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Big Data, The Community and The Commons (May 12, 2014)


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These are the slides from a keynote I gave at the
The Cancer Genome Atlas (TCGA) Third Annual Scientific Symposium on May 12, 2014.

Published in: Data & Analytics, Technology
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Big Data, The Community and The Commons (May 12, 2014)

  1. 1. Big  Data,  The  Community  and     The  Commons   Robert  Grossman   University  of  Chicago   Open  Cloud  Consor?um   May  12,  2014   TCGA  Third  Annual  Scien?fic  Symposium  
  2. 2. Outline   1.  Big  data  and  the  problems  it  creates   2.  Compu?ng  over  big  data     3.  Science  clouds     4.  Data  analysis  at  scale   5.  Genomic  clouds   6.  How  might  we  organize?  
  3. 3. Four  ques?ons  and     one  challenge  
  4. 4. 1.  What  is  the  same  and  what  is  different   about  big  biomedical  data  vs  big  science   data  and  vs  big  commercial  data?   2.  What  instrument  should  we  use  to  make   discoveries  over  big  biomedical  data?   3.  Do  we  need  new  types  of  mathema?cal   and  sta?s?cal  models  for  big  biomedical   data?   4.  How  do  we  organize  large  biomedical   datasets  to  maximize  the  discoveries  we   make  and  their  impact  on  health  care?  
  5. 5. One  Million  Genome  Challenge   •  Sequencing  a  million  genomes  would  likely   change  the  way  we  understand  genomic   varia?on.   •  The  genomic  data  for  a  pa?ent  is  about  1  TB   (including  samples  from  both  tumor  and  normal   ?ssue).   •  One  million  genomes  is  about  1000  PB  or  1  EB   •  With  compression,  it  may  be  about  100  PB   •  At  $1000/genome,  the  sequencing  would  cost   about  $1B   •  Think  of  this  as  one  hundred  studies  with  10,000   pa?ents  each  over  three  years.  
  6. 6. Part  1:   Biomedical  compu?ng  is  being   disrupted  by  big  data   Source:  Michael  S.  Lawrence,  Petar  Stojanov,  Paz  Polak,  et.  al.,  Muta?onal  heterogeneity  in  cancer  and  the  search  for   new  cancer-­‐associated  genes,  Nature  449,  pages  214-­‐218,  2013.  
  7. 7. Standard  Model  of  Biomedical  Compu?ng   Public  data   repositories   Private  local   storage  &   compute   Network   download   Local  data  ($1K)   Community   soeware   Soeware  &  sweat  and   tears  ($100K)  
  8. 8. We  have  a  problem  …   Image:  A  large-­‐scale  sequencing  center  at  the  Broad  Ins?tute  of  MIT  and  Harvard.   Growth  of  data   New  types  of  data   It  takes  over  three   weeks  to  download   the  TCGA  data  at  10   Gbps     Analyzing  the  data  is  more   expensive  than  producing  it  
  9. 9. The  Smart  Phone  is  Becoming  a     Home  for  Medical  &  Environmental  Sensors   Source:  LifeWatch  V  from  LifeWatch  AG,  
  10. 10. Source:  Interior  of  one  of  Google’s  Data  Center,  
  11. 11. Computa?onal  Adver?sing  and  Marke?ng   •  Computa?onal  adver?sing  finds  the  “best  match”   between  a  given  user  in  a  given  context  and  a   suitable  adver?sement*.   •  In  2011,  over  $100  billion  was  spent  in  online   adver?sing  (eMarketer  es?mates)   •  Contexts  include:   –  Web  search  context  (SERP  adver?sing)   –  Web  page  content  context  (content  match  adver?sing   and  banners)   –  Social  media  context   –  Mobile  context       *Andrei  Broder  and  Vanja  Josifovski,  Introduc?on  to  Computa?onal  Adver?sing.  
  12. 12. Why  Do  We  Care?   •  A  modern  adver?sing  analy?c  planorm:   – Will  build  behavioral  profiles  on  100  million  plus   individuals     – Use  full  sta?s?cal  models  (not  rules)  for  targe?ng   – Re-­‐analyze  all  of  the  data  each  night   – Serve  10,000’s  of  ads  per  second  using  sta?s?cal   models   – Respond  <  100  ms  (with  analy?cs  <  10  ms)   – Use  real  ?me  geoloca?on  data   – Do  analy?cs  at  machine  speed     – Be  driven  by  an  analyst  with  only  modest  training   •  More  than  pay  for  the  data  centers  we  just  saw.  
  13. 13. New  Model  of  Biomedical  Compu?ng   Public  data  repositories   Private  storage  &  compute  at   medical  research  centers   Community  soeware   Compute  &     storage   Community  resources  
  14. 14. The  Tragedy  of  the  Commons   Source:  Garrep  Hardin,  The  Tragedy  of  the  Commons,  Science,  Volume  162,  Number  3859,  pages   1243-­‐1248,  13  December  1968.   Individuals  when  they  act  independently  following  their   self  interests  can  deplete  a  deplete  a  common  resource,   contrary  to  a  whole  group's  long-­‐term  best  interests.  
  15. 15. 1. Create  community  commons  of  biomedical  data.   2. Use  a  cloud  compu?ng  and  automa?on  to   manage  the  commons  and  to  compute  over  it.   3. Interoperate  the  data  commons.  
  16. 16. 2005  -­‐  2015   Bioinforma)cs  tools  &  their  integra)on.   Examples:  Galaxy,  GenomeSpace,   workflow  systems,  portals,  etc.   2010  -­‐  2020   ???   2015  -­‐  2025   ???  
  17. 17. Part  2   Data  Center  Scale  Compu?ng     (aka  “Cloud  Compu?ng”)   Source:  Interior  of  one  of  Google’s  Data  Center,  
  18. 18. What  instrument  do  we  use  to  make  big  data   discoveries  in  cancer  genomics  and  big  data   biology?   How  do  we  build  a  “datascope?”  
  19. 19. Source:  Luiz  André  Barroso,  Jimmy  Clidaras  and  Urs  Hölzle,  The  Datacenter  as  a  Computer,  Morgan  &  Claypool   Publishers,  Second  Edi?on,  2013,  
  20. 20. Self  Service   Scale   Soeware  stack   that  scales  to  a   data  center   Forgot  cloud   compu?ng.    Focus  on   data  centers  &  the   soeware  they  run.   Use  of   automa?on  
  21. 21. Sevng  up  and  opera?ng  large  scale  efficient,  secure   and  compliant  racks  of  compu?ng  infrastructure  is  out   of  reach  for  most  labs,  but  essen?al  for  the  community.   This  is  not  a  cloud…  
  22. 22. Commercial  Cloud  Service  Provider  (CSP)     15  MW  Data  Center   100,000  servers   1  PB  DRAM   100’s  of  PB  of  disk   Automa?c   provisioning  and   infrastructure   management   Monitoring,   network  security   and  forensics   Accoun?ng  and   billing   Customer   Facing   Portal   Data  center  network   ~1  Tbps  egress  bandwidth     25  operators  for  15  MW  Commercial  Cloud  
  23. 23.   …  
  24. 24. Open  Science  Data  Cloud  (Home  of  Bionimbus)   6  PB   (OpenStack,   GlusterFS,   Hadoop)   Infrastructure   automa?on  &   management   (Yates)   Compliance,  &   security  (OCM)   Accoun?ng  &   billing   Customer  Facing   Portal  (Tukey)   Data  center  network   ~10-­‐100  Gbps  bandwidth     6  engineers  to  operate  0.5  MW  Science  Cloud   Science  Cloud  SW   &  Services  
  25. 25. Why  not  just  use  (only)  Amazon  Web  Services  (AWS)?   Community  science  and   biomedical  clouds   •  Scale  /  capacity   •  Simplicity  of  a  credit  card   •  Wide  variety  of  offerings.     vs.   It  is  s?ll  essen?al  to  interoperate  with  CSP  whenever  possible  by   compliance  and  security  policies.   Commercial  Cloud  Service   Providers  (CSP)   •  Lower  cost  (at  medium   scale)   •  We  can  build  specialized   infrastructure  for  science.   •  We  can  build  specialized   infrastructure  for  security  &   compliance.   •  The  data  is  too  important  to   trust  exclusively  with  a   commercial  provider.  
  26. 26. Cost  of  a  medium  private/community  cloud   vs  large  public  cloud.   Source:  Allison  P.  Heath,  Maphew  Greenway,  Raymond  Powell,  Jonathan  Spring,  Rafael  Suarez,  David  Hanley,  Chai   Bandlamudi,  Megan  McNerney,  Kevin  White  and  Robert  L  Grossman,  Bionimbus:  A  Cloud  for  Managing,  Analyzing   and  Sharing  Large  Genomics  Datasets,  Journal  of  the  American  Medical  Informa?cs  Associa?on,  2014.   PB   Cost     (thousands  of  $)  
  27. 27. Reliability  over  Commodity  Compu?ng   Components  Is  Difficult  as  is  Data  Locality   •  Hadoop  enables  reliable  computa?on  over   thousands  of  low  costs,  unreliable  compu?ng  nodes.   •  Hadoop  efficiently  computes  over  the  data  instead  of   moving  the  data.   •  The  programming  model  of  Hadoop  (MapReduce)  is   in  prac?ce  more  efficient  in  terms  of  soeware   development  than  the  programming  tradi?onally   used  by  high  performance  compu?ng  (message   passing)  (but  usually  does  not  fully  u?lize  the   underlying  hardware)  
  28. 28. The  Tail  at  Scale,  Jeffrey  Dean,  Luiz  André  Barroso    Communica?ons  of  the  ACM,   Volume  56  Number  2,  Pages  74-­‐80   Latency  is  Difficult  
  29. 29. Call  an  algorithm  and   compu?ng  infrastructure   is  “big-­‐data  scalable”  if   adding  a  rack  of  data  (and   corresponding  processors)   does  not  increase  the  ?me   required  to  complete  the   computa?on  but  enables   the  computa?on  to  run  on   a  rack  more  of  data.    Most   of  our  community’s   algorithms  today  fail  this   test.  
  30. 30. 2005  -­‐  2015   Bioinforma)cs  tools  &  their  integra)on.   Examples:  Galaxy,  GenomeSpace,   workflow  systems,  portals,  etc.   2010  -­‐  2020   Data  center  scale  science.     Examples:  Bionimbus/OSDC,  CG  Hub,   Cancer  Collaboratory,  GenomeBridge,  etc.   2015  -­‐  2025   ???  
  31. 31. Part  3   Science  Clouds   Source:  Lincoln  Stein  
  32. 32. Discipline   Dura)on   Size   #  Devices   HEP  -­‐  LHC   10  years   15  PB/year*   One   Astronomy  -­‐  LSST   10  years   12  PB/year**   One   Genomics  -­‐  NGS   2-­‐4  years   0.4  TB/genome   1000’s   Genomics  as  a  Big  Data  Science   *At  full  capacity,  the  Large  Hadron  Collider  (LHC),  the  world's  largest  par?cle  accelerator,  is  expected  to  produce  more  than  15   million  Gigabytes  of  data  each  year.    …  This  ambi?ous  project  connects  and  combines  the  IT  power  of  more  than  140  computer   centres  in  33  countries.    Source:  hpp://­‐en.html     **As  it  carries  out  its  10-­‐year  survey,  LSST  will  produce  over  15  terabytes  of  raw  astronomical  data  each  night  (30  terabytes   processed),  resul?ng  in  a  database  catalog  of  22  petabytes  and  an  image  archive  of  100  petabytes.    Source:  hpp:// News/enews/teragrid-­‐1004.html  
  33. 33. vs   Source:  A  picture  of  Cern’s  Large  Hadron  Collider  (LHC).    The  LHC  took  about  a  decade  to  construct,  and  cost  about  $4.75  billion.       Source  of  picture:  Conrad  Melvin,  Crea?ve  Commons  BY-­‐SA  2.0,   •  Ten  years  and  $10B   •  No  business  value   •  Big  data  culture   •  Liple  compliance   •  Five  years  and  $1M   •  Business  value   •  Culture  of  small  data   •  Compliance   Common  compu?ng,    storage  &  transport    infrastructure  
  34. 34. UDT  Tuning:  Buffers  and  CPUs     Configuration Change Observed Transfer Rate Time to Transfer 1 TB (minutes) UDT and Linux Defaults 1.6 Gbps 85 Setting buffers sizes to 64 MB 3.3 Gbps 41 Improved CPU on sending side with processor affinity 3.7 Gbps 36 Improved CPU on receiving side with processor affinity 4.6 Gbps 29 Improved CPU on both sides with processor affinity on both sides 6.3 Gbps 21 Turn off CPU frequency scaling and set to max clock speed 6.7 Gbps 20
  35. 35. Science  vs  Commercial  Clouds   Science  CSP   Commercial  CSP   Perspec?ve   Democra?ze  access  to   data.    Integrate  data   to  make  discoveries.     Long  term  archive.   As  long  as  you  pay  the   bill;  as  long  as  we  keep   the  our  business  model.   Data   Data  intensive   compu?ng   Internet  style  scale  out   Flows   Large  data  flows  in   and  out   Lots  of  small  web  flows   Lock  in   Data  and  compute   portability  essen?al   Lock  in  is  good  
  36. 36. A  Key  Ques?on   •  Is  biomedical  compu?ng  at  the  scale  of  a  data   center  important  enough  for  the  research   community  to  do  or  do  we  only  outsource  to   commercial  cloud  service  providers  (certainly   we  will  interoperate  with  commercial  cloud   service  providers)?  
  37. 37. Open  Science  Data  Cloud  
  38. 38. Part  4:   Analyzing  Data  at  the  Scale  of  a  Data  Center   Source:  Jon  Kleinberg,  Cornell  University,­‐book/  
  39. 39. experimental   science   simula?on   science   data  science   (big  data  biology,   medicine)   1609   30x   1670   250x   1976   10x-­‐100x   2004   10x-­‐100x  
  40. 40. Is  More  Different?    Do  New  Phenomena   Emerge  at  Scale  in  Biomedical  Data?  
  41. 41. Complex  models   over  small  data  that   are  highly  manual.   Simpler  models   over  large  data  that   are  highly   automated.   Small  data   Medium  data   GB   TB   PB   W   KW   MW  
  42. 42. Several  ac?ve  voxels  were  discovered  in  a  cluster  located   within  the  salmon’s  brain  cavity  (Figure  1,  see  above).  The  size   of  this  cluster  was  81  mm3  with  a  cluster-­‐level  significance  of   p  =  0.001.  Due  to  the  coarse  resolu?on  of  the  echo-­‐planar   image  acquisi?on  and  the  rela?vely  small  size  of  the  salmon   brain  further  discrimina?on  between  brain  regions  could  not   be  completed.  Out  of  a  search  volume  of  8064  voxels  a  total   of  16  voxels  were  significant.      
  43. 43. Environmental  Factors  and  Cancer  
  44. 44. Building  Models  over  Big  Data   •  We  know  about  the  “unreasonable  effec?veness  of   ensemble  models.”  Building  ensembles  of  models   over  computer  clusters  works  well  …   •  …  but,  how  do  machine  learning  algorithms  scale  to   data  center  scale  science?   •  Ensembles  of  random  trees  built  from  templates   appear  to  work  beper  than  tradi?onal  ensembles  of   classifiers   •  The  challenge  is  oeen  decomposing  large   heterogeneous  datasets  into  homogeneous   components  that  can  be  modeled.  
  45. 45. New  Ques?ons   •  How  would  research  be  impacted  if  we  could   analyze  all  of  the  data  each  evening?   •  How  would  health  care  be  impacted  if  we   could  analyze  of  the  data  each  evening?  
  46. 46. 2005  -­‐  2015   Bioinforma)cs  tools  &  their  integra)on.   Examples:  Galaxy,  GenomeSpace,   workflow  systems,  portals,  etc.   2010  -­‐  2020   Data  center  scale  science.     Interoperability  and  preserva?on/peering/ portability  of  large  biomedical  datasets.     Examples:  Bionimbus/OSDC,  CG  Hub,   Cancer  Collaboratory,  GenomeBridge,  etc.   2015  -­‐  2025   New  modeling  techniques.  The   discovery  of  new  &  emergent  behavior   at  scale.    Examples:    What  are  the   founda?ons?    Is  more  different?  
  47. 47. Part  5:   Genomic  Clouds   Cancer  Genome   Collaboratory  (Toronto)   Cancer  Genomics  Hub   (Santa  Cruz)   Bionimbus  Protected   Data  Cloud  (Chicago)   (Cambridge)   (Mountain  View)  
  48. 48.  
  49. 49. Analyzing  Data  From     The  Cancer  Genome  Atlas  (TCGA)   1.  Apply  to  dbGaP  for  access   to  data.   2.  Hire  staff,  set  up  and   operate  secure  compliant   compu?ng  environment  to   mange  10  –  100+  TB  of  data.       3.  Get  environment  approved   by  your  research  center.   4.  Setup  analysis  pipelines.   5.  Download  data  from  CG-­‐ Hub  (takes  days  to  weeks).     6.  Begin  analysis.   Current  Prac)ce   With  Bionimbus  Protected  Data   Cloud  (PDC)   1.  Apply  to  dbGaP  for  access   to  data.   2.  Use  your  exis?ng  NIH  grant   creden?als  to  login  to  the   PDC,  select  the  data  that   you  want  to  analyze,  and   the  pipelines  that  you  want   to  use.     3.  Begin  analysis.  
  50. 50. 1.  What  scale  is  required  for  biomedical  clouds?   2.  What  is  the  design  for  biomedical  clouds?   3.  What  tools  and  applica?ons  do  users  need  to  make   discoveries  in  large  amounts  of  biomedical  data?   4.  How  do  different  biomedical  clouds  interoperate?  
  51. 51. 6.  How  Do  We  Organize?  
  52. 52. Cyber  Condo  Model   •  Research  ins?tu?ons  today   have  access  to  high   performance  networks  –  10G   &  100G.   •  They  couldn’t  afford  access  to   these  networks  from   commercial  providers.   •  Over  a  decade  ago,  they  got   together  to  buy  and  light   fiber.         •  This  changed  how  we  do   scien?fic  research.   •  Cyber  condos  interoperate   with  commercial  ISPs  
  53. 53. Science  Cloud  Condos   •  Build  Science  Cloud  condo.   •  To  provide  a  sustainable   home  for  large  commons  of   research  data  (and  an   infrastructure  to  compute   over  it).   •  “Tier  1”  Science  Clouds  need   to  establish  peering   rela?onships.   •  And  to  interoperate  with  CSPs   •  The  Open  Cloud  Consor?um  is   planning  to  develop  a  science   cloud  condo.  
  54. 54. Some  Biomedical  Data  Commons  Guidelines  for   the  Next  Five  Years   •  There  is  a  societal  benefit  when  biomedical  data  is  also   available  in  data  commons  operated  by  the  research   community  (vs  sold  exclusively  as  data  products  by   commercial  en??es  or  only  offered  for  download  by   the  USG).   •  Large  data  commons  providers  should  peer.   •  Data  commons  providers  should  develop  standards  for   interopera?ng.   •  Standards  should  not  be  developed  ahead  of  open   source  reference  implementa?ons.   •  We  need  a  period  of  experimenta?on  as  we  develop   the  best  technology  and  prac?ces.   •  The  details  are  hard  (consent,  scalable  APIs,  open  vs   controlled  access,  sustainability,  security,  etc.)  
  55. 55. Source:  David  R.  Blair,  Christopher  S.  Lyple,  Jonathan  M.  Mortensen,  Charles  F.  Bearden,  Anders  Boeck   Jensen,  Hossein  Khiabanian,  Rachel  Melamed,  Raul  Rabadan,  Elmer  V.  Bernstam,  Søren  Brunak,  Lars   Juhl  Jensen,  Dan  Nicolae,  Nigam  H.  Shah,  Robert  L.  Grossman,  Nancy  J.  Cox,  Kevin  P.  White,  Andrey   Rzhetsky,  A  Non-­‐Degenerate  Code  of  Deleterious  Variants  in  Mendelian  Loci  Contributes  to  Complex   Disease  Risk,  Cell,  September,  2013     7.     Recap  
  56. 56. 100,000  pa?ents   100  PB   1,000,000  pa?ents   1,000  PB   10,000  pa?ents   10  PB   1000  pa?ents   •  What  are  the  key   common  services  &  APIs?   •  How  do  the  biomedical   commons  clouds   interoperate?   •  What  is  the  governance   structure?   •  What  is  the  sustainability   model?  
  57. 57. 2005  -­‐  2015   Bioinforma)cs  tools  &  their  integra)on.   Examples:  Galaxy,  GenomeSpace,   workflow  systems,  portals,  etc.   2010  -­‐  2020   Data  center  scale  science.     Interoperability  and  preserva?on/peering/ portability  of  large  biomedical  datasets.     Examples:  Bionimbus/OSDC,  CG  Hub,   Cancer  Collaboratory,  GenomeBridge,  etc.   2015  -­‐  2025   New  modeling  techniques.  The   discovery  of  new  &  emergent  behavior   at  scale.    Examples:    What  are  the   founda?ons?    Is  more  different?  
  58. 58. Thanks  To  My  Colleagues  &  Collaborators   •  Kevin  White   •  Nancy  Cox   •  Andrey  Rzhetsky   •  Lincoln  Stein   •  Barbara  Stranger  
  59. 59. Thanks  to  My  Lab   Allison   Heath   Ray   Powell   Jonathan   Spring   Renuka   Ayra   David   Hanley   Maria   Paperson   Map   Greenway   Rafael   Suarez     Stu?   Agrawal     Sean   Sullivan   Zhenyu   Zhang    
  60. 60. Thanks  to  the  White  Lab   Jason   Grundstad   Chaitanya   Bandlamidi   Jason  Pip   Megan   McNerney  
  61. 61. Ques?ons?   62  
  62. 62. For  more  informa?on   •   •  For  more  informa?on  and  background,  see  Robert  L.   Grossman  and  Kevin  P.  White,  A  Vision  for  a  Biomedical   Cloud,  Journal  of  Internal  Medicine,  Volume  271,  Number  2,   pages  122-­‐130,  2012.   •  You  can  find  some  more  informa?on  on  my  blog:                                           •  My  email  address  is  robert.grossman  at  uchicago  dot  edu.     Center for Research Informatics
  63. 63. Major  funding  and  support  for  the  Open  Science  Data  Cloud  (OSDC)  is  provided  by  the  Gordon  and   Bepy  Moore  Founda?on.    This  funding  is  used  to  support  the  OSDC-­‐Adler,  Sullivan  and  Root  facili?es.     Addi?onal  funding  for  the  OSDC  has  been  provided  by  the  following  sponsors:     •  The  Bionimbus  Protected  Data  Cloud  is  supported  in  by  part  by  NIH/NCI  through  NIH/SAIC  Contract   13XS021  /  HHSN261200800001E.     •  The  OCC-­‐Y  Hadoop  Cluster  (approximately  1000  cores  and  1  PB  of  storage)  was  donated  by  Yahoo!   in  2011.   •  Cisco  provides  the  OSDC  access  to  the  Cisco  C-­‐Wave,  which  connects  OSDC  data  centers  with  10   Gbps  wide  area  networks.   •  The  OSDC  is  supported  by  a  5-­‐year  (2010-­‐2016)  PIRE  award  (OISE  –  1129076)  to  train  scien?sts  to   use  the  OSDC  and  to  further  develop  the  underlying  technology.   •  OSDC  technology  for  high  performance  data  transport  is  support  in  part  by    NSF  Award  1127316.   •  The  StarLight  Facility  in  Chicago  enables  the  OSDC  to  connect  to  over  30  high  performance   research  networks  around  the  world  at  10  Gbps  or  higher.   •  Any  opinions,  findings,  and  conclusions  or  recommenda?ons  expressed  in  this  material  are  those   of  the  author(s)  and  do  not  necessarily  reflect  the  views  of  the  Na?onal  Science  Founda?on,  NIH  or   other  funders  of  this  research.     The  OSDC  is  managed  by  the  Open  Cloud  Consor?um,  a  501(c)(3)  not-­‐for-­‐profit  corpora?on.  If  you  are   interested  in  providing  funding  or  dona?ng  equipment  or  services,  please  contact  us  at