Modeling at Computer: Getting Started
The dynamics of a synthetic gene circuit is obtained by solving a system of ordinary differential equations. However, even simple ODE systems can be too difficult to be tackled analytically. Hence, you shall recur to numerical methods. In this Chapter we will show how to use the software COPASI to write a model for a biological system and compute the dynamics of it. In particular, we will consider some of the models we derived in Chap. 2. You will learn how to build and simulate a model based on mass action kinetics and Hill functions. Moreover, useful features provided by COPASI – such as the definition of a report and the “parameter scan” function – are here described. We have chosen COPASI because it is open-source and easy to use thanks to an intuitive graphical user interface.