Mark Ellisman, Ph.D. Professor of Neurosciences and Bioengineering Director, BIRN Coordinating Center Center for Research on Biological Systems University of California San Diego - School of Medicine La Jolla, California Building on the BIRN March 22, 2004

BIRN is Team Science Applied to Stretch Goals A Big Challenge or Vision: A Big Challenge or Vision: “Enable new understanding of the healthy and diseased brain by linking data about macroscopic brain function to its molecular and cellular underpinnings” Taking practical steps toward a grand goal using cyberinfrastructure: Taking practical steps toward a grand goal using cyberinfrastructure: Federate geographically distributed brain data of the same & different types Federate geographically distributed brain data of the same & different types Accommodate requirements to collaboratively interact with shared databases of large-scale data, share methods, and computational resources Accommodate requirements to collaboratively interact with shared databases of large-scale data, share methods, and computational resources Scales of NS data from Maryann Martone

BIRN Project Coordination Internet 2 Functional Imaging BIRN Test-bed Human Morphometry BIRN Test-bed Mouse BIRN Test-bed BIRN Coordinating Center The BIRN-CC leads… the deployment and maintenance of a network infrastructure capable of quickly moving large amounts of data between BIRN sites across the country. the deployment and maintenance of a network infrastructure capable of quickly moving large amounts of data between BIRN sites across the country. the creation of a federation of databases pertaining to the BIRN scientific projects. the creation of a federation of databases pertaining to the BIRN scientific projects. the development and integration of software to refine, combine, compare, and analyze complex biomedical data. the development and integration of software to refine, combine, compare, and analyze complex biomedical data. and cultivates group activities to overcome cultural barriers to building a forum for collaborative research, co-authoring research papers, and sharing methods/tools/codes across institutions. and cultivates group activities to overcome cultural barriers to building a forum for collaborative research, co-authoring research papers, and sharing methods/tools/codes across institutions.

The BIRN’s Interwoven Teams Information Tech. SRB / Database IRB Callibration Statistics Project Manager Scientific Director Information Tech. SRB / Database IRB Callibration Statistics Project Manager Scientific Director Information Tech. SRB / Database Project Manager Scientific Director PI Information Tech. SRB / Database IRB Statistics Project Manager Scientific Director PI MouseMorphometryFunctionBIRN-CC Statistics Callibration BIRN All Hands meeting held annually BIRN PIs meet quarterly as part of the BIRN Steering Committee IRB Task Forces SRB / 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 Task Forces Intellectual Property Utilization Data Sharing Working Groups

 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…

“CYBERINFRASTRUCTURE” What is a Grid? What do we mean? GRID technologies bring remote resources togetherGRID technologies bring remote resources together

Evolution of the Computational Infrastructure Source: Dr. Deborah Crawford Chair, NSF CyberInfrastructure Working Group (CIWG) Supercomputer Centers PACI Terascale | | | | | | 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 Development Tools & Libraries Applications Environmental Science High Energy Physics Biomedical Informatics Geoscience Domain- specific Cybertools (software) Shared Cybertools (software) Distributed Resources (computation, communication storage, etc.) Education and Training Discovery & Innovation

BIRN 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 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 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” Parallel Distributed High Performance Computing The End User is Shielded from the Complexities of the Grid Platform Independent Domain Independent

Example 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 Structure Wrapper Clinical Wrapper Mediator

BIRN is using Domain Maps to Navigate Data Sources These are Rule-based ontology maps or a “data model”These are Rule-based ontology maps or a “data model” They Encode conceptual and semantic relationships (“domain knowledge”They Encode conceptual and semantic relationships (“domain knowledge” Ontologies can be linked or joined to data models of other biomedical databases (PDB, Yale’s Sense Lab, etc.)Ontologies can be linked or joined to data models of other biomedical databases (PDB, Yale’s Sense Lab, etc.) Brain Cerebellum Purkinje Cell Layer Purkinje cell neuron has a is a

Purkinje neuron Registering My Data UMLS Spatial Registration

Annual Meeting 3 rd Annual BIRN All-Hands Meeting October 2003 Scripps Institution of Oceanography 3 rd Annual BIRN All-Hands Meeting October 2003 Scripps Institution of Oceanography