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Internet2 Support for Biomedical Research

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  • 1. AAMC  2013  Informa0on  Technology  in  Academic  Medicine  Conference   Vancouver  CA      June  5-­‐7,  2013     Michael  Sullivan,  M.D.   Associate  Director,  Health  Sciences,  Internet2   Internet2  Support  for  Biomedical  Research  
  • 2. Overview   Internet2  Research  Support   •  •  •  •  Community  and  Network   Data-­‐intensive  Science   Interna0onal  Collabora0on   Innova0on  PlaLorm     Big  Data  Challenges   •  Transport   •  Security   •  Storage  and  Compute   2  –  6/7/13,  ©  2012  Internet2  
  • 3. Internet2  Community                  220  Universi0es                    60  Corpora0ons                    70  Government  agencies                    38  Regional  and  state  networks                    65  Interna0onal  R&E  networks   3  –  6/7/13,  ©  2010  Internet2  
  • 4. Advanced  100G  Produc0on  and  Research  Network   4  –  6/7/13,  ©  2010  Internet2  
  • 5. Data  Tsunami   Life  Sciences   Physics   Large  Hadron  Collider   Image by: CERN " 5  –  6/7/13,  ©  2012  Internet2   Magne0c  Resonance  Imager  (MRI)  
  • 6. Visualizing  Big  Data   Physics   Life  Sciences   LHC  –  Lead  Ion  Collision   MRI  –  Monkey  Brain   Source: CERN (ALICE detector) " Source: Van Wedeen, M.D., Martinos Center and Dept. of Radiology, Massachusetts General Hospital and Harvard University Medical School " 6  –  6/7/13,  ©  2012  Internet2  
  • 7. Sequencing:  Smaller,  Faster,  Cheaper   Illumina HiSeq 2500/1500   Source: http://www.illumina.com/systems/hiseq_systems/hiseq_2500_1500.ilmn " 7  –  6/7/13,  ©  2012  Internet2   Handheld USB Sequencer " Image: Oxford Nanopore Technologies "
  • 8. Democra0za0on  of  Sequencing   2,386  Genome  Sequencers  Worldwide  –  30  May  2013   Source: Map of High-throughput Sequencers" 8  –  6/7/13,  ©  2012  Internet2  
  • 9. North  American  Genome  Sequencers   998  Sequencers  in  NA  –  30  May  2013   Source: Map of High-throughput Sequencers" 9  –  6/7/13,  ©  2012  Internet2  
  • 10. Sequencing  in  Vancouver   13  Sequencers  at  the  Genome  Science  Center   Source: Map of High-throughput Sequencers" 10  –  6/7/13,  ©  2012  Internet2  
  • 11. Canarie  Weathermap   11  –  6/7/13,  ©  2012  Internet2  
  • 12. US-­‐based  Interna0onal  Exchange  Points   US-­‐based  Exchange  Points   StarLight,  Chicago  IL   MAN  LAN,  New  York  NY   NGIX-­‐East,  College  Park  MD   Atlan0cWave  (distributed)   AMPATH,  Miami  FL   PacificWave-­‐S,  Los  Angeles  CA   PacificWave-­‐N,  Seahle  WA   12  –  6/7/13,  ©  2011  Internet2  
  • 13. GEANT  Interna0onal     13  –  6/7/13,  ©  2011  Internet2  
  • 14. APAN   14  –  6/7/13,  ©  2012  Internet2   14  –  6/7/13,  ©  2011  Internet2  
  • 15. Synchronized  Genomic  Repositories:  NCBI,  EBI,  DDBJ   15  –  6/7/13,  ©  2012  Internet2  
  • 16. US  –  China  10  Gbps  Link     Dr.  Lin  Fang   Fed  Ex:    2  days   Internet  +  FTP:   26  hours   China-­‐US  10G  Link:   30  seconds   Sample.fa   (24GB)   16  –  6/7/13,  ©  2012  Internet2   Dr.  Dawei  Lin  
  • 17. Innovation Platform 100  GigE  Layer  2  ConnecOon   Science  DMZ   SoWware  Defined  Networking   SDN  Control  Server   Internet2   innovaOon   backbone   delivered   as  100G  L1   High-­‐Performance   Layer  2/3   Switch/Router   TradiOonal   regional  and   commodity   providers   Performance  Node   Switches,  data  stores  for   data-­‐intensive  science   IP  Network   Layer  3   GENI   Experiments   Your  Research   StaOc   Layer  2   Dynamic   Layer  2   GENI   ?   For  more  informaOon,  see   fasterdata.es.net   InnovaOon  Services   TradiOonal  Switch   Substrate   TradiOonal  L3  Campus  Border  Security   17  –  6/7/13,  ©  2012  Internet2   TR-­‐CPS   TradiOonal  Services   TradiOonal   Campus   Border  Router   Campus   Enterprise   Network   R&E  IP   SoWware  Defined  Networking   Substrate   OpOcal  System   Dark  Fiber   www.internet2.edu  
  • 18. Innova0on  PlaLorm  Pilot  Sites   18  –  6/7/13,  ©  2012  Internet2  
  • 19. Mee0ng  the  Big  Data  Challenges   Transport   •  •  •  •  Science  DMZ   PerfSONAR  Toolkit   MaDDash  Tes0ng  Mesh   File  Transfer  Tools   Security   •  Science  DMZ  Hardening   •  Federated  IdM:  InCommon  and  NSTIC   Storage  and  Compute   •  Storage  and  Compute     19  –  6/7/13,  ©  2012  Internet2  
  • 20. Challenge  #1:  Transport   Science  DMZ   hhp://fasterdata.es.net/science-­‐dmz/science-­‐dmz-­‐security/   20  –  6/7/13,  ©  2012  Internet2  
  • 21. Performance  Monitoring   21  –  6/7/13,  ©  2012  Internet2  
  • 22. MaDDash  XSEDE  Tes0ng  Mesh   22  –  6/7/13,  ©  2012  Internet2  
  • 23. File  Transfer  Tools   Unix   LAN  Tools   TCP  –  based   Open  Source   •  scp,  smp,  rsync  –  poor  choices  for  WAN  (RTT  >  25ms)   •  scp  with  HPN  patch  –  beher  but  s0ll  has  limita0ons   •  Globus  Online  –  hhp://www.globusonline.org   –  Uses  GridFTP  with  TCP  op0miza0ons   –  Friendly  GUI,  Fire  and  Forget,  Galaxy  integra0on   UDP  –  based   •  Aspera:  hhp://www.asperasom.com/   Commercial   •  Annai  Systems:  hhp://www.annaisystems.com   23  –  6/7/13,  ©  2012  Internet2  
  • 24. Tool  Speeds   Berkeley,  CA    çè  Argonne,  IL      RTT=53   24  –  6/7/13,  ©  2012  Internet2  
  • 25. Challenge  #2:  Security   Hardening  the  Science  DMZ   •  •  •  •  ESnet  Big  Data  design  pahern   Internet2  Innova0on  PlaLorm   NSF  CC-­‐NIE  grants   University  of  Florida   –  –  –  –  HIPAA  alignment   Efficient  encryp0on   Comprehensive  logging   Robust  authen0ca0on   25  –  6/7/13,  ©  2012  Internet2   Source:  www.securearc.com    
  • 26. Federated  Iden0ty  Management   450 Number of Participants 400 350 300 250 200 150 100 50 0 2004 26  –  6/7/13,  ©  2012  Internet2   2005 2006 2007 2008 2009 2010 2011 2012 (June)
  • 27. NSTIC  –  Na0onal  Strategy  for  Trusted  Iden00es  in  Cyberspace   •  •  •  •  White  House  iniOaOve  administered  by  NIST   Goal  is  to  create  an  “IdenOty  Ecosystem”   IDEGS  –  IdenOty  Ecosystem  Steering  Group   Five  awards  for  pilots  spanning  mulOple  sectors:   –  –  –  –  –  Resilient  Network  Systems,  AMA,  Aetna,  ACC,  NeHC,  …   Criterion  Systems,  ID/DataWeb,  AOL,  Experian,  Ping  Iden0ty,  …   Daon,  Inc.,  AARP,  PayPal,  Purdue,  …   American  Assoc.  of  Motor  Vehile  Admins,  Microsom,  AT&A,  etc…     Internet2,  Carnegie  Mellon,  Brown,  MIT,  U.  of  Texas,  U.  of  Utah…   27  –  6/7/13,  ©  2012  Internet2  
  • 28. Challenge  #3:  Storage  and  Compute   •  Cloud  CompuOng  –  many  iniOaOves   –  –  –  –  Private:  NCI  bake-­‐off  to  create  Cancer  Knowledge  Clouds   Public/Private:  AWS  EC2  instances  ––  [100G]  ––  NCBI  repository   Open  Cloud:  BioNimbus  Protected  Data  Cloud   Proprietary:  BGI  EasyGenomics  Cloud   •  NaOonal  Cyberinfrastructure   –  XSEDE   –  Internet2   –  NCGAS     28  –  6/7/13,  ©  2012  Internet2  
  • 29. NCI:  Cancer  Knowledge  Cloud  -­‐  RFI   Summary  of  Community  Input   hhps://wiki.nci.nih.gov/display/NCIPinput/Summary+of+Input+Request%3A+Computa0onal+Needs+to+Support+Large-­‐Scale+Genomics+Inves0ga0ons   29  –  6/7/13,  ©  2012  Internet2  
  • 30. NCBI:  Four  Different  Approaches   Reduced  Data   Size   Incrementally   Transfer   Large  Files   High  Speed   Network   Connec0ons   Cloud  Access   and  Support   Source:  Don  Preuss,  NCBI  Experiences  and  Big  Data  Strategy,  presented  at  2013  Internet2  Annual   Mee0ng,  Arlington,  VA   30  –  ©  2013  Internet2  
  • 31. BioNimbus:  An  Open  Cloud  with  Protected  Data   bionimbus.opensciencedatacloud.org  
  • 32. EasyGenomics:  BGI’s  Cloud  Solu0on   Source:  Xu  Xing,  Managing  Big  Data:  The  Genome  Center  PerspecBve,  presented  at  Bio-­‐IT  World   Conference  &  Expo  ‘13,  Boston,  MA   32  –  6/7/13,  ©  2012  Internet2  
  • 33. Na0onal  Cyberinfrastructure   •  XSEDE   –  NSF-­‐funded   –  Supercomputers   –  HPC  resources   •  Internet2   –  220  universi0es   –  XSEDEnet   •  NCGAS   –  –  –  –  Indiana  University   TACC   SDSC   PSC   33  –  6/7/13,  ©  2012  Internet2   Source:  hhps://www.xsede.org/networking  
  • 34. NCGAS Virtual Instrument Indiana  University   6  PB     Storage   NSF-­‐Funded  or    XSEDE  Alloca0on   NCGAS   Galaxy     Portal   5.5  PB     Storage   SDSC   Mason   5  PB     D.C.   POD   Galaxy     Portal   TACC   100  Gig    Internet2   POD   4  PB     Storage   Federally  Funded   10  Gig    NLR   Sequencing  Center   Source:  Barneh,  W.K.,  and  R.D.  LeDuc,  Next  GeneraBon  Cyberinfrastructures  for  Next  GeneraBon   Sequencing  and  Genome  Science,  presented  at  2013  AAMC  GIR  Conference,  Vancouver,  BC   NCBI   PSC  
  • 35. Networking  Issues  for  Life  Sciences  Research   Focused  Technical  Workshop  on  July  17-­‐  18,  2013   Lawrence  Berkeley  NaOonal  Laboratory   Berkeley,  California     •  Building  on  the  success  of  Joint  Techs,  mee0ng  will  bring  together   technical  experts  in  a  smaller  seyng  with  domain  scien0sts.     •  Workshop  will  include  a  slate  of  invited  speakers  and  panels.   •  Format  to  encourage  lively,  interac0ve  discussions  with  the  goal  of   developing  a  set  of  tangible  next  steps  for  suppor0ng  this  data-­‐intensive   science  community   •  Four  sub-­‐topic  areas:    Network  Architectures,  Workflow  Engines,  Public   and  Private  Cloud  Architectures,  and  Data  Movement  Tools   •  See:    hhp://events.internet2.edu/2013/mw-­‐life-­‐sciences/index.cfm   35  –  6/7/13,  ©  2012  Internet2  
  • 36. Resources   •  The  Fourth  Paradigm  –  Data-­‐Intensive  Scien0fic  Discovery   –  http://research.microsoft.com/en-us/collaboration/fourthparadigm/   •  Internet2  Network  and  Innova0on  PlaLorm   –  http://www.internet2.edu/network/   •  Science  DMZ   –  http://fasterdata.es.net/science-dmz/   •  perfSONAR   –  http://www.perfsonar.net/   Contact   •  Internet2  Research  Support  Center   –  rs@internet2.edu •  Internet2  Life  Sciences  –  Michael  Sullivan,  MD,  Associate  Director   –  msullivan@internet2.edu   36  –  6/7/13,  ©  2012  Internet2  
  • 37. Thank  You   INTERNET2  SUPPORT  FOR  BIOMEDICAL  RESEARCH   AAMC  2013  Informa0on  Technology  in  Academic  Medicine  Conference   Vancouver  CA      June  5-­‐7,  2013     Michael  Sullivan,  M.D.   Associate  Director,  Health  Sciences,  Internet2   37  –  6/7/13,  ©  2012  Internet2  

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