1. A method for determining a reduced genome, comprising: providing a set of metabolic reactions; forming an optimization problem in a suitably programmed computer having a stoichiometric model of metabolism; applying binary logic variables to associate gene activations and gene inactivations with the metabolic reactions and simultaneously solving the optimization problem to determine the effect of the set of metabolic reactions on a growth rate target; selecting a minimal set of reactions from the set of metabolic reactions that meets the growth rate target; and mapping enzymes catalyzing the minimal set of reactions to a corresponding set of coding genes to determine a reduced genome, and providing an output to a user of said reduced genome.