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Michael Marron, Ph.D., Director Division of Biomedical Technology National Center for Research Resources National Institutes of Health Department of Health and Human Services Bethesda, Maryland, USA Biomedical Informatics Biomedical Informatics Research Network Research Network

Biomedical Informatics Research Network

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Michael Marron, Ph.D., Director Division of Biomedical Technology National Center for Research Resources National Institutes of Health Department of Health and Human Services Bethesda, Maryland, USA. Biomedical Informatics Research Network. Biomedical Informatics Research Network - PowerPoint PPT Presentation

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Page 1: Biomedical Informatics Research Network

Michael Marron, Ph.D., DirectorDivision of Biomedical Technology

National Center for Research ResourcesNational Institutes of Health

Department of Health and Human ServicesBethesda, Maryland, USA

Biomedical Informatics Biomedical Informatics Research NetworkResearch Network

Page 2: Biomedical Informatics Research Network

22January 2003January 2003

Biomedical Informatics Research NetworkBiomedical Informatics Research NetworkTestbed for biomedical knowledge infrastructure

Page 3: Biomedical Informatics Research Network

33

BIRN BIRN Biomedical Informatics Biomedical Informatics Research NetworkResearch Network

A testbed for a biomedical knowledge infrastructure

Federated database of neuroimaging data

Fusion of diverse data sources (location; level of aggregation)

Grid access to computational resources

Datamining software

Scalable and extensibleScalable and extensible

Driven by research needs-pull, not technology-pushDriven by research needs-pull, not technology-push

Page 4: Biomedical Informatics Research Network

BIRNBIRN SitesSites

Page 5: Biomedical Informatics Research Network

BIRNBIRN Information Integration Information Integration

protein localization

What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1?

Integrated View

Mediator

morphometry neurotransmission

WebWeb

CaBP, Expasy

Wrapper WrapperWrapper Wrapper

Integrated View Definition

Page 6: Biomedical Informatics Research Network

66January 2003January 2003

BIRNBIRN Grid Infrastructure Grid Infrastructure• The BIRN Portal is built on many

“layers”

• Layers are modular, allowing for extension of any layer without great disruption to the entire system

• Every Layer has its own complexity and administration that was previously passed on to the end-user

• Portal centralizes all adminis-trative details of each layer into a single username and pass phrase

Page 7: Biomedical Informatics Research Network

BIRNBIRN Grid InfrastructureGrid Infrastructure

BIRN Toolkit

Viewing/Visualization Queries/ResultsApplications Data Management

Computation

MCAT

Data Storage

Grid Middleware

Collaboration

Globus

Distributed Resources

Mediator

DatabaseDatabase

GridPort Toolkit

SRB

BIRN Portal

Custom APIs

Mediator APIVisualization APIsSecurity API

Page 8: Biomedical Informatics Research Network

88January 2003January 2003

BIRNBIRN Knowledge IntegrationKnowledge IntegrationSupports queries across heterogeneous data sources

Query

Mediator Layer

Wrapper Layer

Mediator Services API

Query interface Result interface

Query FormulationSource Model

Lifting

SourceRegistration

DeductiveEngine

Query Processing

HTML

Files

XML

RDBOODB

Model Reasoner

Optimizer

SRB

Page 9: Biomedical Informatics Research Network

99January 2003January 2003

MouseMouse BIRNBIRN

Studying animal models of disease across dimensional scales to test hypothesis with human neurological disorders

Experimental Allergic Encephalomyelitis (EAE) mouse models (both chemically induced and transgenic) exhibit episodic weakness and demyelination characteristic of multiple sclerosis

Dopamine Transporter (DAT) knockout mouse for studies of schizophrenia, attention-deficit hyperactivity disorder (ADHD), Tourette’s disorder and substance abuse

Using an alpha-synuclein mouse to model the symptoms/pathology of Parkinson’s Disease

Duke, UCLA, UC San Diego, Cal Tech

Page 10: Biomedical Informatics Research Network

1010January 2003January 2003

MouseMouse BIRNBIRN

Duke - CIVM

UCSD-NCMIR & Duke - CIVN

UCSD-NCMIR

Reconstructed spiny dendrite

Integrating brain data across scales and disciplines

Coronal sections of mouse brains

Page 11: Biomedical Informatics Research Network

1111January 2003January 2003

MorphologyMorphology BIRNBIRN

Examining neuroanatomical correlates of neuropsychiatric illnesses, including Unipolar Depression, mild Alzheimer’s Disease and mild cognitive impairment

Combining data from multiple acquisition sites

Increase statistical power for study of rare populations

Harvard (MGH and BWH), Duke, UCLA, UC–San Diego, Johns Hopkins

Page 12: Biomedical Informatics Research Network

MorphologyMorphology BIRNBIRN

Model based three dimensional medical image segmentation

Harvard-BWH

3D-Slicer - An Integrated visualization system for surgical planning and guidance using image fusion and interventional imaging

Dynamics of gray matter loss rates, mapped in a

schizophrenia population

UCLA-LONI

Harvard-MGH

Surface based coordinate

system

Harvard-BWH

Page 13: Biomedical Informatics Research Network

1313January 2003January 2003

FunctionalFunctional BIRNBIRN

Developing a common fMRI protocol to study regional brain dysfunction related to the progression and treatment of schizophrenia

Investigating techniques to insure interoperability of existing tools for multi-modal analysis

Correlating functional data with anatomical data acquired from the Morphology test-bed to study if there are neuroanatomical correlates with cognitive dysfunction across disorders

UCLA, UC San Diego, UC Irvine, Harvard (MGH and BWH), Stanford, Minnesota, Iowa, New Mexico, Duke/U. North Carolina

Page 14: Biomedical Informatics Research Network

1414January 2003January 2003

FunctionalFunctional BIRNBIRN

Stanford – Lucas Center

fMRI response at 3T and 1.5T with identical software

and hardware platforms

Patients with schizophrenia show abnormal modulation of temporal and frontal regions during semantic processing

Harvard-MGH

neocortical network mediates semantic processing of

sentences in healthy individuals

Page 15: Biomedical Informatics Research Network

1515January 2003January 2003

BIRNBIRN Coordinating CenterCoordinating Center

Deploy a network infrastructure capable of quickly moving large amounts of data between BIRN sites across the country

Create federated databases pertaining to the BIRN scientific test-beds

Develop software to find, compare, and analyze complex neurological imaging data

Ensure regulatory compliance (HIPAA) without inhibiting collaboration

UC San Diego

Page 16: Biomedical Informatics Research Network

1616January 2003January 2003

BIRN NOCMonitoring

24x7 OperationsMonitoring

Gigabit Network Probes

Internet 2

GB Switches

UCSD/SDSCNetwork

BIRN Network Management

BIRN Site Rack

BIRN Network Operations Center BIRN Network Operations Center Standardized Site RackStandardized Site Rack

N2400 NAS

1 - 10 TB

Cisco 4006

DL380 Grid POP

DL380 - Network Stats

GigE Net Probe

APC UPS

DL380

• Network Switch

• BIRN Statistics

• BIRN Network Probe

• Network Attached Storage

• Grid POP/SRB, Globus

• General purpose ( eg., encryption)

• UPS for Rack

NCRR

Ultimately, access from anywhere to BIRN data

everywhere

Wired and Wireless

NOC Servers and Testers/Analyzers

Page 17: Biomedical Informatics Research Network

1717January 2003January 2003

BIRNBIRN CC ServicesCC Services

Network MonitoringNetwork Monitoring Statistics & MeasurementStatistics & Measurement 7 x 24 Help Desk7 x 24 Help Desk Problem TrackingProblem Tracking High Level Project ManagementHigh Level Project Management Portal Services & Tools IntegrationPortal Services & Tools Integration TrainingTraining Data IntegrationData Integration Visualization ToolsVisualization Tools Documentation – web site, best practices, lessons learned, Documentation – web site, best practices, lessons learned,

checklistschecklists

Page 18: Biomedical Informatics Research Network

1818January 2003January 2003

ChallengesChallengesLarge data sets

ISCAR - information storage, curation, archiving, and retrieval

Bandwidth issues Quality control of data only analyzed by machine Visual interfaces for complex data sets

Fostering collaboration Reward structures in government and academic

institutions Intellectual property issues Data integrity Resistance to collaborate with competitors

Data sharing issues (ownership, privacy, authorship)

Page 19: Biomedical Informatics Research Network

1919January 2003January 2003

More ChallengesMore Challenges

Federated DB /Knowledge Engineering Dictionaries & Ontologies Integrating different data types Accessing legacy systems Distributed query computations

High-level management of projects Overcome technical & institutional

barriers Degree of centralization needed Role of standards Project subdivision and optimization

Page 20: Biomedical Informatics Research Network

2020January 2003January 2003

BIRNBIRN Future Future Addition of new sites in a rapid, well-defined,

affordable fashion Grid-based National Clinical Research Network Cross-species integration of data Characterization of treatment at multiple levels Expand model to other areas of biomedical

research