  so3ware	
  is	
  openly	
  accessible	
  
and	
  reusable	
  for	
  everyon...
OpenStack	
  Contribu6ons	
  

Source:	
  Bitergia,	
  hfp://blog.bitergia.com/2013/10/17/the-­‐openstack-­‐havana-­‐relea...
How	
  does	
  open	
  source	
  work	
  with	
  
scien6sts	
  in	
  academia?	
  
Let’s	
  zoom	
  in	
  on	
  a	
  well-...
In	
  2003…	
  

(Ancient	
  history;	
  before	
  Facebook)	
  
Yet	
  Another	
  ‘New’	
  Web-­‐based	
  Solu6on	
  for	
  
the	
  Management	
  of	
  Microarray	
  Data	
  ?!	
  
Not	
  Invented	
  Here	
  Syndrome	
  

Image	
  from	
  Rob	
  Hoo3,	
  CTO	
  Netherlands	
  Bioinforma6cs	
  Centre	
 ...
Different	
  Non-­‐Func6onal	
  
Requirements	
  
•  Bioinforma6cian	
  in	
  academics:	
  solve	
  a	
  novel	
  
problem...
share	
  

reuse	
  

specialize	
  
Sharing?!	
  
Pharma	
  IT	
  as	
  the	
  proverbial	
  fortress.	
  
• Browse	
  clinical	
  Brials	
   clinical	
  trials	
  
•  trowse	
  
• Import	
  /	
  load	
  • Import	
  rial	
  data	...
There	
  has	
  to	
  be	
  a	
  befer	
  way.	
  
February	
  2012	
  
Janssen	
  makes	
  a	
  bold	
  move.	
  

is	
  now	
  Open	
  Source!	
  
No-­‐brainer,	
  zero	
 ...
TranSMART	
  Open	
  Source	
  History	
  
•  February	
  2012:	
  J&J	
  releases	
  tranSMART	
  as	
  
open	
  source	
...
Amsterdam,	
  June	
  2013:	
  tranSMART	
  Workshop
Afendees	
  from	
  10	
  Pharma	
  companies,	
  11	
  University	
 ...
TranSMART	
  in	
  a	
  nutshell	
  
•  Datawarehouse	
  bringing	
  together	
  scien6sts	
  
from	
  clinical	
  science...
eTRIKS	
  Consor6um	
  
tranSMART	
  Founda6on	
  Board	
  
Brian	
  Athey,	
  PhD,	
  University	
  of	
  Michigan	
  
Michael	
  Braxenthaler,	
...
Center for Translational Molecular Medicine
(CTMM)
•  Public-private consortium
•  Dedicated to the development of Molecul...
TraIT February 2013: 26 partners

EUR	
  16	
  million	
  /	
  4	
  years	
  

Growing	
  TraIT	
  project	
  team	
  
CTMM	
  TraIT	
  Goal	
  
•  To	
  build	
  an	
  IT	
  infrastructure	
  for	
  transla6onal	
  
research	
  for	
  all	
...
TraIT	
  ‘Founda6on	
  Team’	
  
2 FTE
4 FTE
2 FTE

•  Core	
  infrastructure	
  
development:	
  adopt	
  &	
  
adapt	
  ...
TraIT	
  tools	
  &	
  applica6ons:	
  the	
  landscape	
  
Hospital	
  (IT)	
  

Transla6onal	
  Research	
  (IT)	
  
dat...
Day	
  to	
  day	
  virtual	
  collabora6on	
  
Day	
  to	
  day	
  virtual	
  collabora6on	
  
TranSMART	
  seems	
  to	
  do	
  well	
  and	
  
certainly	
  has	
  a	
  lot	
  of	
  momentum	
  at	
  
this	
  point.	...
So…	
  is	
  open	
  source	
  a	
  silver	
  bullet	
  to	
  
make	
  so3ware	
  collabora6ons	
  work?	
  
Let’s	
  look...
What	
  about	
  all	
  these	
  great	
  FP6,	
  
FP7,	
  IMI,	
  …	
  projects?	
  
Source	
  code	
  of	
  major	
  projects	
  is	
  
readily	
  available	
  on	
  GitHub	
  	
  
That’s	
  great!	
  
But…	
  I’m	
  afraid	
  it’s	
  s6ll	
  up	
  to	
  you	
  
and	
  me	
  to	
  put	
  the	
  pieces	...
Phenotype	
  Database	
  
Wrifen	
  in	
  Grails,	
  supports	
  several	
  types	
  of	
  omics	
  
data,	
  provides	
  ...
R	
  and	
  Bioconductor	
  
Who	
  doesn’t	
  love	
  R?	
  
Website	
  looks	
  as	
  if	
  dates	
  from	
  Stone	
  Age.	
  
Must	
  be	
  those	
  LaTeX-­‐loving	
  physicists.	
 ...
Very	
  ac6ve	
  community,	
  and…	
  
lots	
  of	
  packages.	
  
Governance	
  of	
  R	
  community	
  
Brian	
  Ripley:	
  “ The	
  R	
  Project	
  is	
  governed	
  by	
  a	
  
self-­‐p...
Galaxy	
  
Galaxy	
  is	
  the	
  most	
  widely	
  used	
  open	
  
source	
  bioinforma6cs	
  web	
  interface	
  AFAIK.	
  
Probab...
Galaxy	
  Toolshed	
  
I2B2	
  (from	
  Harvard)	
  is	
  deployed	
  in	
  
~100	
  medical	
  centers	
  across	
  U.S.	
  
I2B2	
  is	
  clini...
Apps	
  in	
  a	
  hospital:	
  SMART	
  
•  SMART	
  =	
  Subs6tutable	
  Medical	
  Apps	
  
Reusable	
  Technologies	
 ...
Pa6ent	
  Level	
  View	
  
App	
  inside	
  hospital	
  firewall:	
  Cardiac	
  Risk	
  
•  An	
  open	
  source	
  CMS	
  (Content	
  Management	
  
System)	
  wrifen	
  in	
  Python,	
  nowadays	
  backing	
  ...
What	
  do	
  all	
  these	
  success	
  stories	
  
have	
  in	
  common?	
  
Bioconductor	
  Packages	
  
Galaxy	
  Tool...
Success	
  factors	
  

Lessons	
  learned	
  about	
  open	
  source	
  projects	
  
Solve	
  an	
  unmet	
  business	
  ...
TranSMART: How open source software revolutionizes drug discovery through cross-pharma collaboration
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TranSMART: How open source software revolutionizes drug discovery through cross-pharma collaboration

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Presentation about the use of open source software in pharmaceutical companies at Global Discovery & Development Innovation Summit (GDDIS) in Princeton, NY, fall 2013.

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TranSMART: How open source software revolutionizes drug discovery through cross-pharma collaboration

  1. 1. TranSMART:   how  open  source  so3ware   revolu6onizes  drug  discovery   through  cross-­‐pharma  collabora6on   Kees  van  Bochove,  CEO  The  Hyve   October  23,  2013,  Princeton  
  2. 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. 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  
  4. 4. OpenStack  Contribu6ons   Source:  Bitergia,  hfp://blog.bitergia.com/2013/10/17/the-­‐openstack-­‐havana-­‐release  
  5. 5. How  does  open  source  work  with   scien6sts  in  academia?   Let’s  zoom  in  on  a  well-­‐known   bioinforma6cs  problem  
  6. 6. In  2003…   (Ancient  history;  before  Facebook)  
  7. 7. Yet  Another  ‘New’  Web-­‐based  Solu6on  for   the  Management  of  Microarray  Data  ?!  
  8. 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. 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.  
  10. 10. share   reuse   specialize  
  11. 11. Sharing?!   Pharma  IT  as  the  proverbial  fortress.  
  12. 12. • Browse  clinical  Brials   clinical  trials   •  trowse   • Import  /  load  • Import  rial  data   clinical  t /  load  clinical  trial  data   • Define  virtual  • Define  virtual  cohorts   cohorts   • Perform  exploratory  analy6cs   • Perform  exploratory  analy6cs   • Search  /  view  • Search  /  vanalysis  results   nalysis  results   published   iew  published  a • Support  for  'omics'  data  or  'omics'  data   • Support  f • Load  public  data  -­‐  TCGA,  1000  G-­‐  TCGA,  1000  Genomes   • Load  public  data   enomes   $$  $$  $$   $$  $$  $$  $$  $$   $$  $$   $$   $$   $$$$$$$$$$$  $$$$$$$$$$$  
  13. 13. There  has  to  be  a  befer  way.  
  14. 14. February  2012   Janssen  makes  a  bold  move.   is  now  Open  Source!   No-­‐brainer,  zero  cost!   Ehm..  wait  a  minute…  
  15. 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. 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. 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  
  18. 18. eTRIKS  Consor6um  
  19. 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. 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. 21. TraIT February 2013: 26 partners EUR  16  million  /  4  years   Growing  TraIT  project  team  
  22. 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  
  23. 23. TraIT  ‘Founda6on  Team’   2 FTE 4 FTE 2 FTE •  Core  infrastructure   development:  adopt  &   adapt  tranSMART,   Galaxy,  OpenClinica,   BMIA,  etc.   •  Distributed  Scrum   Team  
  24. 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  
  25. 25. Day  to  day  virtual  collabora6on  
  26. 26. Day  to  day  virtual  collabora6on  
  27. 27. TranSMART  seems  to  do  well  and   certainly  has  a  lot  of  momentum  at   this  point.   It  s6ll  needs  a  lot  of  work  though,  to   ensure  long  term  success…  
  28. 28. So…  is  open  source  a  silver  bullet  to   make  so3ware  collabora6ons  work?   Let’s  look  at  a  couple  other  projects.  
  29. 29. What  about  all  these  great  FP6,   FP7,  IMI,  …  projects?  
  30. 30. Source  code  of  major  projects  is   readily  available  on  GitHub    
  31. 31. That’s  great!   But…  I’m  afraid  it’s  s6ll  up  to  you   and  me  to  put  the  pieces  together.  
  32. 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  
  33. 33. R  and  Bioconductor   Who  doesn’t  love  R?  
  34. 34. Website  looks  as  if  dates  from  Stone  Age.   Must  be  those  LaTeX-­‐loving  physicists.  
  35. 35. Very  ac6ve  community,  and…   lots  of  packages.  
  36. 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  
  37. 37. Galaxy  
  38. 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.  
  39. 39. Galaxy  Toolshed  
  40. 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. 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  
  42. 42. Pa6ent  Level  View  
  43. 43. App  inside  hospital  firewall:  Cardiac  Risk  
  44. 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. 45. What  do  all  these  success  stories   have  in  common?   Bioconductor  Packages   Galaxy  Toolshed   Plone  Collec6ve   Drupal  Modules   SMART  Apps  
  46. 46. 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!   •  •  •  •  • 

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