Biomedical InformaticsResearch Network

BIRN Overview: BIRN Overview: Building the Biomedical Building the Biomedical Informatics Research NetworkInformatics Research Network

October 9, 2002

2nd Annual All Hands Meeting

Mark Ellisman - UCSDMark Ellisman - UCSD

SynchrotronsSynchrotrons

MoleculesMolecules

MacromolecularMacromolecularComplexes, Complexes, Organelles, CellsOrganelles, Cells

Organs, Organ Organs, Organ Systems, OrganismsSystems, Organisms

MicroscopesMicroscopes

Magnetic Resonance ImagersMagnetic Resonance Imagers

BIG Distributed BIG Distributed INSTRUMENTSINSTRUMENTS

and Shared and Shared Access Access

BIG BIG && Diverse Diverse BIOMEDICALBIOMEDICALDATABASESDATABASES

and Shared and Shared AccessAccess

BIG COMPUTATIONS BIG COMPUTATIONS - DATA REFINEMENT -- DATA REFINEMENT -

THE CHALLENGE THE CHALLENGE OF FUNCTIONAL OF FUNCTIONAL CORRELATIONSCORRELATIONS

from Arthur Toga / from Arthur Toga / UCLAUCLA

THE CHALLENGE OF MULTIPLE SCALESTHE CHALLENGE OF MULTIPLE SCALES

INTEGRATING AND NAVIGATING NEUROIMAGING DATA - INTEGRATING AND NAVIGATING NEUROIMAGING DATA - Mining for New UnderstandingMining for New Understanding of Structure and Functionof Structure and Functionfrom Maryann Martone / from Maryann Martone / UCSDUCSD

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Biomedical Informatics Research NetworkBiomedical Informatics Research NetworkTest-beds for biomedical knowledge infrastructureTest-beds for biomedical knowledge infrastructure

BIRN Project ObjectivesBIRN Project Objectives

Establish a Establish a stable, high performance networkstable, high performance network linking key linking key Biotechnology Centers and General Clinical Research Biotechnology Centers and General Clinical Research CentersCenters

Establish Establish distributed and linked data collectionsdistributed and linked data collections with with partnering groups - create a “Data GRID” for the BIRNpartnering groups - create a “Data GRID” for the BIRN

Facilitate the use of "Facilitate the use of "grid-basedgrid-based" computational " computational infrastructure and integrate BIRN with other GRID infrastructure and integrate BIRN with other GRID middleware projectsmiddleware projects

Enable Enable data miningdata mining from from multiple data collections or multiple data collections or databasesdatabases on neuroimaging and bioinformatics on neuroimaging and bioinformatics

Build a Build a stable software and hardware infrastructurestable software and hardware infrastructure that will that will allow centers to coordinate efforts to allow centers to coordinate efforts to accumulate larger accumulate larger studiesstudies than can be carried out at one site. than can be carried out at one site.

What BIRN is Doing…….What BIRN is Doing…….

Integrating the activities of the most advanced Integrating the activities of the most advanced biomedical imaging and clinical research centers in biomedical imaging and clinical research centers in the US - the US - Serving as a model for programs everywhere.Serving as a model for programs everywhere.

Developing hardware and software infrastructure for Developing hardware and software infrastructure for managing distributed data managing distributed data - - creation of data gridscreation of data grids..

Exploring data using “intelligent” query engines that Exploring data using “intelligent” query engines that can make inferences upon locating “interesting” data.can make inferences upon locating “interesting” data.

Building bridges across tools and data formats.Building bridges across tools and data formats.

Changing the use pattern for research data from the Changing the use pattern for research data from the individual laboratory or project to shared use.individual laboratory or project to shared use.

Provide a scalable, open and available tool kit for Provide a scalable, open and available tool kit for querying, accessing and viewing the BIRN data. querying, accessing and viewing the BIRN data.

Define processes, procedures and establish best Define processes, procedures and establish best practices so that the BIRN is reliable, scalable and practices so that the BIRN is reliable, scalable and extensible to biomedical research programs extensible to biomedical research programs outside of the pioneering Neuroimaging Test-beds outside of the pioneering Neuroimaging Test-beds - - able to support the work of thousands of researchers.able to support the work of thousands of researchers.

Push the envelop of biomedical informatics and Push the envelop of biomedical informatics and computer science by causing the development of computer science by causing the development of new techniques in databases, information new techniques in databases, information retrieval, visualization and computational retrieval, visualization and computational processing.processing.

What BIRN Must Do…….What BIRN Must Do…….

BIRN Test-bedsBIRN Test-beds (1) Mouse Models of Disease; (2) Human Brain (1) Mouse Models of Disease; (2) Human Brain Morphometrics; (3) Functional Imaging of Schizophrenic HumansMorphometrics; (3) Functional Imaging of Schizophrenic Humans

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BIRN NOCBIRN NOCMonitoringMonitoring

24x7 Operations24x7 OperationsMonitoringMonitoring

NOC Servers and NOC Servers and Testers/AnalyzersTesters/Analyzers

Gigabit Network ProbesGigabit Network Probes

Internet 2Internet 2

SiSi SiSi

GB SwitchesGB Switches

UCSD/SDSCUCSD/SDSCNetworkNetwork

BIRN Network BIRN Network ManagementManagement

BIRN Site RackBIRN Site Rack

BIRN Network Operations Center (NOC) BIRN Network Operations Center (NOC) Logical Description with Standardized Site RackLogical Description with Standardized Site Rack

N2400 N2400 NAS NAS

1 - 10 TB1 - 10 TB

Cisco 4006Cisco 4006

DL380 DL380 Grid POPGrid POP

DL380 - DL380 - Network StatsNetwork Stats

GigE Net ProbeGigE Net Probe

APC UPSAPC UPS

DL380 DL380

•Network Network Switch Switch

•BIRN StatisticsBIRN Statistics

•BIRN Network BIRN Network ProbeProbe

• Network Network Attached Attached Storage – Storage –

• Grid POP/ Grid POP/ SRB, GlobusSRB, Globus

•General General purpose purpose ( eg., ( eg., encryption)encryption)

• UPS for RackUPS for Rack

NCRRNCRR

Ultimately, Access from Ultimately, Access from Anywhere to BIRN DATA Anywhere to BIRN DATA EverywhereEverywhere

Wired and Wired and WirelessWireless

CREATING BIRN TEST-BED PARTNERSHIPSCREATING BIRN TEST-BED PARTNERSHIPS

Three Research Project “Application Test Beds” Three Research Project “Application Test Beds” have been Assembled to Shape BIRN and Guide have been Assembled to Shape BIRN and Guide Infrastructure Development: Infrastructure Development:

Multi-scale Mouse BIRNMulti-scale Mouse BIRN - - Animal Models of disease / Multi Animal Models of disease / Multi Scale/Multi Method - Examples: MS Mouse, DAT KOM (a Scale/Multi Method - Examples: MS Mouse, DAT KOM (a schizophrenic and otherwise interesting mouse animal model) and schizophrenic and otherwise interesting mouse animal model) and a Parkinson’s Disease Mousea Parkinson’s Disease Mouse

Brain MorphometricsBrain Morphometrics (Human Structure BIRN) (Human Structure BIRN) -- Targets: Targets: neuroanatomical correlates of neuropsychiatric illness (Unipolar neuroanatomical correlates of neuropsychiatric illness (Unipolar Depression, mild Alzheimer's Disease (AD), mild cognitive Depression, mild Alzheimer's Disease (AD), mild cognitive impairment (MCI)impairment (MCI)

Functional Imaging BIRNFunctional Imaging BIRN – – Development of a common Development of a common functional magnetic resonance imaging (fMRI) protocol and to functional magnetic resonance imaging (fMRI) protocol and to study regional brain dysfunction related to the progression and study regional brain dysfunction related to the progression and treatment of schizophrenia - attack on treatment of schizophrenia - attack on underlyingunderlying causecause of disease of disease

5 mm3

4 x 10-5 mm3

~110,000 X

P Advanced Imaging - Correlating Human and MouseAdvanced Imaging - Correlating Human and Mouse

Caltech/Beckman Inst.

MOUSE BIRN:MOUSE BIRN: TheThe Multiscale Multimodal Multiscale Multimodal Mouse Brain Imaging Research NetworkMouse Brain Imaging Research Network

Brain Morphometry BIRNBrain Morphometry BIRNClinical Specific AimsClinical Specific Aims

Do structural differences contribute to specific symptoms Do structural differences contribute to specific symptoms such as memory dysfunction or depression?such as memory dysfunction or depression?

Do specific structural differences distinguish specific Do specific structural differences distinguish specific diagnostic categories?diagnostic categories?

Technological Specific AimsTechnological Specific Aims Attempt to overcome obstacles to the use of neuroimaging data Attempt to overcome obstacles to the use of neuroimaging data

as quantitative outcome measures for clinical investigation as quantitative outcome measures for clinical investigation including the issues raised by longitudinal and multi-site including the issues raised by longitudinal and multi-site studies.studies.

Functional Imaging BIRNFunctional Imaging BIRNClinical Specific AimsClinical Specific Aims

Is Frontal and Temporal Lobe Dysfunction the Cause of Is Frontal and Temporal Lobe Dysfunction the Cause of Schizophrenia?Schizophrenia?

How can Treatment Reverse this Dysfunction?How can Treatment Reverse this Dysfunction?

Technological Specific AimsTechnological Specific Aims Integration of 4D Data from Multiple Sites - Acquired with Integration of 4D Data from Multiple Sites - Acquired with

Different Non-Invasive Imaging DevicesDifferent Non-Invasive Imaging Devices Integration of Information Obtained with Different Brain Integration of Information Obtained with Different Brain

Activation Tasks.Activation Tasks.

BIRN - Challenges BIRN - Challenges && Opportunities Opportunities

• Understanding how to integrate and calibrate Understanding how to integrate and calibrate MR data from different sites and equipmentMR data from different sites and equipment

• Incorporating processes for Multi-sites studies Incorporating processes for Multi-sites studies and sharing of human dataand sharing of human data

• HIPPA ComplianceHIPPA Compliance• Patient confidentialityPatient confidentiality• Institutional Review Board (IRB) approvalsInstitutional Review Board (IRB) approvals

• Developing guidelines - Developing guidelines - for sharing data & authorshipfor sharing data & authorship

• Training across tools and disciplinesTraining across tools and disciplines

• Developing research projects leveraging BIRN Developing research projects leveraging BIRN

• Extending to health care industry andExtending to health care industry and translational research projects translational research projects - - eg., drugeg., drug trial networks and clinical care environmentstrial networks and clinical care environments

Ongoing Activities……..Ongoing Activities……..

Tuning and optimization of the Tuning and optimization of the networking infrastructure networking infrastructure for the BIRN for the BIRN – – Integration with Internet2 - establishing enhanced Integration with Internet2 - establishing enhanced performance testbeds to prototype upgradesperformance testbeds to prototype upgrades

Build the BIRN virtual data grid Build the BIRN virtual data grid – – Storage Resource Broker and Storage Resource Broker and NSF / National MiddIeware Initiative tools - evolve BIRN with the gridNSF / National MiddIeware Initiative tools - evolve BIRN with the grid

Coupling BIRN data grid to the computational grid – Coupling BIRN data grid to the computational grid – Globus, Globus,

NMI, NMI, etc -etc - picking high performance computational projects picking high performance computational projects

Assimilating and Integrating Data Refinement or Metadata Assimilating and Integrating Data Refinement or Metadata Production tools into the BIRN Projects: Production tools into the BIRN Projects: Tools from Partner Tools from Partner sites like: GridPortals, FreeSurfer, LONI Pipeline, 3-D Slicer, etcsites like: GridPortals, FreeSurfer, LONI Pipeline, 3-D Slicer, etc

Incorporating and adapting data integration and data Incorporating and adapting data integration and data mediation technologies into BIRN test-bed projects. mediation technologies into BIRN test-bed projects.

Building Interaction Environments for the BIRN Building Interaction Environments for the BIRN - - Incorporating Visualization Tools from BIRN partners and others.Incorporating Visualization Tools from BIRN partners and others.

Challenges……..Challenges……..

Breaking down the barriersBreaking down the barriersMistrustMistrustOpen sharing of informationOpen sharing of informationWho gets creditWho gets creditCommercial productsCommercial productsGovernanceGovernance

Integrating new participantsIntegrating new participantsProviding an architecture to allow for Providing an architecture to allow for

technology improvements with the existing technology improvements with the existing infrastructureinfrastructure

Guaranteeing security versus ease of useGuaranteeing security versus ease of use

All Hands Meeting…...All Hands Meeting…...

ObjectivesObjectives

Review the current scope of the BIRN and current Review the current scope of the BIRN and current accomplishments of each teamaccomplishments of each team

Identify research efforts for the next 12 months, define Identify research efforts for the next 12 months, define how it will be accomplished and specify the specific how it will be accomplished and specify the specific tasks of each research teamtasks of each research team

Breakout SessionsBreakout Sessions

This is a working conference !This is a working conference !Emphasis is on discussions, building Emphasis is on discussions, building

relationships and getting questions answered.relationships and getting questions answered.Three types of breakout sessions are have been Three types of breakout sessions are have been

planned:planned:BIRN Interactions - Interdisciplinary & Cross Training BIRN Interactions - Interdisciplinary & Cross Training BIRDs of a Feather - Detailed DiscussionsBIRDs of a Feather - Detailed DiscussionsA Focused Session for each Test-bed Partnering Group A Focused Session for each Test-bed Partnering Group

to Discuss and Define their Near-term Implementation to Discuss and Define their Near-term Implementation PlansPlans

Breakout Sessions (continued)Breakout Sessions (continued)

Breakout Sessions #1 & #2Breakout Sessions #1 & #2

Identify key impediments for accomplishing our goalsIdentify key impediments for accomplishing our goals

Define suggested approaches to resolve the Define suggested approaches to resolve the impedimentsimpediments

Identify action items and specify responsible persons Identify action items and specify responsible persons for reporting back to the teamfor reporting back to the team

Breakout Sessions (continued)Breakout Sessions (continued)

Breakout Session #3Breakout Session #3

Identify three (or more) research aims to be completed Identify three (or more) research aims to be completed over the next 8 to 12 monthsover the next 8 to 12 months

Specify the steps needed to accomplish these goalsSpecify the steps needed to accomplish these goals

Identify which individuals will be responsible for Identify which individuals will be responsible for accomplishing these tasksaccomplishing these tasks