Mark Ellisman, Ph.D. Professor of Neurosciences and Bioengineering Director, BIRN Coordinating Center Center for Research on Biological Systems University.

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



IRBIRB

CallibrationCallibration








PIPI PIPI PIPI



IRBIRB




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


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.)

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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

Project Workflows

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

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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

Purkinje neuron

Registering My Data

UMLS

Spatial RegistrationSpatial Registration

QuickTime™ and aCinepak decompressor

are needed to see this picture.

Annual MeetingAnnual Meeting

3rd Annual BIRN All-Hands Meeting

October 2003UCSD @ Scripps Institution of Oceanography

3rd Annual BIRN All-Hands Meeting

October 2003UCSD @ Scripps Institution of Oceanography

Mark Ellisman, Ph.D. Professor of Neurosciences and Bioengineering Director, BIRN Coordinating Center Center for Research on Biological Systems University.

Documents

birn sites

birn coordinating centercenter

birn scientific projects

distributed brain data

large amounts of data

complex biomedical data

integrated system

nsf cyberinfrastructure