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Internet2 Support for Biomedical Research

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Michael Sullivan, M.D. Associate Director, Health Sciences, Internet2

Michael Sullivan, M.D. Associate Director, Health Sciences, Internet2
AAMC 2013 Information Technology in Academic Medicine Conference Vancouver CA June 5-7, 2013

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Internet2 Support for Biomedical Research Internet2 Support for Biomedical Research Presentation Transcript

  • 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  
  • 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  Overview  
  • 3  –  6/7/13,  ©  2010  Internet2  Internet2  Community                  220  Universi0es                    60  Corpora0ons                    70  Government  agencies                    38  Regional  and  state  networks                    65  Interna0onal  R&E  networks  
  • 4  –  6/7/13,  ©  2010  Internet2  Advanced  100G  Produc0on  and  Research  Network  
  • Physics  Large  Hadron  Collider  5  –  6/7/13,  ©  2012  Internet2  Data  Tsunami  Life  Sciences  Magne0c  Resonance  Imager  (MRI)  Image by: CERN"
  • 6  –  6/7/13,  ©  2012  Internet2  Visualizing  Big  Data  Physics  LHC  –  Lead  Ion  Collision  Life  Sciences  MRI  –  Monkey  Brain  Source: Van Wedeen, M.D., Martinos Center and Dept. of Radiology,Massachusetts General Hospital and Harvard University Medical School"Source: CERN (ALICE detector)"
  • Illumina HiSeq 2500/1500  7  –  6/7/13,  ©  2012  Internet2  Sequencing:  Smaller,  Faster,  Cheaper  Handheld USB Sequencer"Image: Oxford Nanopore Technologies"Source: http://www.illumina.com/systems/hiseq_systems/hiseq_2500_1500.ilmn"
  • 8  –  6/7/13,  ©  2012  Internet2  Democra0za0on  of  Sequencing  2,386  Genome  Sequencers  Worldwide  –  30  May  2013  Source: Map of High-throughput Sequencers"
  • 9  –  6/7/13,  ©  2012  Internet2  North  American  Genome  Sequencers  998  Sequencers  in  NA  –  30  May  2013  Source: Map of High-throughput Sequencers"
  • 10  –  6/7/13,  ©  2012  Internet2  Sequencing  in  Vancouver  13  Sequencers  at  the  Genome  Science  Center  Source: Map of High-throughput Sequencers"
  • 11  –  6/7/13,  ©  2012  Internet2  Canarie  Weathermap  
  • 12  –  6/7/13,  ©  2011  Internet2  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  
  • 13  –  6/7/13,  ©  2011  Internet2  GEANT  Interna0onal    
  • 14  –  6/7/13,  ©  2011  Internet2  APAN  14  –  6/7/13,  ©  2012  Internet2  
  • 15  –  6/7/13,  ©  2012  Internet2  Synchronized  Genomic  Repositories:  NCBI,  EBI,  DDBJ  
  • 16  –  6/7/13,  ©  2012  Internet2  US  –  China  10  Gbps  Link    Fed  Ex:  Internet  +  FTP:  China-­‐US  10G  Link:    2  days  26  hours  30  seconds  Sample.fa  (24GB)  Dr.  Dawei  Lin  Dr.  Lin  Fang  
  • 100  GigE  Layer  2  ConnecOon  www.internet2.edu  Innovation PlatformSDN  Control  Server  Performance  Node  Switches,  data  stores  for  data-­‐intensive  science  TradiOonal  L3  Campus  Border  Security  High-­‐Performance  Layer  2/3  Switch/Router  TradiOonal  Campus  Border  Router  Campus  Enterprise  Network  Science  DMZ  For  more  informaOon,  see  fasterdata.es.net  SoWware  Defined  Networking  GENI  Experiments  Dark  Fiber  OpOcal  System  GENI   ?  Dynamic  Layer  2  IP  Network  Layer  3  StaOc  Layer  2  R&E  IP   TR-­‐CPS  InnovaOon  Services  TradiOonal  Services  SoWware  Defined  Networking  Substrate  TradiOonal  Switch  Substrate  Your  Research  Internet2  innovaOon  backbone  delivered  as  100G  L1  TradiOonal  regional  and  commodity  providers  17  –  6/7/13,  ©  2012  Internet2  
  • 18  –  6/7/13,  ©  2012  Internet2  Innova0on  PlaLorm  Pilot  Sites  
  • 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  Mee0ng  the  Big  Data  Challenges  
  • 20  –  6/7/13,  ©  2012  Internet2  Challenge  #1:  Transport  hhp://fasterdata.es.net/science-­‐dmz/science-­‐dmz-­‐security/  Science  DMZ  
  • 21  –  6/7/13,  ©  2012  Internet2  Performance  Monitoring  
  • 22  –  6/7/13,  ©  2012  Internet2  MaDDash  XSEDE  Tes0ng  Mesh  
  • •  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  •  Aspera:  hhp://www.asperasom.com/  •  Annai  Systems:  hhp://www.annaisystems.com  23  –  6/7/13,  ©  2012  Internet2  File  Transfer  Tools  TCP  –  based  Open  Source  UDP  –  based  Commercial  Unix  LAN  Tools  
  • 24  –  6/7/13,  ©  2012  Internet2  Tool  Speeds  Berkeley,  CA    çè  Argonne,  IL      RTT=53  
  • 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  Challenge  #2:  Security  Source:  www.securearc.com    
  • 0501001502002503003504004502004 2005 2006 2007 2008 2009 2010 2011 2012 (June)NumberofParticipants26  –  6/7/13,  ©  2012  Internet2  Federated  Iden0ty  Management  
  • •  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  NSTIC  –  Na0onal  Strategy  for  Trusted  Iden00es  in  Cyberspace  
  • •  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  Challenge  #3:  Storage  and  Compute  
  • 29  –  6/7/13,  ©  2012  Internet2  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  
  • Reduced  Data  Size  Incrementally  Transfer  Large  Files  High  Speed  Network  Connec0ons  Cloud  Access  and  Support  30  –  ©  2013  Internet2  NCBI:  Four  Different  Approaches  Source:  Don  Preuss,  NCBI  Experiences  and  Big  Data  Strategy,  presented  at  2013  Internet2  Annual  Mee0ng,  Arlington,  VA  
  • bionimbus.opensciencedatacloud.org  BioNimbus:  An  Open  Cloud  with  Protected  Data  
  • 32  –  6/7/13,  ©  2012  Internet2  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  
  • •  XSEDE  –  NSF-­‐funded  –  Supercomputers  –  HPC  resources  •  Internet2  –  220  universi0es  –  XSEDEnet  •  NCGAS  –  Indiana  University  –  TACC  –  SDSC  –  PSC  33  –  6/7/13,  ©  2012  Internet2  Na0onal  Cyberinfrastructure  Source:  hhps://www.xsede.org/networking  
  • NSF-­‐Funded  or    XSEDE  Alloca0on  Federally  Funded  NCGAS  Galaxy    Portal  POD  Galaxy    Portal  5  PB    D.C.  6  PB    Storage  5.5  PB    Storage  4  PB    Storage  TACC  SDSC  PSC  Mason  POD  Sequencing  Center   NCBI  100  Gig    Internet2  10  Gig    NLR  NCGAS Virtual InstrumentIndiana  University  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  
  • 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  Networking  Issues  for  Life  Sciences  Research  
  • •  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/  •  Internet2  Research  Support  Center  –  rs@internet2.edu•  Internet2  Life  Sciences  –  Michael  Sullivan,  MD,  Associate  Director  –  msullivan@internet2.edu  36  –  6/7/13,  ©  2012  Internet2  Resources  Contact  
  • 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  Thank  You  37  –  6/7/13,  ©  2012  Internet2