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

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.

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

    • TranSMART:   how  open  source  so3ware   revolu6onizes  drug  discovery   through  cross-­‐pharma  collabora6on   Kees  van  Bochove,  CEO  The  Hyve   October  23,  2013,  Princeton  
    • 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  
    • 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  
    • OpenStack  Contribu6ons   Source:  Bitergia,  hfp://blog.bitergia.com/2013/10/17/the-­‐openstack-­‐havana-­‐release  
    • How  does  open  source  work  with   scien6sts  in  academia?   Let’s  zoom  in  on  a  well-­‐known   bioinforma6cs  problem  
    • 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   hfp://nothinkingbeyondthispoint.blogspot.nl/2011/11/decision-­‐tree-­‐for-­‐scien6fic.html  
    • 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.  
    • share   reuse   specialize  
    • Sharing?!   Pharma  IT  as  the  proverbial  fortress.  
    • • 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   $$  $$  $$   $$  $$  $$  $$  $$   $$  $$   $$   $$   $$$$$$$$$$$  $$$$$$$$$$$  
    • There  has  to  be  a  befer  way.  
    • February  2012   Janssen  makes  a  bold  move.   is  now  Open  Source!   No-­‐brainer,  zero  cost!   Ehm..  wait  a  minute…  
    • 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  
    • 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  
    • 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  
    • eTRIKS  Consor6um  
    • 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  
    • 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
    • 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  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  
    • TraIT  ‘Founda6on  Team’   2 FTE 4 FTE 2 FTE •  Core  infrastructure   development:  adopt  &   adapt  tranSMART,   Galaxy,  OpenClinica,   BMIA,  etc.   •  Distributed  Scrum   Team  
    • 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  
    • 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.   It  s6ll  needs  a  lot  of  work  though,  to   ensure  long  term  success…  
    • So…  is  open  source  a  silver  bullet  to   make  so3ware  collabora6ons  work?   Let’s  look  at  a  couple  other  projects.  
    • 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  together.  
    • 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  
    • 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-­‐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  
    • Galaxy  
    • 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.  
    • Galaxy  Toolshed  
    • 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.  
    • 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  
    • Pa6ent  Level  View  
    • App  inside  hospital  firewall:  Cardiac  Risk  
    • •  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  
    • What  do  all  these  success  stories   have  in  common?   Bioconductor  Packages   Galaxy  Toolshed   Plone  Collec6ve   Drupal  Modules   SMART  Apps  
    • 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!   •  •  •  •  •