Practical 2

Part 1 - Exploring Python

Before staring with the modelling exercises, start to familiarise yourself with Python and the Idle environment using this tutorial

Part 2 - Creating Models

Have a look at this tutorial before starting. We will look at the last two subsections, Elementary modes and Enzyme subsets, tomorrow, so don't worry about those yet.

(a) Create and load toy_model.spy as described in the tutorial.

(b) See what happens if you remove the tilde sign (~) from any of the reactions in the model file. Implement the modification either by selecting ScrumPy > Compile in the model file, or do:

   1 >>> m.Reload()

in the ScrumPy window (after saving the modification in the model file).

(c) Modify the reaction stoichiometry in any of the reactions in toy_model.spy so that all reactants are identical, e.g.:

   1 A_tx:
   2     A -> A
   3     ~

Reload or compile the model as above. What happens?

Part 3 - The Stoichiometry Matrix and Null-space

(a) Familiarise yourself with the stoichiometry matrix of the toy model, e.g. repeat the examples in the section of the tutorial relating to the stoichiometry matrix.

(b) Generate a kernel of the stoichiometry matrix (using the .NullSpace() method).

(c) Multiply the stoichiometry matrix by the kernel matrix, using the .Mul() method of the stoichiometry matrix.

(d) Repeat the multiplication above using the external stoichiometry matrix instead.

(e) Create a kernel of the external stoichiometry matrix - what is different?

(f) Multiply the internal and external stoichiometry matrices by your new kernel.

(g) Try adding or removing reactions from the model, and repeat the exercises above, explain the new results.