Developing Reusable Software Infrastructure

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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
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Modeling Synaptic Activity
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Transformation Based Backprojection for Volume
Reconstruction (TxBR)
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Enabling Biomedical Applications with Grid
Technology -- Cyberinfrastructure
Cyberinfrastructure raw resources, middleware
and execution environment
Virtual Organizations
Web Service
Workflow Management
NBCR Rocks Clusters
Vision
Virtual Filesystem
KEPLER
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Service Oriented Architecture
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Opal Web Service Wrapper
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GAMA Grid Account Management Architecture
K. Mueller
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Rapid Grid Deployment
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Web Service based Workflow Composition
S. Krishnan
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Opal WSRF Operation Provider
K. Ichikawa
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Opal Web services in Vision
M. Sanner
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PMV developments

• Secure web servicesfor AutoDock on NBCR cluster

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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

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My WorkSphere Overview
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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

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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

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Integrating Image Analysis, Mesh Generation, and
Simulation

• Pipeline

Image Pre-processing
Feature Extraction
Geometric Modeling
Physical Modeling
Simulation
Z. Yu
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Relaxed Complex Method and Virtual Screening
AutoDock
Post-processing ranking schemes
Set of docked complexes, BEs
R. Amaro
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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
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Continuity Data Format Beeler-Reuter 1977

• Stuart Campbell