Divide-and-conquer approach to the parallel computation of elementary flux modes in metabolic networks

Dimitrije Jevremovic, Daniel L Boley, Carlos P. Sosa

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations

Abstract

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.

Original languageEnglish (US)
Title of host publication2011 IEEE International Symposium on Parallel and Distributed Processing, Workshops and Phd Forum, IPDPSW 2011
Pages502-511
Number of pages10
DOIs
StatePublished - Dec 20 2011
Event25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011 - Anchorage, AK, United States
Duration: May 16 2011May 20 2011

Publication series

NameIEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum

Other

Other25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011
CountryUnited States
CityAnchorage, AK
Period5/16/115/20/11

Keywords

  • Computational biology
  • Divide-and-conquer
  • Metabolic network pathways
  • Parallel algorithms

Fingerprint Dive into the research topics of 'Divide-and-conquer approach to the parallel computation of elementary flux modes in metabolic networks'. Together they form a unique fingerprint.

Cite this