Developing Reusable Software

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5 Νοε 2013 (πριν από 3 χρόνια και 10 μήνες)

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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

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 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 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

Feature

Extraction

Geometric

Modeling

Physical

Modeling

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