neuroinformatics, the iconic grid, and oregon’s science industry
DESCRIPTION
Neuroinformatics, the ICONIC Grid, and Oregon’s Science Industry. Allen D. Malony University of Oregon. Professor Department of Computer and Information Science. Director NeuroInformatics Center Computational Science Institute. May 10, 2004. Oregon’s 2004 Bioscience Conference. Outline. - PowerPoint PPT PresentationTRANSCRIPT
Neuroinformatics, the ICONIC Grid, and Oregon’s Science Industry
Allen D. Malony
University of Oregon
Oregon’s 2004 Bioscience ConferenceMay 10, 2004
ProfessorDepartment of Computerand Information Science
DirectorNeuroInformatics Center
Computational Science Institute
May 10, 2004 2004 Bioscience Conference
Outline
Computational science High-performance computing research at UO Brain, Biology, and Machine Initiative Neuroinformatics and the ICONIC Grid
NeuroInformatics Center (NIC) Electrical Geodesics, Inc. (EGI) ICONIC Grid system and application
HPC / Grid computing for Oregon’s science industry Services delivery (research, clinical, medical, …) HPC resource centers High-bandwidth state-wide networking
May 10, 2004 2004 Bioscience Conference
Computational Science
Integration of computerscience in traditionalscientific disciplines
Increasingly acceptedmodel of scientificresearch
Application of high-performancecomputation, algorithms, networking, database,and visualization Parallel and grid computing Integrated problem-solving environments
Computer science research at the core
ComputerScience
Biology
Neuroscience
PsychologyPaleontology
Geoscience
Math
May 10, 2004 2004 Bioscience Conference
Computational Science Projects at UO Geological science
Model coupling for hydrology Bioinformatics
Zebrafish Information Network (ZFIN) Evolution of gene families Oregon Bioinformatics Toolkit
Neuroinformatics Paleontology
Dinosaur skeleton and motion modeling Artificial intelligence
Computational Intelligence Research Lab (CIRL) Oregon Computational Science Institute
May 10, 2004 2004 Bioscience Conference
HPC Research Project Areas at UO
Parallel performance evaluation and tools Parallel language systems Tools for parallel system and software interaction Source code analysis Parallel component software Computational services Grid computing Parallel modeling and simulation Scientific problem solving environments
May 10, 2004 2004 Bioscience Conference
HPC Research Affiliations at UO
Strong associations with DOE national laboratories Los Alamos National Lab, Lawrence Livermore
National Lab, Sandia National Lab, Argonne National Lab, Pacific Northwest National Lab
DOE funding Office of Science, Advance Scientific Computing
Research Accelerated Strategic Computing Initiative
(ASCI/NNSA) NSF funding
Academic Research Infrastructure Major Research Instrumentation
May 10, 2004 2004 Bioscience Conference
Brain, Biology, and Machine Initiative
UO 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 of neuroimaging resources Magnetic Resonance Imaging (MRI) systems Dense-array EEG systems Computation clusters for high-end analysis
Establish and support institutional centers
May 10, 2004 2004 Bioscience Conference
BBMI Sponsored Research
$40 million research attracted by BBMI DoD TATRC funding
Telemedicine Advanced Technology Research Center $10 million gift from Robert and Beverly Lewis family
Established Lewis Center for Neuroimaging (LCNI) Dr. Ray Nunnally, Director
NIH NSF Oregon bond funds UO foundation funds
May 10, 2004 2004 Bioscience Conference
BBMI Research and Development Plan
Imaging technology and integration Dense-array EEG and MRI Coil development Simultaneous measurement
Computational analysis problems Image segmentation, analysis, identification EEG signal decomposition, component analysis, source
localization Internet-based capabilities for analysis services, data
archiving, and data mining Computation and data grid for bio and neuro sciences
May 10, 2004 2004 Bioscience Conference
Computational Science and 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, informatic, and collaborative
May 10, 2004 2004 Bioscience Conference
Brain Dynamics Analysis Problem
Identify functional components Different cognitive neuroscience research contexts Clinical and medical applications
Interpret with respect to physical and cognitive models Requirements: spatial (structure), temporal (activity) Imaging techniques for analyzing brain dynamics
Blood flow neuroimaging (PET, fMRI) good spatial resolution functional brain mapping temporal limitations to tracking of dynamic activities
Electromagnetic measures (EEG/ERP, MEG) msec temporal resolution to distinguish components spatial resolution sub-optimal (source localization)
May 10, 2004 2004 Bioscience Conference
Integrated Electromagnetic Brain Analysis
IndividualBrain Analysis
Structural /FunctionalMRI/PET
DenseArray EEG /
MEG
ConstraintAnalysis
Head Analysis
Source Analysis
Signal Analysis
Response Analysis
Experimentsubject
temporaldynamics
neuralconstraints
CorticalActivity Model
ComponentResponse Model
spatial patternrecognition
temporal patternrecognition
Cortical ActivityKnowledge Base
Component ResponseKnowledge Base
good spatialpoor temporal
poor spatialgood temporal neuroimaging
integration
May 10, 2004 2004 Bioscience Conference
Experimental Methodology and Tool Integration
source localization constrained to cortical surface
processed EEG
BrainVoyager
BESA
CT / MRI
EEG segmentedtissues
16x256bits permillisec(30MB/m)
mesh generation
EMSEInterpolator 3D
NetStation
May 10, 2004 2004 Bioscience Conference
NeuroInformatics Center (NIC)
Application of computational science methods to human neuroscience problems (cognitive, clinical) Understand functional activity of the brain Help to diagnosis brain-related disorders Utilize high-performance computing and simulation Support large-scale data analysis and visualization
Advanced techniques for integrated neuroimaging Coupled modeling (EEG/ERP and MR analysis) Advanced statistical analysis (PCA, ICA) FDM/FEM brain models (EEG, CT, MRI) Source localization (dipole, linear inverse models)
Problem-solving environment for brain analysis
May 10, 2004 2004 Bioscience Conference
Electrical Geodesics Inc. (EGI)
EGI Geodesics Sensor Net Dense-array sensor technology
64/128/256 channels 256-channel geodesics sensor net
AgCl plastic electrodes Carbon fiber leads
Net Station Advanced EEG/ERP data analysis
Stereotactic EEG sensor registration Research and medical services
Stroke monitoring and localization
May 10, 2004 2004 Bioscience Conference
UO MRI Facility (Lewis Center for Neuroimaging)
Siemens Head-Only 3T MRI System Tailored to performing
functional imaging Human subjects Monitor common
physiologic parameters heart rate, respiration peripheral pulse oxygenation eye location and eye movement
Audio and visual stimulus Special RF screening room MRI coil development
May 10, 2004 2004 Bioscience Conference
Source Localization Problem
Mapping of scalp potentials to cortical generators Single time sample and time series
Requirements Accurate head model and physics
High-resolution 3D structural geometry Precise tissue identification and segmentation Correct tissue conductivity assessment
Computational head model formulation Finite element model (FEM) Finite difference model (FDM) Forward problem calculation
Dipole search strategy
May 10, 2004 2004 Bioscience Conference
Advanced Image Segmentation
Native MR gives high gray-to-white matter contrast
Edge detection finds region boundaries
Segments formed by edge merger
Color depicts tissue type Investigate more advanced
level set methods and hybrid methods
May 10, 2004 2004 Bioscience Conference
Building Finite Element Brain Models
MRI segmentation of brain tissues Conductivity model
Measure head tissue conductivity Electrical impedance tomography
small currents are injectedbetween electrode pair
resulting potential measuredat remaining electrodes
Finite element forward solution Source inverse modeling
Explicit and implicit methods Bayesian methodology
May 10, 2004 2004 Bioscience Conference
Computational Integrated Neuroimaging System
… …
raw
storageresources
virtualservices
compute resources
May 10, 2004 2004 Bioscience Conference
UO ICONIC Grid
NSF Major Research Instrumentation (MRI) proposal “Acquisition of the Oregon ICONIC Grid for Integrated
COgnitive Neuroscience Informatics and Computation” PIs
Computer Science: Malony, Conery Psychology: Tucker, Posner, Nunnally
Senior personnel Computer Science: Douglas, Cuny Psychology: Neville, Awh, White
Computational, storage, and visualization infrastructure
May 10, 2004 2004 Bioscience Conference
SMPServerIBM p655
GraphicsSMP
SGI MARS
SAN 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
ICONIC Grid
5 TerabytesTapeBackup
May 10, 2004 2004 Bioscience Conference
Human Neuroscience and ICONIC Grid
Common questions to be explored Identifying brain networks Critical periods during normal development Network involvement in psychopathologies Training interventions in network development
Research areas Development of attentional networks Brain plasticity in normal & altered development Attention and emotion regulation Spatial working memory and selective attention Psychopathology
May 10, 2004 2004 Bioscience Conference
Computer Science and ICONIC Grid
Scheduling and resource management Assign hardware resources to computation tasks Scheduling of workloads for quality of service
Problem-solving computational science environments Provide scientists an entrée to the ICONIC Grid without
requiring specialized knowledge of parallel execution Interactive / immersive three-dimensional visualization
Explore multi-sensory visualization Merge 3D graphics with force-feedback haptics
Parallel performance evaluation
May 10, 2004 2004 Bioscience Conference
NIC Relationships
Biology
CISCSI
OHSUUtah
UCSD
USC
Academic Labs / Centers
LANL Argonne
SDSCInternet2
EGI
Industry
Intel IBMNIC
UO Departments
UO Centers/Institutes
BBMI CDSI
LCNI
Physics
NSI
LLNL
SGI
OSU
PSU
Psychology
Math
May 10, 2004 2004 Bioscience Conference
Technology Transfer in Human Neuroscience
UO’s BBMI is conducting pioneering research and development in human neuroscience, genetics and proteomics, and computational science for future neurological medicine and health care
Greater precision and speed in brain imaging has high research and medical relevance Integrated medical imaging (EEG/MEG, MRI, radiology) Automatic image assessment (detection and diagnosis) Neurological evaluation and surgical planning
Linking of genetics factors with complex cognitive traits (personality, learning, attention) has potential for therapies and pharmaceutical clinical drug development
May 10, 2004 2004 Bioscience Conference
Leveraging Internet, HPC, and Grid Computing
Telemedicine imaging and neurology Distributed EEG and MRI measurement and analysis Neurological medical services Shared brain data repositories Remote and rural imaging capabilities
Neet to enhance HPC and grid infrastructure in Oregon Build on emerging web services and grid technology Establish HPC resources with high-bandwidth networks
Create institutional and industry partnerships UO is working closely with EGI to develop high-end
EEG analysis services framework Pilot neuroimaging services model on ICONIC Grid
May 10, 2004 2004 Bioscience Conference
Region 4
Region 1Region 2
Region 3
Region 5
Oregon E-Science Grid
Internet 2 /National LambdaRail
Regional networks
HPC serversRegional clients