Parallel out-of-core algorithm for genome-scale enumeration of metabolic systemic pathways

N. F. Samatova, A. Geist, G. Ostrouchov, A. Melechko

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

8 Scopus citations

Abstract

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 out-of-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, search space reduction, and out-of-core implementation to improve CPU-time and memory requirements by several orders of magnitude. Augmented with a parallel implementation, it provides extremely scalable performance. No previous parallel and/or out-of-core algorithms for the enumeration of systemically defined metabolic pathways are known.

Original languageEnglish
Title of host publicationProceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages185-192
Number of pages8
ISBN (Electronic)0769515738, 9780769515731
DOIs
StatePublished - 2002
Event16th International Parallel and Distributed Processing Symposium, IPDPS 2002 - Ft. Lauderdale, United States
Duration: Apr 15 2002Apr 19 2002

Publication series

NameProceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002

Conference

Conference16th International Parallel and Distributed Processing Symposium, IPDPS 2002
Country/TerritoryUnited States
CityFt. Lauderdale
Period04/15/0204/19/02

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