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TitleAnalyzing and designing cell factories with OptFlux
Author(s)Vilaça, Paulo Ricardo Carvalho
Maia, Paulo
Giesteira, Hugo Miguel Melo
Rocha, Isabel
Rocha, Miguel
KeywordsComputational biology and bioinformatics
Systems biology
Metabolic engineering
Flux-balance analysis
Issue date2018
JournalMethods in Molecular Biology
CitationVilaça, P.; Maia, Paulo; Giesteira, Hugo; Rocha, Isabel; Rocha, Miguel, Analyzing and designing cell factories with Optflux. In Marco Fondi, Metabolic Network Reconstruction and Modeling: Methods and Protocols, Vol. Methods in Molecular Biology 1716, Springer, 2018. ISBN: 978-1-4939-7528-0, 37-76
Abstract(s)OptFlux was launched in 2010 as the first open-source and user-friendly platform containing all the major methods for performing metabolic engineering tasks in silico. Main features included the possibility of performing microbial strain simulations with widely used methods such as Flux Balance Analysis and strain design using Evolutionary Algorithms. Since then, OptFlux suffered a major re-factoring to improve its efficiency and reliability, while many features were added in the form of novel plug-ins, such as the BioVisualizer and the over/under expression plug-ins. The current chapter described the main mathematical formulations of the major methods implemented within OptFlux, also providing a detailed guide on the usage of those functionalities.
TypeBook part
Publisher version
AccessRestricted access (UMinho)
Appears in Collections:CEB - Livros e Capítulos de Livros / Books and Book Chapters

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