GENII: Grid-based Environment for Neuroimaging Integration and Interoperation Human Brain Project...
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Transcript of GENII: Grid-based Environment for Neuroimaging Integration and Interoperation Human Brain Project...
GENII: Grid-based Environmentfor Neuroimaging Integration and
Interoperation
Human Brain Project – Neuroinformatics Proposal
Allen D. Malony
DonTucker
ScottMakeig
Gregor von Laszewski
Dennis Gannon
NeuroInformatics Center,
Department of Computer and Information
Science,
University of Oregon
Electrical Geodesics, Inc.,
University of Oregon
Swartz Center for Computational Neuroscience,
Institute for Neural Computation, University of
CaliforniaSan Diego
Argonne National Laboratory
Pervasive Technologies Laboratory,
Department of Computer Science,
Indiana University
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Aim 1 Develop a grid-based computing environment for
dynamic neuroimaging We will apply state-of-the-art technology from the Open
Grid Computing Environment (OGCE) consortium to build GENII
Grid-based domain-specific Environment for dynamic Neuroimaging of human brain activity with support for analysis and modeling tool Integration and Interoperation
Provide access to shared time-series data repositories, and analysis workflow creation and execution on a grid of computational and storage resources
GENII will be publicly-available open-source software designed to maintain both technological and operational consistency with the NIH Biomedical Informatics Research Network (BIRN)
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Aim 2
Enable leading Matlab-based time-series neuroimaging tools to efficiently and conveniently access the GENII environment and benefit from the emerging grid computing infrastructure We will develop mechanisms for Matlab to interface with
GENII using the Java Virtual Machine (JVM) support inherent in current Matlab (R14) installations and the Java CoG and portlet technologies from the OGCE
Utilize this interface to make the widely used Matlab toolsets EEGLAB, BrainStorm, SPM, APECS, and FieldTrip able to access GENII computational, storage, and workflow services
GENII will mediate a high-level interaction between freely available (front-end) Matlab tools and a user’s (back-end) grid computing infrastructure
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Aim 3
Build high-performance analysis and modeling components as GENII neuroimaging services We will select and implement several essential time-
intensive algorithms in signal processing, computational head modeling, image segmentation, and dipole source localization in high-performance sequential and parallel forms
The implementations will support scaling in data size, model resolution, and degree of parallelism
These programs will be wrapped as grid-enabled components to operate as prototypical computational services available within the GENII environment
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Aim 4
Create computational workflows that capture complex, multi-step neuroanalysis processes We will support processing of neurophysiological time-
series data involving a series of analysis steps performed by multiple tools across multiple subjects over multiple experiments
Utilize emerging grid workflow programming technologies (e.g., XCAT and GridAnt) to create multi-component neuroimaging pipelines as high-level GENII services
The workflows can be reused with pluggable analysis components and composed with other workflow processes
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Aim 5
Design and implement a storage schema for managing time-series neuroimaging information Support storage and management of large, multi-
dimensional, and multi-model neurophysiological data (raw, intermediate analyses, final results)
We will develop a robust schema for the storage of neuroimaging data and experimental information compatible with the SRB technology and incorporating a streamlined interface for GENII software access
A range of time-series data formats and types will be supported as well as tools for data conversion and correlation
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Specific Aims – Neuroinformatics Software
The results of the project will be publicly-available open-source software for managing the storage and analysis of neuroinformatic experiment data and for leveraging the power of grid-accessible Unix-based clusters for high-performance computation
The GENII software will allow users to extend freely available Matlab toolsets with grid-enabled capabilities for workflow processing and shared storage
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Integrated Dynamic Brain Analysis Problem
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
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
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
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Experiment Tool Integration (Selected)
Geodesic Sensor Net (EGI)
EEGLAB (Swartz Center)
NetStation (EGI)
BrainStorm, USC/LANL
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
SMPServerIBM p655
GraphicsSMP
SGI Prism
SAN Storage SystemIBM SAN FS
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 at University of Oregon
5 TerabytesTape
Backup
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
ICONIC Grid – Hardwarep690 16 processors
p655 4 nodes 8 processors per node
Dell cluster 16 nodes 2 processors per node
JS20 Blade 16 nodes 2 processors per node
FAStT storage 5 TBSAN FS
FibreChannel
FibreChannel
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Computational Integrated Neuroimaging System
… …
raw
storageresources
virtualservices
compute resources
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
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
Enhanced HPC / grid infrastructure for neuroinformatics Build on emerging web services and grid technology Establish HPC resources with high-bandwidth networks
Further institutional and industry partnerships
GENII - Grid-based Environment for Neuroinformatics Integration and Interoperation
Institution
Year 1 Year 2 Year 3 Year 4 Year 5 Total
UO $300K $300K $300K $300K $300K $1500K
UCSD $175K $175K $175K $175K $175K $875K
Indiana $175K $175K $175K $175K $175K $875K
Argonne $175K $175K $175K $175K $175K $875K
Total $825K $825K $825K $825K $825K $4125K
Proposed Budget
Direct costs