2 Some Simple Kinetic Modelling in ScrumPy

Before you start you may wish to revise the introduction to Python from last year's workshop. Starting ScrumPy and loading a model are described in last year's ScrumPy introduction from Practical 2.

2.0 Preparation

1. Create a directory in your home area called "Practical_2"

   $ mkdir Practical_2

2. cd into this and create 3 more directories: "Revers", "Irrev", and "Cycle"

   $ cd Practical_2
   $ mkdir Revers Irrev Cycle

2.1 Steady-States with Reversible Kinetics

1. Download the TwoReacRever.spy model (right click for saving) and put it in the "Revers" directory.

2. cd into the Revers directory, launch ScrumPy and load the model.

3. Identify the kinetics, Parameter and initial value assignments.
4. On the basis of the network structure, what predictions can you make about relationships of steady-state fluxes ?
5. Investigate the effect of varying the Vmax value of the first reaction, e.g.

   •    1 >>> results = m.AddStatMonitor()
        2 >>> for n in range(20):
        3         m["Vmax1"] += 1
        4         m.FindSS()
        5 
        6 >>> results.SetPlotX("Vmax1")
        7 >>> results.AddToPlot("R1")
     

6. Repeat with some other parameters that could be tested in the lab.

2.2 Steady-States with Irreversible Kinetics

1. Download the TwoReacIrrev.spy model and put it in the "Irrevs" directory.

2. Repeat the investigation in 2.1 on this model.
3. What are the smilarities and differences in behaviour ?
4. What conclusions can you draw ?

2.3 Steady-States of a Moiety Conserved Cycle

1. Download the SimpleCycle.spy model and put it in the "Cycle" directory.

2. Proceed as 2.1 (but this time you need to vary the concentration of the external metabolite, x_A).
3. Now investigate the effect of varying the conserved total (hint: use the parameter 'CSUM_NADH').
4. Now break the conservation relationship and repeat the first part of 2.3
5. What conclusions can you draw ?