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neuGRID

neuGRID. A GRID-BASED e-INFRASTRUCTURE FOR DATA ARCHIVING/ COMMUNICATION AND COMPUTATIONALLY INTENSIVE APPLICATIONS IN THE MEDICAL SCIENCES.

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neuGRID

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  1. neuGRID A GRID-BASED e-INFRASTRUCTURE FOR DATA ARCHIVING/ COMMUNICATION AND COMPUTATIONALLY INTENSIVE APPLICATIONS IN THE MEDICAL SCIENCES Giovanni B Frisoni (P.I.)1, Christian Spenger2, Alex Zijdenbos2, Richard McClatchey3, David Manset4, FrederikBarkhof5, Lars-OlofWahlund6, Tony Solomonides7, Carla Finocchiaro8 1IRCCS Fatebenefratelli – Centro Nazionale per la Malattia di Alzheimer e le Malattie Psichiatriche, Brescia, Italy; 2Neuralyse Europe GmbH, Switzerland; 3University of the West of England, Bristol, UK; 4Maat G Knowledge SL, Toledo, Spain; 5VUmc - Vrije Universitet Medical Center, Amsterdam, The Netherlands; 6Karolinska Institutet, Stockholm, Sweden; 7HealthGrid, France; 8CF consulting, Milano, Italy

  2. neuGRID • European FP7 funded project (I3) • Started Feb 2008 (3 years) • ~3M€ total budget • 8Europeanpartners • Builds on proven technologies: • MammoGrid (MAAT, UWE) • LORIS database infrastructure and CLASP Pipeline (McGill/MNI, Prodema Informatics)

  3. Provincia Lombardo Veneta Fatebenefratelli, ITALY Vrije Universiteit Medical Centre, THE NETHERLANDS Prodema Informatics, SWITZERLAND CF consulting s.r.l., ITALY University of the West of England, Bristol, UK Maat Gknowledge, SPAIN Karolinska institutet, SWEDEN HealthGrid, FRANCE neuGRID

  4. Question Marker of Alzheimer’s progression (like PSA for prostate cancer) *Courtesy of Provincia Lombardo Veneta Fatebenefratelli (FBF)

  5. Common Practice • Technology and expertise exists at select centers • Researchers huddle together at those centers

  6. neuGRID Approach (1) • Expertise and technology available on-line • Computational analyses distributed on a grid

  7. neuGRID Use Case (1)

  8. neuGRID Use Case (2)

  9. neuGRID Approach (2) • Combination of LORIS & MammoGrid • Grid as the technological glue • I.e. « gridification » of the LORIS solution « à la » MammoGrid • Deploymentof the Solution in relevant major centres accross Europe LORIS neuGRID MammoGrid

  10. MammoGrid WP MWS MAS European FP5 Project MG Server Workstation SOA Mammogram Images PACS System MammoGrid Services Patients Clinical Data Grid Connectivity ﾺ Algorithms repository Mammogram Scanner Algo'1' Algo'2' Remote Clinical Centres Algo'n' Digital Mammographer

  11. LORIS (1) Solution Highlights • Originally developed for the NIH-funded “MRI Study of Normal Brain Development” • Centralised Solution • Centraliseddatabase + local cluster • Web-based solution for uploadingimaging data • Brainimage processingalgorithmtoolbox • E.g. Cortical ThicknessMeasurement • User-facing services • Data acquisition and quality control • Querygraphical user-interface • Open Standards *Courtesy of Prodema Informatics

  12. LORIS (2) Solution Highlights Patient Data Management Image Browser JAVA-based 3D Image Overlay *Courtesy of Prodema Informatics

  13. neuGRID Architecture (1) Service-Oriented Architecture

  14. neuGRID Architecture (2) Service-Oriented Architecture LORIS MammoGrid EGEE gLite New Stuff

  15. neuGRID Infrastructure A Layered Infrastructure LEVEL 0 Data Coordination Centre - DCC Grid Coordination Centre - GCC Virtual Database LEVEL 1 Data Archiving & Computing Site – DACS LEVEL 2 . . . . . . Data Collection Site – DCS

  16. The work has started... (1) • Requirementsgatheringand analysis • Visited the 3 clinical sites to fetchrequirements • Functionalrequirements formalisation • Use-cases specifications • Technical brainstorming and specifications • State-of-the-art review • Prototypingongoing • Gluing Service • Workflowauthoring • Data Provenance Service

  17. The work has started... (2) • Deployment logistics preparation • Designed not less than 18 hardware specifications for access points • Considereddifferent types of hardware fromregular rack-mountable servers to blades • Setupdevelopmentenvironment(neuGRIDPoC) • CertificateAuthority • Virtual Organisation • Grid Information System • File Catalogue

  18. neuGRID Infrastructure A Layered Infrastructure Deployedsince Sept 2008 Ongoing Expected 2009 Exploitation 2010

  19. neuGRID Exploitation Exploitation & Business Plan Proof of Concept Pre-Commercial Exploitation Commercial Exploitation Consortium Neuroscience Community ? Pharma Industry Non Neurosci Comm. Post-Project Project

  20. New Related Initiatives • CBRAIN - Canadian Brain Imaging Research Network • Recently funded by CANARIE (Canadian Advanced Network and Research for Industry and Education) • NeuroLOG • Funded by the French ANR A Super Neurosciences Grid-enabled Network?

  21. Conclusions • neuGRID aims to bring sophisticated neuro-imaging analyses “home” • neuGRID consortium has strong ties to international neuro-scientific, grid, and clinical communities • Partners have complementary expertise • Technology based on established, proven software solutions • Deployment has started – DCC and GCC in place • 1st DACS at FBF willbeready in comingmonth • neuGRID prototype being developed with objective to demo mid October 2008

  22. neuGRID A GRID-BASED e-INFRASTRUCTURE FOR DATA ARCHIVING/ COMMUNICATION AND COMPUTATIONALLY INTENSIVE APPLICATIONS IN THE MEDICAL SCIENCES Giovanni B Frisoni (P.I.)1, Christian Spenger2, Alex Zjdenbos2, Richard McClatchey3, David Manset4, FrederikBarkhof5, Lars-OlofWahlund6, Tony Solomonides7, Carla Finocchiaro8 1IRCCS Fatebenefratelli – Centro Nazionale per la Malattia di Alzheimer e le Malattie Psichiatriche, Brescia, Italy; 2Neuralyse Europe GmbH, Switzerland; 3University of the West of England, Bristol, UK; 4Maat G Knowledge SL, Toledo, Spain; 5VUmc - Vrije Universitet Medical Center, Amsterdam, The Netherlands; 6Karolinska Institutet, Stockholm, Sweden; 7HealthGrid, France; 8CF consulting, Milano, Italy Thank You For Your Attention Visitour Booth! SummaryneuGRID will be a user-friendly Grid-based research e-Infrastructure enabling the European neuroscience community to carry out imaging research on degenerative brain diseases. In neuGRID, the collection/archiving of large amounts of imaging data will be paired with computationally intensive data analysis tools (cortical thickness extraction). Networking activities Establishment of EU and international links. Development of ethical standards and privacy protection protocols. Establishment of a medical imaging database. Training courses and dissemination. Promotion of clustering and concertation actions amongst other related projects. Service activitiesneuGRID will result from merging two project infrastructures, a database service specific to neurodegenerative diseases providing data management and computationally intensive community services, and MammoGrid, providing a generic set of services optimizing and facilitating the use of a grid infrastructure. Joint Research ActivitiesneuGRID will implement the cortical extraction pipeline to run in the grid in order to produce results identical to a centralized system. neuGRID will be end-user transparent. The work plan is split into a set of three logical phases: (i) needs assessment, technical evaluation, planning, and implementation; (ii) performance evaluation; (iii) validation. User communitiesNeuroscientists working in the field of imaging of Alzheimer’s disease. Algorithm developers will have a powerful testbed as well as access to a large community of neuroscientists that might exploit their products. Pharma industry (surrogate outcomes for clinical trials) and non neuroscientific communities are prospective users. Action plan Phase 1 - Project Foundation by Month 12 Phase 2 - Project Deployment by Month 24 Phase 3 - Project Final Phases by Month 36 International issuesCollaborative arrangements include the European Alzheimer’s Disease Consortium (EADC), Alzheimer’s Disease Neuroimaging Initiatives (ADNI), the Montreal Neurological Institute, EC InnoMed/AddNeuroMed project, EC NeuroLog, EC NeuroGrid, the Alzheimer’s Association, the LoNI in Los Angeles, the FIL in London, the French IFRAD, the FMRIB in Oxford, and the EFNS. This project has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n°211714

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