S-->X2-->X3-->P

begin name
linear3
end name

begin reactions
v[1] {1}$s = {1}x2
v[2] {1}x2 = {1}x3
v[3] {1}x3 = {1}$p
end reactions

Note that the reactions have a label, e.g. v[1], which is also used to indicate which rate equation is associated with this reaction. Within curly brackets the stoichiometry of the reaction is given. This number is not necessarily an integer but can also be a rational. The dollar sign before s and p, e.g. $s indicates that these metabolites are clamped at their initial values. Thus these metabolites are parameters of the system, their values do not change during the simulation.

begin rate equations
v[1] = Vm1/K1s (s - x2[t]/Keq1) / (1 + s/K1s + x2[t]/K1x2)
v[2] = Vm2/K2x2 (x2[t] - x3[t]/Keq2) / (1 + x2[t]/K2x2 + x3[t]/K2x3)
v[3] = Vm3/K3x3 (x3[t] - p/Keq3) / (1 + x3[t]/K3x3 + p/K3p)
end rate equations

The description of the rate equation, this equation can have any form, it should have a label and make a clear distinction between parameters and variables. All variables are indicated to be functions of the independent variable time by the [t] addition, e.g. x2[t]. Note that s and p are parameters.

begin parameters
Vm1 = 1 (mM/s)
K1s = 1 (mM)
K1x2 = 1 (mM)
Keq1 = 1
Vm2 = 1 (mM/s)
K2x2 = 1 (mM)
K2x3 = 1 (mM)
Keq2 = 1
Vm3 = 1 (mM/s)
K3x3 = 1 (mM)
K3p = 1 (mM)
Keq3 = 1
s = 1 (mM)
p = 0 (mM)
end parameters

begin initial conditions
x2[0] = 0 (mM)
x3[0] = 0 (mM)
end initial conditions