Analyzing and designing cell factories with OptFlux

Abstract

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.