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Synthetic biology is an engineering approach that designs biological systems to have new functions for useful purposes. Rational cell design is crucial for synthetic biology and can be considered a strategy that includes increasing the production efficiency of a cell or developing a new product by changing or adding specific biochemical reactions and regulations using modern metabolic engineering techniques. Metabolic flux and control analyses with models created in silico following cellular genome mapping have also contributed significantly to rational cell design. Models make the prediction of behaviors possible without performing a vast number of experiments when biological systems are modified. The modeling of microbial cells for the biosynthesis of high-value products is gaining increasing attention in biotechnology. In this chapter, the main focus will be on the concept of the genome scale metabolic …