Stochastic Modelling for Systems Biology, Third Edition, 3rd Edition

CHAPTER 2

Representation of biochemical networks

2.1 Coupled chemical reactions

As was illustrated in the first chapter, a powerful and flexible way to specify a model is to simply write down a list of reactions corresponding to the system of interest. Note, however, that the reactions themselves specify only the qualitative structure of a model and must be augmented with additional information before they can be used to carry out a dynamic simulation on a computer. The model is completed by specifying the rate of every reaction, together with initial amounts of each reacting species.

Reconsider the auto-regulation example from Section 1.5.7:

$\begin{array}{ll}\hfill g+P_2& \rightleftharpoons g\cdot P_2\hfill \\ \hfill g& \to g+r\hfill \\ \hfill r& \to r+P\hfill \\ \hfill 2P& \rightleftharpoons P_2\hfill \\ \hfill r\to \cancel{0},& P\to \cancel{0}.\hfill \end{array}$

Although only six reactions are listed, there are actually eight, ...