How to do a simple simulation using Tellurium

November 1, 2016 1:10 pm

The most common requirement is the ability to carry out a simple time course simulation of a model. Consider the model:

$$ S_1 \rightarrow S_2 \rightarrow S_2 $$

Two reactions and three metabolites, S1, S2 and S3. We can describe this system using an Antimony string:

import tellurium as te
import roadrunner

r = te.loada ('''
   S1 -> S2; k1*S1;
   S2 -> S3; k2*S2;

   k1= 0.4; k2 = 0.45
   S1 = 5; S2 = 0; S3 = 0 
''')

m = r.simulate (0, 20, 100)
r.plot()

Run the script by clicking on the green arrow in the tool bar to yield: