Parallel Out-of-Core Algorithm for Genome-Scale Enumeration of Metabolic Systemic Pathways

Systemic pathways-oriented approaches to analysis of metabolic networks are effective for small networks but are computationally infeasible for genome scale networks. Current computational approaches to this analysis are based on the mathematical principles of convex analysis. The enumeration of a complete set of “systemically independent” metabolic pathways is at the core of these approaches and it is computationally the most demanding component. An efficient parallel outof-core algorithm for generating a complete set of systemically independent metabolic pathways, termed “extreme pathways”, is presented. These pathways represent the edges of a high-dimensional convex cone and can be used to derive any admissible steady-state flux distribution (or phenotype) for a specified metabolic genotype. The algorithm can be used for computing “elementary flux modes” that are different but closely related to extreme pathways. The algorithm combines a bitmap data representation, sear...

• Type: Conference
• Year: 2002
• Where: IPPS
• Authors: Nagiza F. Samatova, Al Geist, George Ostrouchov, Anatoli V. Melechko
• Keywords: Distributed And Parallel Computing, Extreme Pathways, Independent Metabolic Pathways, IPPS 2002, Metabolic Pathways