= 1 Simple Kinetic Modelling in ScrumPy =
[[AccliPhot/WorkshopTwo/Tue_3|See notes from this pms lecture.]]

== 1.0 Preparation ==
 1. Create a directory in your home area called "Practical_1"
 {{{
$ mkdir Practical_1
}}}


 1. 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 [[http://mudsharkstatic.brookes.ac.uk/AccliPhot/Workshop2/Models/TwoReacRever.spy|TwoReacRever.spy]] model (right click for saving) and put it in the "Revers" directory.


 1.
 cd into the Revers directory, launch [[http://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] and load the model.


 1. Identify the kinetics, Parameter and initial value assignments.
 1. On the basis of the network structure, what predictions can you make about relationships of steady-state fluxes ?
 1. Investigate the effect of varying the Vmax value of the first reaction, e.g.
  .
  {{{#!python
>>> results = m.AddStatMonitor()
>>> for n in range(20):
        m["Vmax1"] += 1
        m.FindSS()

>>> results.SetPlotX("Vmax1")
>>> results.AddToPlot("R1")
}}}



 1. 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 [[http://mudsharkstatic.brookes.ac.uk/AccliPhot/Workshop2/Models/TwoReacIrrev.spy|TwoReacIrrev.spy]] model and put it in the "Irrevs" directory.


 1. Repeat the investigation in 1.1 on this model.

 1. How many results are in the data set ?
 1. What are the smilarities and differences in behaviour ?
 1. What conclusions can you draw ?

== 1.3 Steady-States of a Moiety Conserved Cycle ==
 1.
 Download the [[http://mudsharkstatic.brookes.ac.uk/AccliPhot/Workshop2/Models/SimpleCycle.spy|SimpleCycle.spy]] model and put it in the "Cycle" directory.


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