= Exercises - ScrumPy and Elementary Modes analysis =


Create a new, blank ScrumPy model window and copy (with line numbering switched off) the [[ Meetings/Riga2013/Practicals/Practical_2/Calvin | Calvin model ]] into it.

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]]

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

{{{#!python
#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?