mark ellisman, ph.d. professor of neurosciences and bioengineering director, birn coordinating...
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Mark Ellisman, Ph.D.Professor of Neurosciences and BioengineeringDirector, BIRN Coordinating CenterCenter for Research on Biological SystemsUniversity of California San Diego - School of MedicineLa Jolla, California email: [email protected]
Building on the BIRNMarch 22, 2004
BIRN is Team Science BIRN is Team Science Applied to Stretch Applied to Stretch
GoalsGoals A Big Challenge or Vision:A Big Challenge or Vision: ““Enable new understanding of Enable new understanding of the healthy and diseased brain the healthy and diseased brain by linking data about by linking data about macroscopic brain function to macroscopic brain function to its molecular and cellular its molecular and cellular underpinnings”underpinnings”
Taking practical steps toward a Taking practical steps toward a grand goal using grand goal using cyberinfrastructure:cyberinfrastructure:
• Federate geographically Federate geographically distributed brain data of the same distributed brain data of the same & different types& different types
• Accommodate requirements to Accommodate requirements to collaboratively interact with collaboratively interact with shared databases of large-scale shared databases of large-scale data, share methods, and data, share methods, and computational resourcescomputational resourcesScales of NS data from Maryann MartoneScales of NS data from Maryann Martone
BIRN Project CoordinationBIRN Project Coordination
Internet 2
SiSi SiSi
Functional Imaging BIRN Test-bed
Human Morphometry BIRN Test-bed
Mouse BIRN Test-bed
BIRN Coordinating
Center
The BIRN-CC leads…The BIRN-CC leads…• • the deployment and maintenance the deployment and maintenance of a network infrastructure capable of a network infrastructure capable of quickly moving large amounts of of quickly moving large amounts of data between BIRN sites across the data between BIRN sites across the country. country.
• • the creation of a federation of the creation of a federation of databases pertaining to the BIRN databases pertaining to the BIRN scientific projects. scientific projects.
• • the development and integration of the development and integration of software to refine, combine, software to refine, combine, compare, and analyze complex compare, and analyze complex biomedical data. biomedical data.
• • and cultivates group and cultivates group activities to overcome activities to overcome cultural barriers to building cultural barriers to building a forum for collaborative a forum for collaborative research, co-authoring research, co-authoring research papers, and research papers, and sharing sharing methods/tools/codes across methods/tools/codes across institutions. institutions.
The BIRN’s Interwoven TeamsThe BIRN’s Interwoven Teams
Information Tech.Information Tech.
SRB / DatabaseSRB / Database
IRBIRB
CallibrationCallibration
StatisticsStatistics
Project ManagerProject Manager
Scientific DirectorScientific Director
Information Tech.Information Tech.
SRB / DatabaseSRB / Database
IRBIRB
CallibrationCallibration
StatisticsStatistics
Project ManagerProject Manager
Scientific DirectorScientific Director
Information Tech.Information Tech.
SRB / DatabaseSRB / Database
Project ManagerProject Manager
Scientific DirectorScientific Director
PIPI PIPI PIPI
Information Tech.Information Tech.
SRB / DatabaseSRB / Database
IRBIRB
StatisticsStatistics
Project ManagerProject Manager
Scientific DirectorScientific Director
PIPI
Mouse Morphometry Function BIRN-CC
StatisticsStatisticsCallibrationCallibration
BIRN All Hands meeting held annually
BIRN PIs meet quarterly as part of the BIRN Steering Committee
IRBIRB
Task ForcesTask Forces
SRB / DatabaseSRB / Database
Cross BIRN working group has video teleconferences monthly
IRB working group holds monthly teleconferences and interacts closely with the Data Sharing Task Force
Task forces commissioned by the BIRN Steering Committee hold monthly video teleconferences
SRB / Database working groups are held weekly covering a wide range of topics
Ad hoc working groups created by the test beds meet according to their needs
TaskForces
Intellectual PropertyIntellectual Property Intellectual PropertyIntellectual PropertyIntellectual PropertyIntellectual Property Intellectual PropertyIntellectual Property
UtilizationUtilization UtilizationUtilizationUtilizationUtilization UtilizationUtilization
Data SharingData Sharing Data SharingData SharingData SharingData Sharing Data SharingData Sharing
WorkingGroups
Producing a fully integrated system and making components or toolkits accessible
Deploying functional infrastructure - at the same time new solutions are being specified, researched, designed, implemented, and hardened
Producing solutions that are driven by test bed specifications AND core requisites for broad scalability, interoperability, and extensibility
Providing ubiquitous access to new IT capabilities
Providing automatic, robust solutions for deployment in truly heterogeneous environments
Producing a fully integrated system and making components or toolkits accessible
Deploying functional infrastructure - at the same time new solutions are being specified, researched, designed, implemented, and hardened
Producing solutions that are driven by test bed specifications AND core requisites for broad scalability, interoperability, and extensibility
Providing ubiquitous access to new IT capabilities
Providing automatic, robust solutions for deployment in truly heterogeneous environments
The BIRN is…The BIRN is…
Components of Cyberinfrastructure(Grid)-enabled science & engineering
CollaborationServices
Knowledge managementinstitutions for collection buildingand curation of data, information,
literature, digital objects
High-performance computingfor modeling, simulation, data
processing/ mining
Individual &Group Interfaces& Visualization
Physical World
Humans
Facilities for activation,manipulation and
construction
Instruments forobservation andcharacterization.
GlobalConnectivity
A broad, systemic, strategic conceptualization
Grid implies global (international) system for collaboration
Source: Dan Atkinshttp://www.communitytechnology.org/nsf_ci_report/
“CYBERINFRASTRUCTURE”What is a Grid? What do we mean?
• GRID technologies bring remote resources togetherGRID technologies bring remote resources together
Evolution of the Computational InfrastructureSource: Dr. Deborah CrawfordChair, NSF CyberInfrastructure Working Group (CIWG)
Supercomputer Centers
PACI
Terascale
1985 1990 1995 2000 2005 2010
| | | | | |
NPACI and Alliance
SDSC, NCSA, PSC, CTC
TCS, DTF, ETF
Cyberinfrastructure
Prior Computing Investments
NSF Networking
Hardware
Integrated Cyberinfrastructure System meeting the needs of multiple communities Source: Dr. Deborah Crawford, Chair, NSF CyberInfrastructure Working Group
Grid Services & Middleware
DevelopmentTools & Libraries
Applications• Environmental Science• High Energy Physics• Biomedical Informatics• Geoscience
Domain-specific
Cybertools (software)
Domain-specific
Cybertools (software)
Shared Cybertools (software)
Shared Cybertools (software)
Distributed Resources
(computation, communicationstorage, etc.)
Distributed Resources
(computation, communicationstorage, etc.)
Ed
uca
tion a
nd
Tra
inin
g
Dis
covery
& In
novati
on
BIRN Virtual Data GridBIRN 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
BIRN PortalBIRN Portal
The Portal is composed of 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 administrative details of each layer into a single username and pass phrase
Building the BIRN PortalBuilding the BIRN Portal
Application environment developed to provide centralized access to BIRN tools, applications, resources with a Single Login from any Internet capable location
Provides simple, intuitive access to Grid resources for data storage, distributed computation, and visualization
BIRN Portal: Launches Scientific Workflow
1. User Login In BIRN Portal, selects data and LONI settings2. LONI Pipeline is launched from Portal3. Results are automatically displayed in Slicer 3D
• No need to manage Globus Certificates• Resources are transparently cross-platform, cross-domain• Tomography tools are used regularly to create 3D image volumes, • Other BIRN project codes now parallelized and going to the GRID
The BIRN Projects are Beginning to Use “GRID-Enabled” The BIRN Projects are Beginning to Use “GRID-Enabled” Parallel Distributed High Performance ComputingParallel Distributed High Performance Computing
The End User is Shielded from the Complexities of the Grid
Platform Independent
Domain Independent
Example Query of Federated DatabaseExample Query of Federated Database
fMRI
Are chronic, but not first-onset patients, associated with superior temporal gyrus dysfunction (MMN)?
Integrated View
Receptor Density ERP
Web
PubMed, Expasy
Wrapper
WrapperWrapper
Wrapper
Structure
Wrapper
Clinical
Wrapper
MediatorMediator
0.150.18
0.140.11
-0.14-0.10-0.06-0.020.020.060.100.140.180.220.260.30
ARIP - 20MG ARIP - 30MG RISP - 06MG PLACEBOTreatment Group
BIRN is using Domain Maps BIRN is using Domain Maps to Navigate Data Sourcesto Navigate Data Sources
• These are Rule-based These are Rule-based ontology maps or a “data ontology maps or a “data model”model”
• They Encode conceptual They Encode conceptual and semantic relationships and semantic relationships (“domain knowledge”(“domain knowledge”
• Ontologies can be linked or Ontologies can be linked or joined to data models of joined to data models of other biomedical other biomedical databases (PDB, Yale’s databases (PDB, Yale’s Sense Lab, etc.)Sense Lab, etc.)
Brain
Cerebellum
Purkinje Cell Layer
Purkinje cell
neuron
has a
has a
has a
is a