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