Title: NPACI Neuroscience
1Molecules
Synchrotrons
Macromolecular Complexes, Organelles, Cells
Microscopes
Organs, Organ Systems, Organisms
Magnetic Resonance Imagers
2Biomedical Informatics Research Network a testbed
for a biomedical knowledge infrastructure
3BIRN Project Objectives
1) establish a stable high performance network
linking key Biotechnology Centers and General
Clinical Research Centers 2) establish
distributed and linked data collections with
partnering groups 3) enable the use of
"grid-based" computing 4) enable data mining
from multiple data collections or databases on
neuroimaging 5) 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.
4EACH BRAIN REPRESENTS A LOT OF DATA
AND COMPARISONS MUST BE MADE BETWEEN MANY
Slide courtesy of Arthur Toga / UCLA
5 6Federate Emerging Databases
Infrastructure to relate, combine produce
meta data
Deformation Segmentation Quantification
Slide courtesy of Arthur Toga
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8Two groups have developed BIRN project
partnerships, so far
- Mouse BIRN - Animal Models of Disease / Multi
Scale/Multi Method - MS Mouse and DAT KOM (a
schizophrenic and otherwise interesting mouse
animal model) - Brain Morphology BIRN - Targets neuroanatomical
correlates of neuropsychiatric illness (Unipolar
Depression, mild Alzheimer's Disease (AD), mild
cognitive impairment (MCI)
9THE BIOMEDICAL INFORMATICS RESEARCH NETWORK
LAYOUT FOR PHASE 1
10Getting down to work - BIRN has had to
- 1) establish Network Infrastructure between NIHs
Research Infrastructure sites Biotechnology
Resources and General Clinical Research Center
sites. The BIRN Coordinating Center (BIRN CC)
defined the infrastructure required and
coordinated the procurement of both hardware and
software installed at the BIRN Partner Sites
(BIRN PS) for networking and caching of data. - 2) establish policies and protocols for use of
the BIRN infrastructure and operating guidelines.
The BIRN CC is coordinating with BIRN PS groups
and NIH - National Center For Research
Resources. - 3) build a Virtual Data Grid (VDG) for the
initial cohort of group projects or test-beds
in the neuroimaging research domain. - 4) develop the data modeling and mediation tools
for complex queries relevant to the proposed
research goals of these test-bed projects.
11BIRN Coordinating Center Activities / Layers
- I. Networking Infrastructure for the BIRN -
Install, commission and tune networks between the
BIRN Partner Sites with I2/Abilene etc. - II. The BIRN Virtual Data Grid - Install and
commission hardware and software layers for
BIRN's Distributed Data - The Storage Resource
Broker Technologies (SRB). - III. Coupling BIRN Data Grid to the Computational
Grid - Make the BIRN system work with NSFs
National Middleware Initiative and leverage on
the NSFs Distributed Terascale Facilities. - IV. Data Integration Technologies for BIRN -
BIRN-CC Tool Development and BIRN-Partner Site
Group-Specific Data Respresentations and Domain
Map Development - V. Interaction Environments for the BIRN - Adding
a Collaborative layer to the BIRN data complex
query Portal, including Volumetric Viewing
Capabilities and link to the BIRN-Partner Site
visualization and analysis tools.
12Networking and Data Storage Infrastructure
Site Hardware Configurations
- Last link included
- Linking Internet 2 to Biotechnology Resource or
General Clinical Research Center sites is of
primary concern - BIRN supplies major networking pieces in BIRN
Racks - Site infrastructure to link from rack to Internet
2 provided by each campus - Each site has a consistent configuration
- A standard base for all network and data services
to run on - - No excuses - local staff to become responsible
for their site - Remote management and measurement tools at each
site - To facilitate expansion of BIRN, alternative
lower cost configurations will be explored and
specified - once test-bed projects are established
13BIRN Network Operations Center (NOC)
Logical Description with Standardized Site Rack
24x7 Operations Monitoring
Internet 2
SDSC Network
BIRN NOC Monitoring
- Network Switch
- BIRN Statistics
- BIRN Network Probe
- Network Attached Storage
- Grid POP/ SRB, Globus Dual Processor
- General purpose ( eg., encryption)
- UPS for Rack
NCRR
Cisco 4006
GB Switches
DL380 - Network Stats
BIRN Network Management
GigE Net Probe
N2400 NAS 0.5- 4 TB
Gigabit Network Probes
DL380 Grid POP
DL380
NOC Servers and Testers/Analyzers
APC UPS
BIRN Site Rack
14Building a Distributed Data Collection
- Provide data handling system to access data
stored in someone elses administration domain - Provide collection management to support
discovery of distributed data sets - Provide knowledge management interface to
differentiate between naming conventions
15BIRN Virtual Data Grid
- Defines a Distributed Data Handling System
- Integrates Storage Resources in the BIRN network
- Integrates Access to Data, to Computational and
Visualization Resources
- Acts as a Virtual Platform for
Knowledge-based Data
Integration Activities - Provides a Uniform
Interface to Users
STORAGE RESOURCES
16BIRN is Integrating Across Data Sources
- The idea
- Different models capture correlated but distinct
aspects of biological reality - How can we express and evaluate queries that
compute data across models - The approach
- For each source create a knowledge-base of the
anatomy of the observations - Attach the data of each source to the respective
knowledge-base - bridge the sources by a simple ontological
mapping - Compute the query across bridged sources
17Data Sources on the Web
Washington Univ
Boston Univ
UCLA
Montana State Univ
Vanderbilt Univ
Yale Univ
18Information Integration
What is the cerebellar distribution of rat
proteins with more than 70 homology with human
NCS-1?
Integrated View
Integrated View Definition
Mediator
Wrapper
Wrapper
Wrapper
Wrapper
Web
protein localization
morphometry
neurotransmission
CaBP, Expasy
19Querying Across Databases
What is the distribution of protein X in
cerebellum?
Source 2
Source 1
Source 3
Cerebellum
- Purkinje Cell Dendrite
- Dendritic spines
- Dendritic shaft
- Endoplasmic reticulum
- Cerebellar Cortex
- Granule Cell Layer
- Purkinje Cell layer
- Molecular Layer
20Additional Glue Knowledge
Source 2
Source 1
Source 3
Cerebellum
Cerebellar Cortex Granule Cell Layer Purkinje
Cell layer Molecular Layer
Purkinje Cell Dendrite Dendritic spines Dendritic
shaft Endoplasmic reticulum
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22Development of Smart Atlases
23From Telescience to BIRN
24Brain Morphometry BIRN
- Clinical Specific Aims
- Attempt to address questions of the following
type - Do structural differences contribute to specific
symptoms such as memory dysfunction or depression
independent of diagnosis? - Do specific structural differences distinguish
specific diagnostic categories? - Technological Specific Aims
- Attempt to overcome obstacles to the use of
neuroimaging data as quantitative outcome
measures for clinical investigation including the
issues raised by longitudinal and multi-site
studies. In other words- to make the Clinical
Specific Aims possible to address.
Harvard
Duke
UCLA
UCSD
25Cortical Thickness Estimation with Sub-Voxel
Accuracy
Gray-white boundary
Pial surface
From Anders Dale / Mass General Hospital -
Harvard
26A Surface-Based Coordinate System
byAnders Dale (MGH)
Subject (native representation)
Inflation (native representation)
Registration (common representation)
Return to Native Configuration (with coordinates)
27Automated Whole-Brain Segmentation (37 Anatomical
Labels, 1 wk 10 min)
Part of Free Surfer
By Bruce Fishl and Anders Dale (MGH)
28Brain BIRN Data Flow
294 x 10-5 mm3 110,000 X
5 mm3
30The Mouse Brain Imaging Research Network MBIRN
Caltech/Beckman Inst.
31 BIRN test-bed sites, with 10 site project for
fMRIs of Schizophrenics - Multiscale Mouse
Models of Disease, Human Brain Morphometrics and
FIRST BIRN