title: A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information.
abstract: OBJECTIVE
  Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events.
  This work proposes a novel software tool that implements methods for the phenotype simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community.
  
  
  BACKGROUND
  The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation.
authors.affiliation: Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal. pvilaca@deb.uminho.pt
authors.forename: Paulo
authors.initials: P
authors.lastname: Vilaça
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
mesh_terms: D000465:Algorithms; D002450:Cell Communication; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D000431:Ethanol / Q000378:metabolism; D005786:Gene Expression Regulation; D016680:Genome, Bacterial; D008660:Metabolism; D008954:Models, Biological; D012984:Software
chemical_list: D000431:Ethanol