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Divide-and-Conquer Approach to the Parallel Computation of Elementary Flux Modes in Metabolic Networks

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3 Author(s)
Jevremovic, D. ; Dept. of Comput. Sci. & Eng., Univ. of Minnesota, Minneapolis, MN, USA ; Boley, D. ; Sosa, C.P.

Elementary flux modes are an important class of metabolic pathways used to characterize the functioning and behavior of metabolic networks of biochemical reactions in a biological cell. The computation of the elementary flux modes is accomplished by using the so-called Nullspace Algorithm whose high computational cost and memory requirements still limit the computation to relatively small metabolic networks. We combine a "combinatorial'' parallelization with a novel divide-and-conquer paradigm into a new implementation of the Nullspace Algorithm with lower memory requirements. We discuss the disadvantages of the combinatorial parallelization and divide-and-conquer ideas and explain why their combination attains more computational power. The improved parallel Nullspace Algorithm is used to compute up to nearly 50 million elementary flux modes for a metabolic network for yeast, a task which was previously not possible using either of the two approaches individually.

Published in:

Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on

Date of Conference:

16-20 May 2011