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• WorkshopTwo
• Practical_1

1 Simple Kinetic Modelling in ScrumPy

See notes from this pms lecture.

1.0 Preparation

1. Create a directory in your home area called "Practical_1"

   $ mkdir Practical_1

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

   $ cd Practical_1
   $ mkdir Revers Irrev Cycle

1.1 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 - e.g. change some consentrations, calculate values of the external metabolites that will result in no steady-state flux.

1.2 Steady-States with Irreversible Kinetics

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

2. Repeat the investigation in 1.1 on this model.
3. How many results are in the data set ?
4. What are the smilarities and differences in behaviour ?
5. What conclusions can you draw ?

1.3 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 ?