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HPC and Grid Computing for Integrative Biomedical Research

CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY, ATLANTA, GA 30322, USA

Shannon Hastings

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA

Vijay Kumar

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA, DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210-1277, USA

Stephen Langella

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA

Ashish Sharma

CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY, ATLANTA, GA 30322, USA

Tony Pan

CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY, ATLANTA, GA 30322, USA

Scott Oster

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA

David Ervin

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA

Justin Permar

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA

Sivaramakrishnan Narayanan

DEPARTMENT OF BIOMEDICAL INFORMATICS, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210, USA, DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING, OHIO STATE UNIVERSITY, COLUMBUS, OH 43210-1277, USA

Yolanda Gil

INFORMATION SCIENCES INSTITUTE, UNIVERSITY OF SOUTHERN CALIFORNIA, LOS ANGELES, CA 90292, USA

Ewa Deelman

INFORMATION SCIENCES INSTITUTE, UNIVERSITY OF SOUTHERN CALIFORNIA, LOS ANGELES, CA 90292, USA

Mary Hall

COLLEGE OF COMPUTING, UNIVERSITY OF UTAH, CEDAR CITY, UT 84720, USA

Joel Saltz

CENTER FOR COMPREHENSIVE INFORMATICS, EMORY UNIVERSITY, ATLANTA, GA 30322, USA

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.

Key Words: integrative biomedical research • system level integrative analysis • multi-scale integrative investigation

This version was published on August 1, 2009

International Journal of High Performance Computing Applications, Vol. 23, No. 3, 252-264 (2009)
DOI: 10.1177/1094342009106192


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