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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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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
22January 2003January 2003
Biomedical Informatics Research NetworkBiomedical Informatics Research NetworkTestbed for biomedical knowledge infrastructure
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
BIRNBIRN SitesSites
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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