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Biomedical Informatics
Research Network
Michael Marron, Ph.D., Director
Division of Biomedical Technology
National Center for Research Resources
National Institutes of Health
Department of Health and Human Services
BIRN
Biomedical Informatics
Research 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 extensible
Driven by research needs-pull, not technology-push
26 Nov 2002
2
BIRN Infrastructure
• Establish a stable high performance network linking key
Biotechnology Centers and General Clinical Research
Centers using Internet2
• Establish distributed and linked data collections with
partnering groups
• Enable the use of "grid-based" computing resources for
project specific data refinements and comparisons
• Enable data mining from multiple data collections or
databases on neuroimaging
• Build a stable software and hardware infrastructure that will
allow centers to coordinate efforts to accumulate larger
studies than can be carried out at one site.
26 Nov 2002
3
BIRN Sites
Information Integration
What is the cerebellar distribution of rat proteins with more
than 70% homology with human NCS-1?
Integrated
View
Integrated
View Definition
Wrapper
Mediator
Wrapper
Wrapper
Wrapper
Web
protein localization
morphometry
neurotransmission
CaBP, Expasy
Mouse BIRN
• Animal Models of Disease /Multi Scale/Multi Method - MS Mouse
and DAT KOM (a schizophrenic and otherwise interesting mouse
animal model)
• Looking at different resolutions by combining data from multiple
modalities
• Duke, UCLA, UC San Diego, Cal Tech
26 Nov 2002
6
Morphology BIRN
• Neuroanatomical correlates of neuropsychiatric illness (unipolar
depression, Alzheimer's disease, mild cognitive impairment)
- Overcome obstacles to the use of neuroimaging data as quantitative outcome measures
for clinical investigation including issues raised by longitudinal and multi-site studies.
- Do structural differences contribute to specific symptoms such as memory dysfunction or
depression independent of diagnosis?
- Do specific structural differences distinguish specific diagnostic categories?
• Harvard (MGH and BWH), Duke, UCLA, UC San Diego, Johns
Hopkins, UC Irvine
26 Nov 2002
7
Functional BIRN
• Characterizing the collection and integration of fMRI data from
multiple sites
• Study schizophrenia through fMRI images collected from patients
around the country using standardized protocols
• UCLA, UC San Diego, UC Irvine, Harvard (MGH and BWH),
Stanford, Minnesota, Iowa, New Mexico, Duke, North Carolina
26 Nov 2002
8
BIRN Coordinating Center
Uniform Hardware for BIRN Sites
NCRR
Cisco 4006
DL380 - Network Stats
GigE Net Probe
N2400 NAS
1.0 TB
DL380 Grid POP
DL380
APC UPS
26 Nov 2002
• Gigabit/10/100 Network
Switch – Cisco4006
• Network Statistics System
• Gigabit Ethernet Network
Probe
• Network Attached Storage –
Gigabit Ether
• 1.0 to 8.0 TB
• Grid POP
• SRB, Globus
• Dual Processor Linux w/
1GB memory
• DL 380 General purpose
• Specialized encryption
• UPS for Rack
• UC San Diego
• Best practices aggregator
• Technical development
center
• Center for training and
experience exchange
• Expert-level technical
support
• High-level project
management
• Oversight bodies point of
contact
9
Challenges
Large 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)
26 Nov 2002
10
More 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
26 Nov 2002
11
BIRN 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
26 Nov 2002
12