Download Wilfred`s talk

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
Modeling Synaptic
Activity
ventricles
multicellular
lattice
crossbridge
filament
Transformation Based Backprojection for
Volume Reconstruction (TxBR)
Enabling Biomedical Applications with
Grid Technology -- Cyberinfrastructure
Cyberinfrastructure: raw resources, middleware and execution environment
Virtual Organizations
Workflow Management
Web Service
NBCR Rocks Clusters
Vision
KEPLER
Virtual Filesystem
Service Oriented Architecture
Opal: Web Service Wrapper
GAMA – Grid Account
Management Architecture
K. Mueller
Rapid Grid Deployment
Web Service based Workflow Composition
S. Krishnan
Opal WSRF Operation Provider
K. Ichikawa
Opal Web services in Vision
M. Sanner
PMV developments
• Secure web services
for AutoDock on
NBCR cluster
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 ligandprotein interaction studies
– Use of small molecules (ligands) to turn
on or off a protein function
My WorkSphere Overview
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
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
Integrating Image Analysis, Mesh Generation,
and Simulation
• Pipeline
Image
Pre-processing
Geometric
Modeling
Physical
Modeling
Z. Yu
Simulation
Feature
Extraction
Relaxed Complex Method and Virtual
Screening
Receptor xtal struct
Ligands
N/A
Org.
synth
Explicit
MD
available
ZINC
ACD
NCI
- Different
methods of
structure
generation
-Reduction of
snapshots
Snapshot
10 ps
Ligand PDBs
Receptor ensemble
AutoDock
Set of docked
complexes, BEs
Post-processing
ranking schemes
R. Amaro
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
Virtual Cell
Continuity
Proposed development
activities:
• Create VCell utilities
to export Continuityready cell model and
geometry
descriptions
• Graphical, intuitive
model authoring
• Database of existing
cell models
• Deploy Continuity as
a grid-based parallel
solving engine
accessible by VCell
Access to parallel solvers for VCell
• Dynamic compilation
of cell model
descriptions
• Highly accessible
parallel solvers
A. McCulloch
Continuity Data Format – BeelerReuter 1977
•
Stuart Campbell