title: An integrated computational environment for elementary modes analysis of biochemical networks.
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.
authors.affiliation: Department of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, Braga, Portugal. paulo.maia@deb.uminho.pt
authors.forename: Paulo
authors.initials: P
authors.lastname: Maia
authors.forename: Paulo
authors.initials: P
authors.lastname: Vilaça
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha
authors.forename: Marcellinus
authors.initials: M
authors.lastname: Pont
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Tomb
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
mesh_terms: D000465:Algorithms; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D010641:Phenotype; D020543:Proteome / Q000032:analysis / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D020543:Proteome