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TitleAn integrated computational environment for elementary modes analysis of biochemical networks
Author(s)Maia, P.
Vilaça, P.
Rocha, I.
Pont, M.
Tomb, J. F.
Rocha, Miguel
elementary flux modes
Biochemical networks
Computational environment
Systems biology
Filtering techniques
Graphical user interface
Issue date2012
PublisherInderscience Enterprises Ltd.
JournalInternational Journal of Data Mining and Bioinformatics
Abstract(s)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.
AccessRestricted access (UMinho)
Appears in Collections:CCTC - Artigos em revistas internacionais
CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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