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Schedule: November 12-18th 2005
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Genome-Scale Computational Approaches to Memory-Intensive Applications in Systems Biology

Session: Bioscience

Event Type: Paper

Time: 2:30pm - 3:00pm

Session Chair: Srinivas Aluru

Speaker(s): Yun Zhang, Faisal N. Abu-Khzam, Nicole E. Baldwin, Elissa J. Chesler, Michael A. Langston, Nagiza F. Samatova

Location: 602-604

Abstract:

Effective graph-theoretical approaches for small biological networks are not computationally feasible for genome-scale analysis. These systems biological problems are typically NP-hard, with exponential run times for finding optimal solutions. Plus they are memory-intensive, requiring effective data sharing across many processors. For example, enumeration of maximal cliques, essential to many biological applications, can yield 3^(n/3) maximal cliques for a graph with n vertices. Memory requirements reach terabyte scales even for modest-sized problems. Emerging hardware architectures with ultra-large globally addressable memory including the SGI Altix and Cray X1 are ideal for data-intensive problems. This paper presents a novel framework providing exact, parallel and scalable solutions to graph-theoretical biological network analysis. The framework exploits large-memory architectures by creating globally addressable bitmap memory indices with high compression rates, fast bitwise-logical operations, and reduced search space. Theoretical advances in fixed-parameter tractability augment performance for computationally feasible solutions to large combinatorial problems of systems biology.

This paper can be found in the ACM and IEEE Digital Libaries
Click here for ACM
Click here for IEEE



Chair/Speaker Details:

Srinivas Aluru (Chair)
Iowa State University

Yun Zhang
Department of Computer Science, University of Tennessee, Knoxville, TN 37996-3450, USA

Faisal N. Abu-Khzam
Division of Computer Science and Mathematics, Lebanese American University, Chouran, Beirut, Lebanon

Nicole E. Baldwin
Computational Biology Institute, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA

Elissa J. Chesler
Department of Anatomy and Neurobiology, University of Tennessee, Memphis, TN 38163, USA

Michael A. Langston
Department of Computer Science, University of Tennessee, Knoxville, TN 37996-3450, USA

Nagiza F. Samatova
Computational Biology Institute, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA