Practical 2 Null space and elementary modes analysis with ScrumPy
Follow the links below to reach the relevant documentation and instructions. Go through the Python related material before the starting with ScrumPy documentation and exercises.
1 Using Python
Follow this link to for a brief reminder of the work covered in yesterdays lecture. Try to replicate the examples shown there, and ask the demonstrators if something appears not to work as expected. Also expect the demonstrators to ask you to explain the results you see on the screen.
2 Exploring the Null Space
This page has instructions for loading a simple model (is it the same as the one described in yesterdays lecture ?) .
Again, replicate the examples shown then attempt the following exercises. You should be able to describe what you expect the result to be before you attempt to do it on the computer. If the result is not as expected you must be able to explain the difference:
a) Generate a kernel of the stoichiometry matrix.
b) Use the matrix ".Mul()" (multiply) to multiply the stoichiometry matrix by it's null space.
c) Multiply the kernel by the external stoichiometry matrix.
d) Create a kernel of the external stoichiometry matrix - what is different ?
d) Multiply the internal and external stoichiomtry matrices by your new kernel.
e) Try adding or removing reactions from the model, and repeat the exercises above, explain the new results.
Further Exercises
We will continue tomorrow, but if you have time today, follow the instructions on the two links below.