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OptFlux : an open-source software platform for in silico metabolic engineering

Background: Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other ex...

OptFlux : a software for metabolic engineering

Natural computation meta-heuristics for the in silico optimization of microbial...

Background: One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only due to the inherent complexity of the metabolic and regulatory networks, but also to the lack o...

An improved evolutionary algorithm-based framework for identifying in silico me...

In metabolic engineering problems, due to the complexity of metabolic networks, it is often difficult to identify a priori which genetic manipulations will originate a given desired phenotype. Genome-scale metabolic models, available for several microorganisms, can be used to simulate the metabolic phenotype and therefore help the tasks of metabolic engineering. This simulation can be performed by calculating t...

Evolutionary programming as a platform for in silico metabolic engineering

Background: Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the complexity of metabolic networks, both in terms of structure and regulation, it is often difficult to predict the effects of genetic modifications on the resulting phenotype. Recently genome-sca...

Fermentation performance and intracellular metabolite patterns in laboratory an...

Heterologous genes for xylose utilization were introduced into an industrial Saccharomyces cerevisiae, strain A, with the aim of producing fuel ethanol from lignocellulosic feedstocks. Two transformants, A4 and A6, were evaluated by comparing the performance in 4-l anaerobic batch cultivations to both the parent strain and a laboratory xylose-utilizing strain: S. cerevisiae TMB 3001. During growth in a ...