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Research Abstracts Online
January 2008 - March 2009

University of Minnesota Twin Cities
Institute of Technology
Department of Computer Science and Engineering

PI: Daniel L. Boley, Fellow
Co-PI: Friedrich Srienc, Associate Fellow

Computation of Metabolic Pathways

This project aims to compute the set of vector pathways called elementary modes of a biochemical reaction network. In this problem, biochemical reaction networks are represented as a steady-state stoichiometric matrix of dimension m x q, where m is the number of metabolites and q is the number of reactions in the metabolism. This computation is based on the so-called Nullspace Algorithm, which is an iterative algorithm for the computation of elementary pathways given the stoichiometric matrix as input. Present software solutions are able to compute metabolic pathways for only relatively small reaction networks, due to the explosive nature of intermediate pathways during computation. These researchers are developing a distributed version of the Nullspace algorithm to be run on a parallel computer, with an aim of computing metabolic pathways of very large and genome-scale metabolic networks. The parallel version of the algorithm will be able to accommodate much larger networks, perhaps with several hundreds of reactions, allowing researchers to model much more complete genome-scale metabolic networks.

Group Member

Dimitrije Jevremovic, Graduate Student