Optimization in computational systems biology

Abstract

Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on applications of mathematical optimization in computational systems biology. Examples are given where optimization methods are used for topics ranging from model building and optimal experimental design to metabolic engineering and synthetic biology. Finally, several perspectives for future research are outlined.

Figure 1

Simple examples (two decision variables, no constraints) of unimodal (1.a) and multimodal (1.b) surfaces, where the z-coordinate of the surface represents the value of the objective function for each pair of decision variables x and y.