Parallel Extreme Pathway Computation for Metabolic Networks

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CSB
2004
2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)
Abstract - Parallel Extreme Pathway Computation for Metabolic Networks

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2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)

Stanford, California

August 16-August 19

ISBN: 0-7695-2194-0

	ASCII Text	x
	Lie-Quan Lee, Jeff Varner, Kwok Ko, "Parallel Extreme Pathway Computation for Metabolic Networks," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 636-639, 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04), 2004.

	BibTex	x
	@article{ 10.1109/CSB.2004.1332526, author = {Lie-Quan Lee and Jeff Varner and Kwok Ko}, title = {Parallel Extreme Pathway Computation for Metabolic Networks}, journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society}, volume = {0}, year = {2004}, isbn = {0-7695-2194-0}, pages = {636-639}, doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2004.1332526}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society TI - Parallel Extreme Pathway Computation for Metabolic Networks SN - 0-7695-2194-0 SP636 EP639 A1 - Lie-Quan Lee, A1 - Jeff Varner, A1 - Kwok Ko, PY - 2004 KW - null VL - 0 JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society ER -

Lie-Quan Lee, Stanford Linear Accelerator Center

Jeff Varner, Genencor International, Inc

Kwok Ko, Stanford Linear Accelerator Center

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2004.1332526

We parallelized the serial extreme pathways algorithm presented by Schilling et al., in J. Theor. Biol. 203 (2000) using the Message Passing Interface (MPI). The parallel algorithm exhibits super-linear scalability because the number of independence tests performed decreases as the number of MPI nodes increases. A subsystem of the metabolic network of Escherichia coli with 140 reactions and 96 metabolites (without preprocessing) is used as a benchmark. The extreme pathways of this system are computed in under 280 seconds using 70 2.4 GHz Intel Pentium-IV CPUs with Myrinet interconnection among the dual-CPU nodes of the Linux cluster.

Citation:

Lie-Quan Lee, Jeff Varner, Kwok Ko, "Parallel Extreme Pathway Computation for Metabolic Networks," csb, pp.636-639, 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04), 2004

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