AWT Ivo D. Dinov, Ph.D., CCB Chief Operations Officer PI: Arthur W. Toga, Ph.D. Co-PI: Tony F. Chan, Ph.D.

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a national infrastructure for biomedical computing CCB Science, SW Development & Infrastructure

Non-Affine Volumetric Registration Shape –Parametric & Implicit Shape Representation –Modeling & Parsing of Biological Shapes –Shape Analysis (e.g., using Integral Invariants) Conformal Mapping (on D 2 or S 2 ) Volumetric Image Segmentation Biosequence analysis (e.g., alternative splicing) Driving Biological Projects CCB Science Developments

DBP 1: Mapping Language Development Longitudinally DBP 2: Mapping Structural and Functional Changes in Aging and Dementia DBP 3: Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis CCB – Driving Biological Projects (current) DBP 4: Correlating Neuroimaging, Phenotype and Genotype in Schizophrenia

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a national infrastructure for biomedical computing CCB Science, SW Development & Infrastructure

CCB Grand Challenges Brain Mapping Challenges Software & Hardware Engineering Challenges Infrastructure & Communication Challenges Data Management Multidisciplinary Science Environment

CCB Brain Mapping Challenges Quantitative analysis of structural & functional data Merging NeuroImaging and Clinical data (e.g., NPI) NeuroImaging Interactions w/ Genotype-Phenotype Understanding Temporal Changes in the Brain Data Management (volume, complexity, HIPAA) Data Integration Across Species, Modalities, Resol. Efficient and Robust Neurocomputation (Grid) SW & Tool Development and Management ( Pipeline )

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a national infrastructure for biomedical computing CCB Science, SW Development & Infrastructure

CCB Computational Atlas Framework

Data Analysis –Image segmentation –Surface methods –DTI Analysis –Genotype-Phenotype analysis Interaction –Grid Pipeline Environment –Pipeline/SCIRun Integration –Pipeline/Slicer Integration –Tools for Integration, Managing, Modeling & Visualization Knowledge Management –Analytic strategy validation –Data Provenance CCB Computational Tools

Computing Infrastructure Develop, implement and maintain the computing resources and network services required for computationally intensive science performed in the CCB Application Deployment Integrate the algorithms, techniques and tools developed in Cores 1 & 2 with the Computing Infrastructure to enable researchers to remotely access and use the computing resources of the CCB Computational Research Support Provide technical support and expertise to enable collaborators to use the resources of the CCB CCB Infrastructure

SW & Computational Tool Development Internal Algorithm & SW design –Mixture of: Sporadic Rapid Prototype development efforts Structured library-based quality developments –SW stages: active development,  &  distributions External SW design, policies, licenses – –Integration/Interoperability ( for now mainly with NAMIC ) Software Management System (SMS) –Based on: –Summary | Admin | Home Page | Forums | Tracker | Bugs | Support | Patches | RFE | Lists | Tasks | Docs | Screenshots | News | CVS | Files|

Example: Shape Representation – New Codebase Specification Explicitly represent points, edges, faces and solids Allow any number of arbitrary objects (e.g., scalars, vectors, tensors, colors) to be associated with topological primitives Modular Java-based architecture designed for collaborative development, including documentation sufficient to support independent development

Grid Pipeline The algorithms have been implemented –Possibly located on different platforms, different machines The data has been gathered –Possibly located on different machines, have different forma Grid Pipeline Processing Environment –A data flow execution environment –Useful for… Any task where you can draw the steps in a flowchart Any task where you need to write instructions for someone

Pipeline GUI v 3.0

Data Mediation

Pipeline Encryption Network communications uses shared secret key –Diffie Hellman key agreement –Advanced Encryption Standard User information –SHA1 digest of passphrase –AES key from digest Data Security and Anonymization

Data Visualization Additional functionality Is integrated via the extension architecture. Mutation Pathways Of HIV-1 Protease

Grid Engine Integration

DB Template Example 1. SW Label (acronym) ShapeViewer 2. Short Description: Provides 3D interactive user interface for viewing parametric shapes commonly used in CCB 3. Data INPUT (format, parameters, etc.): Current version requires UCF format 4. Data OUTPUT (format, parameters, etc.): Scenes, multiples shape objects, associated view reloading 5. Implementation Language: Java 1.4, requires Java3D runs as Application or as Applet 6. Platform(s) tested: Macintosh, PC, Sun 7. Version, date, Stage: 1.0, May 24, 2005, 8. Author(s): Ma, Schwartz, Woods, Dinov 9. URL: DB of Current CCB SW Developments Tool Categories 1.Viewers 1.Java-based 2.C++/VTK/ITK 2.Analysis a.Segmentation b.Sequence Analysis c.Data Alignment d.Shape Analysis e.Preprocessing (skull stripping) 3.Atlasing Tools 1.Construction 2.Mapping 3.Analysis (variation) 4.Data Processing (Pipeline, Debabeler) 5.Data Integration (BrainGraph)

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a national infrastructure for biomedical computing CCB Science, SW Development & Infrastructure

CCB Data Sharing CCB does not acquire data CCB utilizes other resource for test data Test data for internal CCB use: –Algorithm Development (All Problems outlined in CCB SIG Challenges) –Tool Implementation Testing and Validation –Online:

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a national infrastructure for biomedical computing CCB Science, SW Development & Infrastructure

CCB SW Integration with other NCBCs CCB–NAMIC –SLIPIE ( Slicer-LONI Pipeline Integration Environment ) –Java  JNI mediation  C/C++ tools –Level-set segmentation techniques CCB–I2B2 –HIVE cells  Neuroscience Pipelines –Pipeline modules  HIVE Objects –Neurogenetics (e.g., Huntington’s), DB and biosequence analysis CCB–SimBios –Structure Modeling Tools  Pipeline Modules –CCB Compute/Viz Libs  SimTK CCB–Collaborators ( many directions ) –Diffeomorphic shape representation –… –Integration of Gene expression maps and Macro-imaging

Science Developments CCB Grand Challenges SW & Computational Tool Development –Internal Algorithm & SW design –External SW design, policies, licenses –Software Management System (SMS) Data Sharing CCB SW Integration with other NCBCs NCBC as a National Infrastructure for Biomedical Computing CCB Science, SW Development & Infrastructure

NCBCs - Nat’l Infrastructure for Biomed Computing Intra-Center Infrastructure Inter-Center Infrastructure Center-Collaborators Infrastructure

Center for Computational Biology

Core 2: Computational Tools Analysis Data Integration Knowledge Management Core 3: Driving Biological Projects Brain Development Aging & Dementia Multiple Sclerosis Schizophrenia Core 1: Computational Science Registration Shape Modeling Surface Modeling Segmentation Core 7: Administration & Management Committees Science Advisory Board Meetings & Communication Progress & Monitoring Support Core 6: Dissemination Web Publications Education Database Core 5: Education & Training Courses Fellowships Workshops Training Materials Core 4: Infrastructure/Resources Computing Software Informatics CCB Overall Organization