Circuit Analysis with COPASI
In this Chapter you will learn how to carry out, with COPASI, some of the analysis techniques described in Chap. 10. Initially, we will use a new model for the Toggle Switch, which takes into account promoter leakage, to run sensitivity analysis and show that the circuit is not robust against variations in the value of the leakage translation rate constant. We will then use the same model to see how to run a circuit optimization with a stochastic algorithm (Simulated Annealing). This procedure is used to find new values for some selected kinetic parameters such that the circuit performance is improved. As in every optimization problem, you will have to specify a proper objective function. Finally, on a simpler circuit, where a reporter protein is expressed in the presence of an inducer chemical, you will see how to fit a model to two different data sets in order to estimate the Hill constant and coefficient.