Title: An integrated computational environment for elementary modes analysis of biochemical networks

Authors: Paulo Maia; Paulo Vilaça; Isabel Rocha; Marcellinus Pont; Jean-François Tomb; Miguel Rocha

Addresses: Department of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, Braga, Portugal ' Department of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, Braga, Portugal ' Department of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, Braga, Portugal ' E.I. DuPont De Nemours & Co., Inc Wilmington, DE 19898, USA ' E.I. DuPont De Nemours & Co., Inc Wilmington, DE 19898, USA ' Computer Science and Technology Center, Department of Informatics, University of Minho, Campus de Gualtar, Braga, Portugal

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.

Keywords: EFMs; elementary flux modes; biochemical networks; computational environment; systems biology; filtering techniques; Java; graphical user interface; GUI; pathway analysis; bioinformatics; phenotype simulation; strain optimisation.

DOI: 10.1504/IJDMB.2012.049292

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.4, pp.382 - 395

Published online: 17 Dec 2014 *

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