Exercises - ScrumPy and Elementary Modes analysis

Basic ScrumPy

Copy and load the toy model described previously.

1. Using built-in Python methods find out the number of reactions and metabolites in the network.

2. Write a function that given a model, returns a list of reactions that are in singleton subsets.

Hint: What is special about the names of subsets of size > 1.

Elementary Modes analysis

Copy and load the Calvin model.

Familiarise yourself with the following paper Pool_03.pdf.

1. Identify the light only and dark only reactions in Table 1 in your model. You can add comments to your model like this:

   1 #this is a comment

2. Make two new models - one for light conditions (i.e. comment out dark only reactions) and one for dark conditions.

3. Load the new models and analyse the elementary modes. How many modes do they each have? What is their overall stoichiometries?

4. Identify the sedoheptulose-1,7-bisphisphatase and include it in the dark model. What is the impact of this change in network topology on the elementary modes of the model? What is the biological significance?