Developing Reusable Software Infrastructure – Middleware –

for Multiscale Modeling

Wilfred W. Li, Ph.D. National Biomedical Computation ResourceCenter for Research in Biological SystemsSan Diego Supercomputer CenterUniversity of California, San Diego

Modeling Synaptic Activity

crossbridge

lattice

multicellular

filament

ventricles

Modeling the Heart

Transformation Based Backprojection for Volume Reconstruction (TxBR)

Enabling Biomedical Applications with Grid Technology -- Cyberinfrastructure

Cyberinfrastructure: raw resources, middleware and execution environment

NBCR Rocks Clusters

Virtual Organizations Web Service

KEPLER

Workflow Management

Vision 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 servicesfor 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 ligand-protein

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

FeatureExtraction

GeometricModeling

PhysicalModeling

Simulation

Z. Yu

- Different methods of structure generation

-Reduction of snapshots

Relaxed Complex Method and Virtual Screening

AutoDock

Set of docked complexes, BEs

Post-processing ranking schemes

Ligand PDBs

Ligands

ZINC

available

ACD NCI

N/A

Org. synth

Receptor xtal struct

Explicit MD

Snapshot 10 ps

Receptor ensemble

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

Virtual Cell Continuity

• Graphical, intuitive model authoring

• Database of existing cell models

• Dynamic compilation of cell model descriptions

• Highly accessible parallel solvers

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

Cell models for Continuity

Access to parallel solvers for VCell A. McCulloch

Continuity Data Format – Beeler-Reuter 1977

• Stuart Campbell