Kinetic Modelling
The general form of the description of a kinetic model has been covered in the pages on the ScrumPy Model Description Language. Consider the following two enzyme system as an example:
# Two reactions with reversible Michaelis-Menten kinetics R1: x_A <> B Vmax1/K1A * (x_A - B/Keq1)/ ( 1 + x_A/K1A + B/K1B ) R2: B <> x_C Vmax2/K2B * (B - x_C/Keq2)/ ( 1 + B/K2B + x_C/K2C ) x_A = 1 x_C = 1 Vmax1 = 10 K1A = 1 K1B = 1 Keq1 = 2 Vmax2 = 10 K2B = 1 K2C = 1 Keq2 = 2 B=0.4
Note that this file contains two reaction definitions with their kinetic equations, followed by initial assignments of the parameters and the variable (B).
If this model had already been saved as a spy file, then it can be loaded into ScrumPy as follows: