Biomedical Informatics Research Network BIRN Overview: Building the Biomedical Informatics Research Network October 9, nd Annual All Hands Meeting Mark Ellisman - UCSD

Synchrotrons Molecules MacromolecularComplexes, Organelles, Cells Organs, Organ Systems, Organisms Microscopes Magnetic Resonance Imagers BIG Distributed INSTRUMENTS and Shared Access BIG & Diverse BIOMEDICAL DATABASES and Shared Access BIG COMPUTATIONS - DATA REFINEMENT - BIG COMPUTATIONS - DATA REFINEMENT -

THE CHALLENGE OF FUNCTIONAL CORRELATIONS from Arthur Toga / UCLA THE CHALLENGE OF MULTIPLE SCALES INTEGRATING AND NAVIGATING NEUROIMAGING DATA - Mining for New Understanding of Structure and Function Mining for New Understanding of Structure and Function from Maryann Martone / UCSD

Biomedical Informatics Research Network Test-beds for biomedical knowledge infrastructure

BIRN Project Objectives BIRN Project Objectives Establish a stable, high performance network linking key Biotechnology Centers and General Clinical Research Centers Establish a stable, high performance network linking key Biotechnology Centers and General Clinical Research Centers Establish distributed and linked data collections with partnering groups - create a “Data GRID” for the BIRN Establish distributed and linked data collections with partnering groups - create a “Data GRID” for the BIRN Facilitate the use of "grid-based" computational infrastructure and integrate BIRN with other GRID middleware projects Facilitate the use of "grid-based" computational infrastructure and integrate BIRN with other GRID middleware projects Enable data mining from multiple data collections or databases on neuroimaging and bioinformatics Enable data mining from multiple data collections or databases on neuroimaging and bioinformatics 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. 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.

What BIRN is Doing……. What BIRN is Doing……. Integrating the activities of the most advanced biomedical imaging and clinical research centers in the US - Serving as a model for programs everywhere. Integrating the activities of the most advanced biomedical imaging and clinical research centers in the US - Serving as a model for programs everywhere. Developing hardware and software infrastructure for managing distributed data - creation of data grids. Developing hardware and software infrastructure for managing distributed data - creation of data grids. Exploring data using “intelligent” query engines that can make inferences upon locating “interesting” data. Exploring data using “intelligent” query engines that 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 individual laboratory or project to shared use. Changing the use pattern for research data from the individual laboratory or project to shared use.

Provide a scalable, open and available tool kit for querying, accessing and viewing the BIRN data. Provide a scalable, open and available tool kit for querying, accessing and viewing the BIRN data. Define processes, procedures and establish best practices so that the BIRN is reliable, scalable and extensible to biomedical research programs outside of the pioneering Neuroimaging Test-beds - able to support the work of thousands of researchers. Define processes, procedures and establish best practices so that the BIRN is reliable, scalable and extensible to biomedical research programs outside of the pioneering Neuroimaging Test-beds - able to support the work of thousands of researchers. Push the envelop of biomedical informatics and computer science by causing the development of new techniques in databases, information retrieval, visualization and computational processing. Push the envelop of biomedical informatics and computer science by causing the development of new techniques in databases, information retrieval, visualization and computational processing. What BIRN Must Do……. What BIRN Must Do…….

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

BIRN NOC Monitoring 24x7 Operations Monitoring NOC Servers and Testers/Analyzers Gigabit Network Probes Internet 2 GB Switches UCSD/SDSCNetwork BIRN Network Management BIRN Site Rack BIRN Network Operations Center (NOC) Logical Description with Standardized Site Rack BIRN Network Operations Center (NOC) Logical Description with Standardized Site RackN2400NAS TB Cisco 4006 DL380 Grid POP DL380 - Network Stats GigE Net Probe APC UPS DL380 Network SwitchNetwork Switch BIRN StatisticsBIRN Statistics BIRN Network ProbeBIRN Network Probe Network Attached Storage – Network Attached Storage – Grid POP/ SRB, Globus Grid POP/ SRB, Globus General purpose ( eg., encryption)General purpose ( eg., encryption) UPS for Rack UPS for Rack NCRR Ultimately, Access from Anywhere to BIRN DATA Everywhere Wired and Wireless

CREATING BIRN TEST-BED PARTNERSHIPS Three Research Project “Application Test Beds” have been Assembled to Shape BIRN and Guide Infrastructure Development: Three Research Project “Application Test Beds” have been Assembled to Shape BIRN and Guide Infrastructure Development: Multi-scale Mouse BIRN - Animal Models of disease / Multi Scale/Multi Method - Examples: MS Mouse, DAT KOM (a schizophrenic and otherwise interesting mouse animal model) and a Parkinson’s Disease Mouse Multi-scale Mouse BIRN - Animal Models of disease / Multi Scale/Multi Method - Examples: MS Mouse, DAT KOM (a schizophrenic and otherwise interesting mouse animal model) and a Parkinson’s Disease Mouse Brain Morphometrics (Human Structure BIRN) - Targets: neuroanatomical correlates of neuropsychiatric illness (Unipolar Depression, mild Alzheimer's Disease (AD), mild cognitive impairment (MCI) Brain Morphometrics (Human Structure BIRN) - Targets: neuroanatomical correlates of neuropsychiatric illness (Unipolar Depression, mild Alzheimer's Disease (AD), mild cognitive impairment (MCI) Functional Imaging BIRN – Development of a common functional magnetic resonance imaging (fMRI) protocol and to study regional brain dysfunction related to the progression and treatment of schizophrenia - attack on underlying cause of disease Functional Imaging BIRN – Development of a common functional magnetic resonance imaging (fMRI) protocol and to study regional brain dysfunction related to the progression and treatment of schizophrenia - attack on underlying cause of disease

5 mm 3 4 x mm 3 ~110,000 X P Advanced Imaging - Correlating Human and Mouse

Caltech/Beckman Inst. MOUSE BIRN: The Multiscale Multimodal MOUSE BIRN: The Multiscale Multimodal Mouse Brain Imaging Research Network Mouse Brain Imaging Research Network

Brain Morphometry BIRN Brain Morphometry BIRN Clinical Specific Aims Clinical Specific Aims Do structural differences contribute to specific symptoms such as memory dysfunction or depression? Do structural differences contribute to specific symptoms such as memory dysfunction or depression? Do specific structural differences distinguish specific diagnostic categories? Do specific structural differences distinguish specific diagnostic categories? Technological Specific Aims 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. 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.

Functional Imaging BIRN Functional Imaging BIRN Clinical Specific Aims Clinical Specific Aims Is Frontal and Temporal Lobe Dysfunction the Cause of Schizophrenia? Is Frontal and Temporal Lobe Dysfunction the Cause of Schizophrenia? How can Treatment Reverse this Dysfunction? How can Treatment Reverse this Dysfunction? Technological Specific Aims Technological Specific Aims Integration of 4D Data from Multiple Sites - Acquired with Different Non-Invasive Imaging Devices Integration of 4D Data from Multiple Sites - Acquired with Different Non-Invasive Imaging Devices Integration of Information Obtained with Different Brain Activation Tasks. Integration of Information Obtained with Different Brain Activation Tasks.

BIRN - Challenges & Opportunities Understanding how to integrate and calibrate Understanding how to integrate and calibrate MR data from different sites and equipment MR data from different sites and equipment Incorporating processes for Multi-sites studies Incorporating processes for Multi-sites studies and sharing of human data and sharing of human data HIPPA Compliance HIPPA Compliance Patient confidentiality Patient confidentiality Institutional Review Board (IRB) approvals Institutional Review Board (IRB) approvals Developing guidelines - for sharing data & authorship Developing guidelines - for sharing data & authorship Training across tools and disciplines Training across tools and disciplines Developing research projects leveraging BIRN Developing research projects leveraging BIRN Extending to health care industry and Extending to health care industry and translational research projects - eg., drug translational research projects - eg., drug trial networks and clinical care environments trial networks and clinical care environments

Ongoing Activities…….. Ongoing Activities…….. Tuning and optimization of the networking infrastructure for the BIRN – Integration with Internet2 - establishing enhanced performance testbeds to prototype upgrades Tuning and optimization of the networking infrastructure for the BIRN – Integration with Internet2 - establishing enhanced performance testbeds to prototype upgrades Build the BIRN virtual data grid – Storage Resource Broker and NSF / National MiddIeware Initiative tools - evolve BIRN with the grid Build the BIRN virtual data grid – Storage Resource Broker and NSF / National MiddIeware Initiative tools - evolve BIRN with the grid Coupling BIRN data grid to the computational grid – Globus, NMI, etc - picking high performance computational projects Coupling BIRN data grid to the computational grid – Globus, NMI, etc - picking high performance computational projects Assimilating and Integrating Data Refinement or Metadata Production tools into the BIRN Projects: Tools from Partner sites like: GridPortals, FreeSurfer, LONI Pipeline, 3-D Slicer, etc Assimilating and Integrating Data Refinement or Metadata Production tools into the BIRN Projects: Tools from Partner sites like: GridPortals, FreeSurfer, LONI Pipeline, 3-D Slicer, etc Incorporating and adapting data integration and data mediation technologies into BIRN test-bed projects. Incorporating and adapting data integration and data mediation technologies into BIRN test-bed projects. Building Interaction Environments for the BIRN - Incorporating Visualization Tools from BIRN partners and others. Building Interaction Environments for the BIRN - Incorporating Visualization Tools from BIRN partners and others.

Challenges…….. Challenges…….. Breaking down the barriers Breaking down the barriers Mistrust Mistrust Open sharing of information Open sharing of information Who gets credit Who gets credit Commercial products Commercial products Governance Governance Integrating new participants Integrating new participants Providing an architecture to allow for technology improvements with the existing infrastructure Providing an architecture to allow for technology improvements with the existing infrastructure Guaranteeing security versus ease of use Guaranteeing security versus ease of use

All Hands Meeting…... All Hands Meeting…... Objectives Objectives Review the current scope of the BIRN and current accomplishments of each team Review the current scope of the BIRN and current accomplishments of each team Identify research efforts for the next 12 months, define how it will be accomplished and specify the specific tasks of each research team Identify research efforts for the next 12 months, define how it will be accomplished and specify the specific tasks of each research team

Breakout Sessions This is a working conference ! This is a working conference ! Emphasis is on discussions, building relationships and getting questions answered. Emphasis is on discussions, building relationships and getting questions answered. Three types of breakout sessions are have been planned: Three types of breakout sessions are have been planned: BIRN Interactions - Interdisciplinary & Cross Training BIRN Interactions - Interdisciplinary & Cross Training BIRDs of a Feather - Detailed Discussions BIRDs of a Feather - Detailed Discussions A Focused Session for each Test-bed Partnering Group to Discuss and Define their Near-term Implementation Plans A Focused Session for each Test-bed Partnering Group to Discuss and Define their Near-term Implementation Plans

Breakout Sessions (continued) Breakout Sessions #1 & #2 Breakout Sessions #1 & #2 Identify key impediments for accomplishing our goals Identify key impediments for accomplishing our goals Define suggested approaches to resolve the impediments Define suggested approaches to resolve the impediments Identify action items and specify responsible persons for reporting back to the team Identify action items and specify responsible persons for reporting back to the team

Breakout Sessions (continued) Breakout Session #3 Breakout Session #3 Identify three (or more) research aims to be completed over the next 8 to 12 months Identify three (or more) research aims to be completed over the next 8 to 12 months Specify the steps needed to accomplish these goals Specify the steps needed to accomplish these goals Identify which individuals will be responsible for accomplishing these tasks Identify which individuals will be responsible for accomplishing these tasks