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January 2009 - March 2010

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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 and Analysis of Metabolic Pathways

This project aims to compute the set of vector pathways called elementary flux 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. Earlier 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 have developed a parallel version of the nullspace algorithm and run it on parallel platforms at MSI, with an aim of computing metabolic pathways of very large and genome-scale metabolic networks.

The parallel version of the nullspace algorithm and its implementation in the C++ (with MPI, OpenMP) programming language, accompanied with the use of available numeric libraries, still needs improvement with respect to scalability and more efficient use of memory. Genome-scale metabolic networks may have a number of reactions and metabolites of the order of several thousands, and the present challenge is to enable the computation of complete set of elementary modes for these large metabolic networks. The researchers are also working on the alternative divide-and-conquer algorithm, as well as on an algorithm for the processing of the complete set of elementary modes, both of which will require parallel computing capabilities.

Group Member

Dimitrije Jevremovic, Graduate Student