Provides a tutorial on the computational tools that use mathematical optimization concepts and representations for the curation, analysis and redesign of metabolic networks * Organizes, for the first time, the fundamentals of mathematical optimization in the context of metabolic network analysis * Reviews the fundamentals of different classes of optimization problems including LP, MILP, MLP and MINLP * Explains the most efficient ways of formulating a biological problem using mathematical optimization * Reviews a variety of relevant problems in metabolic network curation, analysis and redesign with an emphasis on details of optimization formulations * Provides a detailed treatment of bilevel optimization techniques for computational strain design and other relevant problems