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| = 2 Some Simple Kinetic Modelling in ScrumPy = Before you start you may wish to revise the [[http://mudshark.brookes.ac.uk/Meetings/Delhi2012/Practicals/Practical_2/PyIntro|introduction to Python]] from last year's workshop. Starting ScrumPy and loading a model are described in last year's [[http://mudshark.brookes.ac.uk/Meetings/Delhi2012/Practicals/Practical_2/ScrumPyIntro|ScrumPy introduction]] from Practical 2. |
= 1 Some Simple Kinetic Modelling in ScrumPy = See notes from this pms lecture. |
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| == 2.0 Preparation == 1. Create a directory in your home area called "Practical_2" |
== 1.0 Preparation == 1. Create a directory in your home area called "Practical_1" |
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| $ mkdir Practical_2 | $ mkdir Practical_1 |
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| $ cd Practical_2 | $ cd Practical_1 |
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| == 2.1 Steady-States with Reversible Kinetics == | == 1.1 Steady-States with Reversible Kinetics == |
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DRAFT VERSION
1 Some Simple Kinetic Modelling in ScrumPy
See notes from this pms lecture.
1.0 Preparation
- Create a directory in your home area called "Practical_1"
$ mkdir Practical_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
Download the TwoReacRever.spy model (right click for saving) 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.
- Repeat with some other parameters that could be tested in the lab.
2.2 Steady-States with Irreversible Kinetics
Download the TwoReacIrrev.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 SimpleCycle.spy model and put it in the "Cycle" directory.
- Proceed as 2.1 (but this time you need to vary the concentration of the external metabolite, x_A).
- 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 ?