 Optimization techniques are used in many facets of computational systems biology such as model building, optimal experimental design, metabolic engineering, and synthetic biology.Linear programming has been applied to calculate the maximal possible yields of fermentation products, and to infer gene regulatory networks from multiple microarray datasets as well as transcriptional regulatory networks from high-throughput data.Nonlinear programming has been used to analyze energy metabolism and has been applied to metabolic engineering and parameter estimation in biochemical pathways.