Practical 2 Null space and elementary modes analysis with ScrumPy
ScrumPy is a set of tools for modelling metabolic networks. It has been written as a collection of modules in the programming language Python. Using ScrumPy involves typing commands in the Python interpreter, so you need to learn a little about how Python works. 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 for a brief tutorial on the syntax and data structures in the computer language Python. 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. It can be used to examine the null space of the stoichiometry matrix of a hypothetical metabolic network.
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 its 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.
3 Elementary Modes Analysis
Using the toy model above, determine the elementary modes (see the earlier instructions). What are the reactions involved in each mode ? What are the net stoichiometries of each mode.
Now introduce new reactions into your toy model in order to:
a) Generate new modes with the same net stoichiometries as previously.
b) Generate modes with new net stoichiometries.
Elementary Modes Analysis of a real system
The instructions that you will find here will enable you to replicate some results concerning the Calvin cycle of photosynthesis. In brief, plants have some enzymes that are turned on or off in light or dark conditions. The paper referred to in this exercise examines the significance of this, and the potential impact of deregulating one of the enzymes.