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| Familiarise yourself with the following paper [[attachment:Pool_03.pdf]]. | Download and familiarise yourself with the following [[http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2003.03390.x/abstract;jsessionid=10BEC22414D996E91E588BFA238F268F.d01t03 | paper]] |
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| 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? | 4. Identify the ''sedoheptulose-1,7-bisphosphatase'' reaction 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? |
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.
Download and familiarise yourself with the following paper
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-bisphosphatase reaction 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?