2 Some Simple Kinetic Modelling in ScrumPy

2.0 Preparation

Create a directory in your home area called "Practical_2"
```
$ mkdir Practical_2
```
cd into this and create 3 more directories: "Revers", "Irrev", and "Cycle"
```
$ cd Practical2
$ mkdir Revers Irrev Cycle
```

2.1 Steady-States with Reversible Kinetics

Download the TwoReacRever.spy model and put it in the "Revers" directory.
cd into the Revers directory, launch ScrumPy and load the model.
Identify the kinetics, Parameter and initial value assignments.
On the basis of the network structure, what predictions can you make about relationships of steady-state fluxes ?
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")

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

2.2 Steady-States with Irreversible Kinetics

Download the TwoReacRever.spy model and put it in the "Irrevs" directory.
Repeat the investigation in 2.1 on this model.
What are the smilarities and differences in behaviour ?
What conclusions can you draw ?

2.3 Steady-States of a Moiety Conserved Cycle

Download the TwoReacRever.spy model and put it in the "Cycle" directory.
Proceed as 2.1
Now investigate the effect of varying the conserved total (hint: use the parameter 'CSUM_NADH').
Now break the conservation relationship and repeat the first part of 2.3
What conclusions can you draw ?