Parallel extreme pathway computation for metabolic networks

Author

Lee, Lie-Quan ; Varner, Jeff ; Ko, Kwok

Author_Institution

Stanford Linear Accelerator Center, CA, USA

fYear

2004

fDate

16-19 Aug. 2004

Firstpage

636

Lastpage

639

Abstract

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.

Keywords

biology computing; message passing; parallel algorithms; Escherichia coli; Linux cluster; Myrinet interconnection; dual-CPU nodes; message passing interface; metabolic networks; parallel extreme pathway computation; superlinear scalability; Biochemistry; Chemical processes; Computer networks; Concurrent computing; Linear accelerators; Message passing; Parallel algorithms; Scalability; Steady-state; Vectors;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE

Print_ISBN

0-7695-2194-0

Type

conf

DOI

10.1109/CSB.2004.1332526

Filename

1332526