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Developing Reusable Software Infrastructure – Middleware – for Multiscale Modeling

Developing Reusable Software Infrastructure – Middleware – for Multiscale Modeling. Wilfred W. Li, Ph.D. National Biomedical Computation Resource Center for Research in Biological Systems San Diego Supercomputer Center University of California, San Diego. Modeling the Heart. ventricles.

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Developing Reusable Software Infrastructure – Middleware – for Multiscale Modeling

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  1. Developing Reusable Software Infrastructure – Middleware – for Multiscale Modeling Wilfred W. Li, Ph.D. National Biomedical Computation Resource Center for Research in Biological Systems San Diego Supercomputer Center University of California, San Diego

  2. Modeling the Heart ventricles multicellular lattice crossbridge filament Modeling Synaptic Activity

  3. Transformation Based Backprojection for Volume Reconstruction (TxBR)

  4. Enabling Biomedical Applications with Grid Technology -- Cyberinfrastructure Cyberinfrastructure: raw resources, middleware and execution environment Virtual Organizations Workflow Management Web Service NBCR Rocks Clusters Vision Virtual Filesystem KEPLER

  5. Service Oriented Architecture

  6. Opal: Web Service Wrapper

  7. GAMA – Grid Account Management Architecture K. Mueller

  8. Rapid Grid Deployment

  9. Web Service based Workflow Composition S. Krishnan

  10. Opal WSRF Operation Provider K. Ichikawa

  11. Opal Web services in Vision M. Sanner

  12. PMV developments • Secure web servicesfor AutoDock on NBCR cluster

  13. Ligand Protein Interaction Using Web Services – GEMSTONE • Baldridge, Greenberg, Amoreira, Kondric • GAMESS Service • More accurate Ligand Information • LigPrep Service • Generation of Conformational Spaces • PDB2PQR Service • Protein preparation • APBS Service • Generation of electrostatic information • QMView Service • Visualization of electrostatic potential file • Applications: • Electrostatics and docking • High-throughput processing of ligand-protein interaction studies • Use of small molecules (ligands) to turn on or off a protein function

  14. My WorkSphere Overview

  15. My WorkSphere • Test platform for portlets • Integrate open source solutions for rich functionalities • Customized solutions based on generic web services • Rapid application deployment using Opal • Technology from TeleScience Project • ATOMIC • Session management • Data storage • New development • Generic user interface definition language • Describe application I/O parameters • Workflow monitor • Job Provenance

  16. Workflow Management • Use of Opal WS wrapper for rapid application deployment • Possible to add data type mapping • Leverage semantic web technology for interoperability • Use of Strongly Typed web service for data integrity, and better integration of WS based workflow • Data Integration • XML schema definition for data • Required for database storage, query and interface layer • What other standards to adopt and integrate using different namespaces • The bottom line: • WS enables workflow composition using tools such as KEPLER, TAVERNA, Vision in a visual environment (programming still required) • Reusable services by many other clients • Separation of data access and computation

  17. Integrating Image Analysis, Mesh Generation, and Simulation • Pipeline Image Pre-processing Feature Extraction Geometric Modeling Physical Modeling Simulation Z. Yu

  18. Receptor xtal struct Ligands N/A available Explicit MD Org. synth ZINC NCI ACD • - Different methods of structure generation • Reduction of snapshots Snapshot 10 ps Ligand PDBs Receptor ensemble Relaxed Complex Method and Virtual Screening AutoDock Post-processing ranking schemes Set of docked complexes, BEs R. Amaro

  19. Virtual Cell Virtual Cell – Continuity Integration Plans Objective: Develop utilities and computing infrastructure to join the model authoring environment of Virtual Cell with the parallel computing capabilities of Continuity Cell models for Continuity Continuity • Proposed development activities: • Create VCell utilities to export Continuity-ready cell model and geometry descriptions • Deploy Continuity as a grid-based parallel solving engine accessible by VCell • Graphical, intuitive model authoring • Database of existing cell models • Dynamic compilation of cell model descriptions • Highly accessible parallel solvers Access to parallel solvers for VCell A. McCulloch

  20. Continuity Data Format – Beeler-Reuter 1977 • Stuart Campbell

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