1 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.
- ```
   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 - e.g. change some consentrations, calculate values of the external metabolites that will cuse no flux to flow.

1.2 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 ?

1.3 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 ?

None: Accliphot/WorkshopTwo/Practical_1 (last edited 2014-09-09 06:19:55 by mark)

-  ⇤ ← Revision 1 as of 2014-08-27 12:31:57 → 
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+   ← Revision 9 as of 2014-08-29 10:54:00 → ⇥
  Size: 2318
  Editor: mark
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-Deletions are marked like this.
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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 Simple Kinetic Modelling in ScrumPy =
[[AccliPhot/WorkshopTwo/Tue_3|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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-Line 14:
+Line 15:
-$ cd Practical_2
+$ cd Practical_1
-Line 19:
+Line 20:
-== 2.1 Steady-States with Reversible Kinetics ==
+== 1.1 Steady-States with Reversible Kinetics ==
-Line 21:
+Line 22:
- Download the [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Models/TwoReacRever.spy|TwoReacRever.spy]] model (right click for saving) and put it in the "Revers" directory.
+ 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.
-Line 25:
+Line 27:
-Line 30:
+Line 33:
-        [[http://mudshark.brookes.ac.uk/Meetings/Delhi2013/Practicals/Practical_2#|Toggle line numbers]]
        {{{
+  {{{#!python
>>> results = m.AddStatMonitor()
>>> for n in range(20):
        m["Vmax1"] += 1
        m.FindSS()

>>> results.SetPlotX("Vmax1")
>>> results.AddToPlot("R1")
-Line 36:
+Line 45:
+. 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 cuse no flux to flow.
-Line 37:
+Line 47:
-. Repeat with some other parameters that could be tested in the lab.
+== 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.
-Line 39:
+Line 51:
-== 2.2 Steady-States with Irreversible Kinetics ==
 1.
 Download the [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Models/TwoReacIrrev.spy|TwoReacIrrev.spy]] model and put it in the "Irrevs" directory.
-Line 47:
+Line 56:
-== 2.3 Steady-States of a Moiety Conserved Cycle ==
+== 1.3 Steady-States of a Moiety Conserved Cycle ==
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+Line 58:
- Download the [[http://mudsharkstatic.brookes.ac.uk/Delhi2013/Models/SimpleCycle.spy|SimpleCycle.spy]] model and put it in the "Cycle" directory.
+ Download the [[http://mudsharkstatic.brookes.ac.uk/AccliPhot/Workshop2/Models/SimpleCycle.spy|SimpleCycle.spy]] model and put it in the "Cycle" directory.