High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D....

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High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer and Information Science Director NeuroInformatics Center Computational Science Instit

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Page 1: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

High-Performance and Grid Computing for Neuroinformatics:NIC and Cerebral Data Systems

Allen D. Malony

University of Oregon

ProfessorDepartment of Computerand Information Science

DirectorNeuroInformatics Center

Computational Science Institute

Page 2: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

Neuroinformatics

Understanding brain function requires the integration of information across many levels Physical and functional Gene to behavior Microscopic and macroscopic

Challenges in brain observation and modeling Structure and organization Operational and functional dynamics Physical, functional, and cognitive

Challenges in scale How to create and maintain of integrated views of the

brain for both scientific and clinical purposes?

Page 3: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

Problem solving environment for brain analysis

Computational Science Human Neuroscience

Computational methods applied to scientific research High-performance simulation of complex phenomena Large-scale data analysis and visualization

Understand functional activity of the human cortex Multiple cognitive, clinical, and medical domains Multiple experimental paradigms and methods

Need for coupled/integrated modeling and analysis Multi-modal (electromagnetic, MR, optical) Physical brain models and theoretical cognitive models

Need for robust tools: computational and informatic

Page 4: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

UO Brain, Biology, and Machine Initiative

University of Oregon interdisciplinary research in cognitive neuroscience, biology, computer science

Human neuroscience focus Understanding of cognition and behavior Relation to anatomy and neural mechanisms Linking with molecular analysis and genetics

Enhancement and integration of neuroimaging facilities Magnetic Resonance Imaging (MRI) systems Dense-array EEG system Computation clusters for high-end analysis

Establish and support UO institutional centers

Page 5: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

NeuroInformatics Center (NIC) at UO Application of computational science methods to

human neuroscience problems Tools to help understand dynamic brain function Tools to help diagnosis brain-related disorders HPC simulation, large-scale data analysis, visualization

Integration of neuroimaging methods and technology Need for coupled modeling (EEG/ERP, MR analysis) Apply advanced statistical signal analysis (PCA, ICA) Develop computational brain models (FDM, FEM) Build source localization models (dipole, linear inverse) Optimize temporal and spatial resolution

Internet-based capabilities for brain analysis services, data archiving, and data mining

Page 6: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

NIC Organization

Allen D. Malony, Director Don M. Tucker, Associate Director Sergei Turovets, Computational Physicist Bob Frank, Mathematician Dan Keith, Software Engineer (distributed systems grid) Chris Hoge, Software Engineer (computational) Ryan Martin / Brad Davidson, Systems administrators Gwen Frishkoff, Research Associate, U. Pittsburgh Kai Li, Ph.D. student (brain segmentation) Adnan Salman, Ph.D. student (computational modeling) Performance Research Lab

Page 7: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

ICONIC Grid

SMPServerIBM p655

GraphicsSMP

SGI Prism

Shared Storage System

Gbit Campus Backbone

NIC CIS CIS

Internet 2

SharedMemory

IBM p690

DistributedMemory

IBM JS20

CNI

DistributedMemory

Dell Pentium Xeon

NIC4x8 16 16 2x8 2x16

graphics workstations interactive, immersive viz other campus clusters

40 TerabytesTape

Backup112 totalprocessors

Page 8: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

GEMINI Project

“Grid-based Electromagnetic Integrated Neuroimaging” Goals

Dynamic neuroimaging algorithms and visualization High-end tool integration and environments High-performance computational server integration Grid-based processing, data sharing, and collaboration Neuroinformatics data ontologies

Page 9: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

GEMINI Architecture

Page 10: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

Computational Integrated Neuroimaging System

… …

raw

storageresources

virtualservices

compute resources

Page 11: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

Cerebral Data Systems

Partnership between EGI and University of Oregon Develop and market neuroinformatics services

Neurological medical data transfer, storage, and analysis High-performance and sophisticated EEG and MR analysis Telemedicine and distributed collaboration Shared brain repositories

Target markets Research and clinical Epilepsy diagnosis and pre-surgical planning MR image segmentation

Technology integration Internet and computional grids High-performance computing

Page 12: High-Performance and Grid Computing for Neuroinformatics: NIC and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department of Computer.

NIA Visit April 6, 2006High-Performance and Grid Computing for Neuroinformatics

CDS Computational Server and Imaging Clients


GENII: Grid-based Environment for Neuroimaging Integration and Interoperation Human Brain Project – Neuroinformatics Proposal Allen D. Malony Don Tucker.

GENII: Grid-based Environment for Neuroimaging Integration and Interoperation Human Brain Project – Neuroinformatics Proposal Allen D. Malony Don Tucker.

Sameer Shende, Allen D. Malony {sameer,malony}@cs.uoregon.edu Computer & Information Science Department Computational Science Institute University of Oregon.

Sameer Shende, Allen D. Malony {sameer,malony}@cs.uoregon.edu Computer & Information Science Department Computational Science Institute University of Oregon.

Allen D. Malony, Sameer Shende {malony,shende}@cs.uoregon.edu Department of Computer and Information Science Computational Science Institute University.

Allen D. Malony, Sameer Shende {malony,shende}@cs.uoregon.edu Department of Computer and Information Science Computational Science Institute University.

Sameer Shende, Allen D. Malony {sameer, malony}@cs.uoregon.edu Department of Computer and Information Science Computational Science Institute University.

Sameer Shende, Allen D. Malony {sameer, malony}@cs.uoregon.edu Department of Computer and Information Science Computational Science Institute University.

Performance Tools for GPU-Powered Scalable Heterogeneous Systems Allen D. Malony, Scott Biersdorff, Sameer Shende {malony,scott,sameer}@cs.uoregon.edu.

Performance Tools for GPU-Powered Scalable Heterogeneous Systems Allen D. Malony, Scott Biersdorff, Sameer Shende {malony,scott,sameer}@cs.uoregon.edu.

Allen D. Malony, Kevin Huck {malony,khuck}@cs.uoregon.edu Department of Computer and Information Science Performance.

Allen D. Malony, Kevin Huck {malony,khuck}@cs.uoregon.edu Department of Computer and Information Science Performance.

Neuroinformatics challenges in MRI data integration

Neuroinformatics challenges in MRI data integration

Allen D. Malony malony@cs.uoregon.edu Performance Research Laboratory (PRL) Neuroinformatics Center (NIC) Department.

Allen D. Malony [email protected] Performance Research Laboratory (PRL) Neuroinformatics Center (NIC) Department.

Allen D. Malony Sameer S. Shende Robert Bell {malony, sameer, bertie}@cs.uoregon.edu Department of Computer and Information Science Computational Science.

Allen D. Malony Sameer S. Shende Robert Bell {malony, sameer, bertie}@cs.uoregon.edu Department of Computer and Information Science Computational Science.

Allen D. Malony, Sameer Shende, Robert Ansell-Bell {malony,sameer,bertie}@cs.uoregon.edu Computer & Information Science Department Computational Science.

Allen D. Malony, Sameer Shende, Robert Ansell-Bell {malony,sameer,bertie}@cs.uoregon.edu Computer & Information Science Department Computational Science.

Performance Profiling Overhead Compensation for MPI Programs Sameer Shende, Allen D. Malony, Alan Morris, Felix Wolf {malony,sameer,amorris}@cs.uoregon.edu.

Performance Profiling Overhead Compensation for MPI Programs Sameer Shende, Allen D. Malony, Alan Morris, Felix Wolf {malony,sameer,amorris}@cs.uoregon.edu.

Introduction to Neuroinformatics: Support Vector Machinesml.informatik.uni-freiburg.de/_media/teaching/ss13/ml/riedmiller/ried... · Introduction to Neuroinformatics: Support Vector

Introduction to Neuroinformatics: Support Vector Machinesml.informatik.uni-freiburg.de/_media/teaching/ss13/ml/riedmiller/ried... · Introduction to Neuroinformatics: Support Vector

Allen D. Malony, Aroon Nataraj {malony,anataraj}@cs.uoregon.edu Department of Computer and Information Science Performance.

Allen D. Malony, Aroon Nataraj {malony,anataraj}@cs.uoregon.edu Department of Computer and Information Science Performance.

神经信息学 Neuroinformatics

神经信息学 Neuroinformatics

Sameer Shende, Allen D. Malony, and Alan Morris {sameer, malony, amorris}@cs.uoregon.edu Department of Computer and Information Science NeuroInformatics.

Sameer Shende, Allen D. Malony, and Alan Morris {sameer, malony, amorris}@cs.uoregon.edu Department of Computer and Information Science NeuroInformatics.

N2A A neuroinformatics framework

N2A A neuroinformatics framework

Global coordination in neuroinformatics

Global coordination in neuroinformatics

Chee Wai Lee, Allen D. Malony, Alan Morris {cheelee,malony,amorris}@cs.uoregon.edu Department of Computer and Information Science Performance Research.

Chee Wai Lee, Allen D. Malony, Alan Morris {cheelee,malony,amorris}@cs.uoregon.edu Department of Computer and Information Science Performance Research.

Neuroscience, Neuroinformatics, Neurotechnology and Neuro ...

Neuroscience, Neuroinformatics, Neurotechnology and Neuro ...

High-Performance and Grid Computing for Neuroinformatics: EGI, UO, and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department.

High-Performance and Grid Computing for Neuroinformatics: EGI, UO, and Cerebral Data Systems Allen D. Malony University of Oregon Professor Department.