HPC and Grid Computing for Integrative Biomedical Research

Authors:
Tahsin Kurc;Shannon Hastings;Vijay Kumar;Stephen Langella;Ashish Sharma;Tony Pan;Scott Oster;David Ervin;Justin Permar;Sivaramakrishnan Narayanan;Yolanda Gil;Ewa Deelman;Mary Hall;Joel Saltz
Affiliations:
CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY,ATLANTA, GA 30322, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA, DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING, OHIOSTATE UNIVERSITY, COLUMBUS, OH 43210-1277, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA;CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY,ATLANTA, GA 30322, USA;CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY,ATLANTA, GA 30322, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA;DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY,COLUMBUS, OH 43210, USA, DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING, OHIOSTATE UNIVERSITY, COLUMBUS, OH 43210-1277, USA;INFORMATION SCIENCES INSTITUTE, UNIVERSITY OF SOUTHERNCALIFORNIA, LOS ANGELES, CA 90292, USA;INFORMATION SCIENCES INSTITUTE, UNIVERSITY OF SOUTHERNCALIFORNIA, LOS ANGELES, CA 90292, USA;COLLEGE OF COMPUTING, UNIVERSITY OF UTAH, CEDAR CITY,UT 84720, USA;CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY,ATLANTA, GA 30322, USA
Venue:
International Journal of High Performance Computing Applications
Year:
2009

Citing 10
Cited 5

Design patterns: elements of reusable object-oriented software

Design patterns: elements of reusable object-oriented software
ANTLR: a predicated-LL(k) parser generator

Software—Practice & Experience
Distributed processing of very large datasets with DataCutter

Parallel Computing - Clusters and computational grids for scientific computing
Jess in Action: Java Rule-Based Systems

Jess in Action: Java Rule-Based Systems
Distributed computing in practice: the Condor experience: Research Articles

Concurrency and Computation: Practice & Experience - Grid Performance
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid

Bioinformatics
e-Science, caGrid, and Translational Biomedical Research

Computer
An integrated framework for performance-based optimization of scientific workflows

Proceedings of the 18th ACM international symposium on High performance distributed computing
Wings for Pegasus: creating large-scale scientific applications using semantic representations of computational workflows

IAAI'07 Proceedings of the 19th national conference on Innovative applications of artificial intelligence - Volume 2
OWLIM – a pragmatic semantic repository for OWL

WISE'05 Proceedings of the 2005 international conference on Web Information Systems Engineering

High-performance systems for in silico microscopy imaging studies

DILS'10 Proceedings of the 7th international conference on Data integration in the life sciences
Review: interactive knowledge capture in the new millennium: How the semantic web changed everything

The Knowledge Engineering Review
High performance computing techniques for scaling image analysis workflows

PARA'10 Proceedings of the 10th international conference on Applied Parallel and Scientific Computing - Volume 2
Large-scale multimedia content analysis using scientific workflows

Proceedings of the 21st ACM international conference on Multimedia
Structured analysis of the ISI Atomic Pair Actions dataset using workflows

Pattern Recognition Letters

Quantified Score

Hi-index	0.00

Visualization

Abstract

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.