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An integrated computational environment for elementary modes analysis of biochemical networks

By P. Maia, P. Vilaça, I. Rocha, M. Pont, J. F. Tomb and Miguel Rocha

Abstract

Elementary Flux Modes (EFMs) have been claimed as one of the most promising approaches for pathway analysis. These are a set of vectors that emerge from the stoichiometric matrix of a biochemical network through the use of convex analysis. The computation of all EFMs of a given network is an NP–hard problem and existing algorithms do not scale well. Moreover, the analysis of results is difficult given the thousands or millions of possible modes generated. In this work, we propose a new plug–in, running on top of the OptFlux Metabolic Engineering workbench (Rocha et al., 2010), whose aims are to ease the analysis of these results and explore synergies among EFM analysis, phenotype simulation and strain optimisation. Two case studies are shown to illustrate the capabilities of the proposed tool.The authors wish to thank the financial support of the Portuguese FCT for the PhD grant SFRH/BD/61465/2009 and the project MIT-PT/BS-BB/0082/2008. Also, thanks to the company Dupont under the scope of the Dupont European University Support Program Award

Topics: EFMs, elementary flux modes, Biochemical networks, Computational environment, Systems biology, Filtering techniques, Java, Graphical user interface, Science & Technology
Publisher: 'Inderscience Publishers'
Year: 2012
DOI identifier: 10.1504/IJDMB.2012.049292
OAI identifier: oai:repositorium.sdum.uminho.pt:1822/23394
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