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Artur  Binczewski  Krzysztof  Kurowski,  Cezary Mazurek,  Juliusz  Pukacki  

 

Best practices for e-Healt and ICT cooperation in PSNC

Center  of  e-­‐Infrastructure  

National  Research  and  Education  Network  PIONIER  Research  Metropolitan  Area  Network  -­‐  POZMAN  HPC  Center  Data  repositories  and  Digital  Libraries  Federation    

 

New  Generation  Networks  HPC  and  Grids  Center  Data  Management  services  Digital  Libraries  and  Portals  Technology,  Applications  and  Services  for  IS    Future  Internet  Cyber  Security  

Center  for  R  &  D  

From  6  people  in  1993  

to  275  people  in  2010  

National  Research  and  Education  Network    -­‐  PIONIER  (topology)  

 Area                                                              312k  sq  km  

 Population                                                                38M  

 Main  academic  centers                            21  

 State  universities                                        165+  

 Students                                                                  2M+        R&D  institutions        and  Univ.  interconnected        via  PIONIER  network                              700+  

         22  MANs  and  5  HPC  Centers  in  PIONIER  Consortium  with  PSNC  as  Operator  

5854  km  of  fiber  infrastructure  in  Poland      763  km  of  fiber  in  Germany  (IRU)  

   6617  km  of  fiber  in  total  

HPC  Center  

Environment:    -­‐  300+  sqm  of  data  center    -­‐  air,  liquid  coolled  systems    -­‐  video  monitoring,  fire  protection    -­‐  24h  monitoring    Systems:    -­‐  HPC  infrastructure    -­‐  PC  clusters      -­‐  Graphical  servers    -­‐  Data  storage      Part  of  -­‐  European  HPC  infrastructure  (PRACE)  -­‐  European  and  national  grid  infrastructure  -­‐  National  data  storage      

Total peak performance 72 TFlops, total RAM 174 TB, disk arrays 0,8 PB, storage capacity 3,7 PB (4Q2010)                                                                                            4xTOP500  

European  R&D  projects  

COORDINATED PARTNERSHIP IN FP7

PARTNERSHIP IN FP5

PARTNERSHIP IN FP6

PARTNERSHIP IN EUROPEAN INITIATIVES

Telemedicine  of  Wielkopolska  

Budget:  2.44  mln  euro  Funding:    

EEA  Financial  Mechanism  (85%)  Ministry  of  Science  and  Higher  Education  /  Ministry  of  Health  (15%)  

Partners:  Pozna  Supercomputing  and  Networking  Center  Pozna  University  of  Medical  Sciences  Pozna  University  of  Technology  26  hospitals  from  the  area  of  the  Wielkopolska  province  

Telemedicine  of  Wielkopolska  

3.4  mln  inhabitants  (Wielkopolska  province)  35  counties  

each  county  operates  a  hospital  with  surgery  and/or  trauma-­‐orthopedic  ward  

Main  city:  Poznan  Poznan  University  of  Medical  Sciences  (PUMS)  reference  centers  

Trauma  reference  center:  Division  of  Trauma,  Burns  and  Plastic  Surgery  (PUMS)  cooperating  clinical  departments  

Telemedicine  of  Wielkopolska  -­‐  goal  

Improvement  and  standardization  of  communication:  regional  

department  in  the  area  of  trauma  Safety  increase  for  patients  with  multiple  body  injuries  Effective  utilization  of  scarce  human  resources  Increase  of  qualification  level  of  the  Wielkopolska  hospitals  personnel  

Clinical  hospitals  (reference  centers)  

Hospitals    

Communication  'hospital      reference  center'  

Communication  

department      clinical  

 

Education'University  of  Medical  Sciences    hospital'  

Medical  Sciences  

Telemedicine  of  Wielkopolska  -­‐  scope  

Construction  of  effective,  flexible  and  secure  system   for   medical   teleconsultations   in  trauma  and  radiology  

teleconsultations   hospital     university  clinical  department  telecouncils   of   specialists   for   specially  difficult  cases  possibility   of   teleconsultations   hospital    hospital  (pilot  deployment    for  radiology)  

 Construction  of  medical  digital  library  

medical  teleeducation  clinical  decision  support  reporting  to  regional  specialist  supervisor  

Open  HD  videoconferencing  platform  

HDVIPER:  International  project  (9  partners),  CELTIC  program,  duration:  2007-­‐2009  Goals:  

To   create   an   open   and   scalable   High   Definition   (HD)   videoconferencing   platform  prototype    To   develop   additional   services   based   on   the   Service   Oriented   Architecture   (SOA)  paradigm  to  enable  new  functionality  beyond  videoconferencing  To  evaluate  the  platform  in  the  following  scenarios:  residential,  business,  education  and  healthcare  To  create  an  affordable  solution  to  promote  common  usage  of  HD  videoconferencing  

HIPERMED:  Follow-­‐up  to  HDVIPER  16  partners,  CELTIC  program,  duration:  2010-­‐2012  Goal:  extending  HD  videoconferencing  platform  prototype  created  during  the   HDVIPER   project   focusing   on   enriching   audio-­‐video   communication  for  use  in  healthcare  scenarios  

 

HIPERMED  

New  functionality:  multiple  video  streams  from  endoscopes  and  other  medical  instruments  stereoscopic  video  streams  providing  true  depth  perception  measurement  data  from  sensors  on  patients  sharing  of  high  resolution  digital  images  (X-­‐ray,  NMR,  ultrasound,  etc)  DICOM  and  HL7  standards  support  

Scenarios:  Professional-­‐to-­‐professional  

multidisciplinary  decision  making  second  opinion  (remote  consultations)  diagnostic  support  basic  education  

Professional-­‐to-­‐patient  follow-­‐up  of  patients  out  of  the  hospital  recovery  at  home  teleassistance  

   

ENT  Surgery  Live  

 Supercomputing  and    Networking  Center  Department  of  Otolaryngology,    

 University  of  Medical  Sciences      

ENT  Surgery  Live  

To   enable   remote   education   for   young   doctors   and   medical  students  by  performing  reference  surgeries  by  professors  in  clinical  hospitals  To  provide  live  surgery  transmissions  over  the  Internet  

Full  PAL  video  resolution  (HD  possible)  Multiple   cameras:   operation   field   camera,   microscope   camera,   overall  camera  Surgeon  verbally  comments  the  procedure  while  he  operates  Users  access  the  transmission  and  can  ask  questions  via  a  dedicated  Internet  portal  

To   allow   reviewing   recorded   surgeries   at   any   time   as   Video   on  Demand  (VoD)  Archieve:  

http://orl.amp.edu.pl/teksty.php?plik=index.php&lang=eng      

ENT  Surgery  Live  -­‐  architecture  

ENT  Surgery  Live  -­‐  statistics  

Up  to  500  concurrent  video  stream  views  Viewers   not   only   from   Poland,   but  also   from   Germany,   UK,   USA,  Switzerland,  Holland  and  Finland  Approximately  350  GB  of  data  

         transmitted  per  session  Already  6  live  surgery  events  transmitted  Extremely  positive  response  of  the  medical  community,  possible  transmissions  in  other  medical  areas    

eHealth  European  Union  level  projects  

ACGT  -­‐  Advancing  Clinico-­‐Genomic  Trial  on  Cancer  EU  founded  project  (IP)  of  6th  FP  February  2006    July  2010  Total  budget:  16M  euro  

P-­‐medicine  -­‐  From  data  sharing  and  integration  via  VPH  models  to  personalized  medicine  

EU  founded  project  (IP)  of  7th  FP  February  2011    January  2015  Budget:  14  M  euro  

AirPROM     -­‐  Airway  Disease  PRedicting  Outcomes   through  Patient  Specific  Computational  Modelling  

EU  founded  project  (IP)  of  7th  FP  March    2011    February  2016  Budget  15,5  M  euro  

 

ACGT  -­‐  Consortium  

ERCIM  FORTH  Phillips  Research  Universiteit  van  Amsterdam  Universidad  Politechnica  de  Madrid  Universidad  de  Malaga  Lunds  Universitet  Institut  Suisse  de  Bioinformatique  Fraunhofer-­‐Gesellschaft  Universitaet  des  Saarlandes  Istituto  Europeo  di  Oncologia  Custodix  Biovista  Healthgrid  Hokkaido  University  PSNC  

The  ACGT  vision  &  principles  

The  ultimate   objective   of   the  ACGT  project  was   the   provision   of   a  unified  technological  infrastructure  which  will  facilitate    

integrated  access  to  multi-­‐level  biomedical  data  development  or  re-­‐use  of  open  source  analytical  tools,  accompanied  with  the  appropriate   meta-­‐data   allowing   their   discovery   and   orchestration   into  complex  workflows.  

ACGT  delivered  a  European  Biomedical  GRID   infrastructure  offering  seamless   mediation   services   for   sharing   data   and   data-­‐processing  methods  and  tools,  and  advanced  security;  

focuses  on  clinical  trials  on  Cancer  (Wilms  tumor,  Breast)  and  is  based  on  the  principles  of    

Open  access  (among  trusted  partners)  Open  source  

Is  not  a  standards  generating  exercise  but  a  standards  adopting  one.  

Main  challenges  in  ACGT  

Grid  middleware   services,   enabling   large-­‐scale   (semantic,   structural,   and  syntactic)  interoperation  among  biomedical  resources  and  services  Master   ontology   (on   Cancer)   through   semantic   modeling   of   biomedical  concepts  using  existing  ontologies  and  ontologies  developed  for  the  needs  of  the  project  Open  source  bioinformatic  tools  and  other  analytical  services  Semantic  annotation  and  advertisement  of  biomedical  resources,  to  allow  metadata-­‐based  discovery  and  query  of  tools,  and  services  Orchestration  of  data  access  and  analytical  services  into  complex  eScience  workflows  for  post  genomic  clinical  research  and  trials  on  cancer  Meta-­‐data   descriptions   of   clinical   trials   to   provide   adequate   provenance  information  for  future  re-­‐use,  comparison,  and  integration  of  results  

PSNC in ACGT  

Overall  architecture  design  Biomedical  Grid  infrastructure  

Common  Grid  layer  based  on  Globus  Advanced  services  based  on  PSNC  Gridge    Toolkit  

GRMS    resource  management  and  allocation  in  the  Grid  DMS    data  management  GAS    grid  authorization  service  and  VO  management  

Support  for  execution  simulations  in  the  Grid  environment    Oncosimulator  application  

P-­‐medicine  -­‐  consortium  

Biovista  (USA/Greece)  Christian  Albrecht    zu  Kiel  (Germany)  Custodix  (Belgium)  eCancer  (Germany)  Eurice  -­‐  European  Research  and  Project  Office  GmbH  (Germany)  FhG-­‐IAIS  -­‐  Institute  for  Intelligent  Analysis  and  Information  Systems  (Germany)  FhG-­‐IBMT    -­‐  Institut    Biomedizinische  Technik  (Germany)  FORTH  -­‐  Foundation  for  Research  and  Technology    Hellas  (Greece)  ICCS  -­‐    Institute  of  Communication  and  Computer  Systems  (Greece)  IEO  -­‐    Istituto  Europeo  di  Oncologia  s.r.l.  (Italy)  LUH    Leibniz    Hannover,  Institute  for  Legal  Informatics    Institut    Rechtsinformatik  (Germany)  Philips  -­‐    Royal  Philips  Electronics  (Holland)  PSNC  -­‐  Poznan  Supercomputing  and  Networking  Center  (Poland)  SIB  -­‐    Swiss  Institute  of  Bioinformatics  (Switzerland)  UCL  -­‐    University  College  London  (United  Kingdom)  UDUS  -­‐    Heinrich-­‐Heine-­‐University,  Coordination  Centre  for  Clinical  Trials  (Germany)  UHok  -­‐  Hokkaido  University  (Japan)  The  Chancellor,  Masters  and  Scholars  of  the  University  of  Oxford  (United  Kingdom)  UPM  -­‐    Universidad  Politecnica  de  Madrid,  Facultad  de  Informatica  (Spain)  USAAR  -­‐    Saarland  University  (Germany)    

P-­‐medicine  general  goals    

Scenarios  and  structures  that  help  to  run  more  clinical  trials  and  to  bridge  the  gap  between  treatment  given  to  patients  today  and  research  Building  infrastructure  that  will  facilitate  the  development  from  current  medical  practice  to  personalized  medicine  

P-­‐medicine  objectives  

Creating   a   collaborative   environment   facilitating   clinically   driven   multiscale   VPH  modelling  leading  to  personalized  medicine    Developing,  sharing  and  running  VPH  simulations  for  clinical  decision  support  Building  a  data  warehouse  for  the  secure  storage  and  sharing  of  heterogeneous  data  to  be  used  by  the  scientific  community    Building   a   p-­‐medicine   workbench   as   a   central   access   point   for   tools,   models,   services  workflows  and  to  data  resources        Exploiting  the  potential  of  high  performance  computing  and  cloud  storage  for  the  use  of  VPH  models  and  data  services  Improvement  of  semantic  interoperability  and  data  integration  Increasing  the  quality  of  data  mining  in  biomedical  research    Establishing  a  service  framework  for  access  to  biomaterial  resources  Empowering  patients  through  respective  tools,  which   include  them  more  actively   in  the  health  care  decision  process  and  in  clinical  research  Linking   the   p-­‐medicine   environment   with   important   European   Research   infrastructure  initiatives  Develop  a  business  plan  to  maintain  and  further  develop  p-­‐medicine  into  a  self-­‐sustaining  entity  

P-­‐medicine  -­‐  PSNC  role  

Overall  architecture  design  Cloud  based  data  management  solutions  

Implementing  and  deploying  cloud  interfaces  for  p-­‐medicine  Data  Warehouse  and  other  services  and  tools  Reliable  long  term  data  storage  in  the  background  (National  Data  Storage  infrastructure)  

Access  to  HPC  infrastructure  Oncosimulator  application  optimization    and  adaptation  to  new  architectures  (GPU)  

AirPROM  -­‐  consortium  

  University  of  Leicester  (United  Kingdom)     Helemholtz   Zentrum   Muechen   Deutsches   Forschungszentrum  

Gesundheit  Und  Umwelt  GMBH  (Germany)     Academisch   Medisch   Centrum   bij   de   Universiteit   van  

Amsterdam  (Holland)     Imperial   College  Of  Science,  Technology  And  Medicine   (United  

Kingdom)      University  Belfast  (United  Kingdom)     The  Chancellor  Masters  And  Scholars  of  the  University  of  Oxford  

(United  Kingdom)     The  University  of  Nottingham  (United  Kingdom)     The  University  of  Sheffield  (United  Kingdom)     Institut  Telecom  (France)     The  University  of  Warwick  (United  Kingdom)     Fundacio  Privada  Parc  Cientific  De  Barcelona  (Spain)       Materialise  Nv  (Belgium)     Ansys  UK  Limited  (United  Kingdom)     Fluidda  Nv  (Belgium)     Biomax  Informatics  AG  (Germany)     European  Respiratory  Society    (Switzerland)     Biosci  Consulting    (Belgium)     University  Of  Southampton  (United  Kingdom)     Universita  Degli  Studi  Di  Catania  (Italy)     Semmelweis  Egyetem  (Hungary)  

  The  University  Of  Manchester  (United  Kingdom)     Universite  De  La  Meditarranee    -­‐  Marseille  (France)     Umea  Universitet  (Sweden)     Karolinska  Institutet  (Sweden)     Objet  Geometries  GMBH  (Germany)     Universitata  Degli  Studi  Di  Ferrara    (Italy)     European  Federation  Of  Asthma  &  Allergy  Associations  Ideell  

Forening  (Belgium)     Instytut    i  Chorob  Pluc    (Poland)     Vastra  Gotlands  Lans  Landsting  (Sweden)     Orszagos  Koranyi  Tbe  Es  Pulmonologiai  Intezet  (Hungary)     Commissatiat   a   l   Energie   Atomique   et   Aux   Energies  

Alternatives  (France)     University   Hospitals   Coventry   And   Warwickshire   National  

Health  Service  Trust  (United  Kingdom)     European  Lung  Foundation  (United  Kingdom)     Poznan  Supercomputing  and  Networking  Center  (Poland)  

AirPROM  general  goals  

The  main  goal  of  the  project  is  to  develop  multi-­‐scale  airway  model  that  will  allow  to  predict  progression  of  airway  diseases  and  response  to  treatment.  This  model  will  be  based  on  extensive  clinical  characterization,  standard  physiological  measurements,  CT-­‐scans,  functional  imaging  (MRI)  and  biological  phenotyping.  AirPROM  will  also  enable  improving  and  personalizing  management  of  airway  diseases,  precisely  asthma  and  Chronic  Obstructive  Pulmonary  Disease.  

AirPROM  objectives  

Development  of  a  patient-­‐specific,  integrated,  multi-­‐scale  computational  model,  to  predict  the  natural  history  and  response  to  therapy  in  airway  disease.  Increase  the  armamentarium  to  fight  airway  disease,  select  the  right  therapy  for  the  right  patient  Understanding  the  complexity  of  airways  disease  

Tissue  to  organ:  image  functional  modeling  Cellular  to  tissue:  airway  remodeling  

omics  Measuring  the  environment:  metagenomics  

Implementation  of  statistical  modeling  of  airways  disease:  phenotyping  the  heterogeneity  Implementation  of  patient-­‐specific  multi-­‐scale  computational  models  

PSNC  role  in  AirPROM  

Integration  of  computational  tools  for  large  airway  high-­‐throughput  modeling  Optimization  of  CFD  modeling  tools  Preparing  high-­‐throughput  semi-­‐automated  framework  for  large  airway  modeling  

Macro-­‐large  airway  model  Integration  and  application  of  tools  and  methods  delivered  to  CFD  simulations  

Knowledge  management  and  security  Integration  of  federated  data  resources  and  algorithms  

API  based  service-­‐oriented  architecture  approach  

Supporting  the  interactive  and  automatic  AirPROM  data  flows  Quality  and  security  assessment  Support  on  security  aspects  

Providing  data  storage  system  for  AirPROM  project  Providing  different  types  of  computational  systems  depending  on  requirements  

Challenges  

 Establish  new  cooperation    Active  promotion  new  ICT  services  in  medical  community                 in  Poland      International  relation  

 International  Update  session  and  Shared  Cyberinfrastructure  for  Global                    Medical  Research  session  at  the  Fall  2011  Internet2  meeting          (October  3-­‐6,  2011)    Poland-­‐US  Cooperation  in  Cancer  Research  

 Deployment  of  advanced  network  and  ICT  services  in  e-­‐Health          applications  

 Digital  libraries,  Bandwidth  on  Demand    (e.g.  AutoBahn),          HD  videoconferencing,  Federation  (e.g.  EduGain),  etc.  

 Promotion  of  open  standards          

     

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