Modelling and analysing MAPK signalling pathways -- Lab

Aim

Exercises

1. Ensure that Snoopy has been installed on your computer.
   If it has not been installed, then you can get it from
   \\uxisapp1\apps\Snoopy\snoopy.exe
   • If you can't install Snoopy, you can try to use the web animation, although this gives very limited functionality.

2. You can get all the models from:
   • \\uxisapp1\apps\Snoopy\Examples
     or from here:-
   • zip file of snoopy models
   • Note that in the following, when downloading a Snoopy model, right-click and use the option 'Download Linked File As...' in order to preserve its name. Otherwise you will get an extra '.xml' extension, which you will have to remove!

3. Play with some simple reactions:
   • Simple a->b, you can try:
     
     qualitative
     continuous
     stochastic
     
   • Simple H2O

4. Using the qualitative Petri net model for an enzymatic reaction, of type MA1 (simple mass action), explore the behaviour of this model using token game. Play with the relationship between the number of tokens for the substrate and for the enzyme.
   The model can be obtained by the following link ma1.pn.

5. Explore the behaviour of the MA1 continuous quantitative model. You can also try to modify the MA1 model: the rates can be changed by selecting a reaction (square - transition), opening it and changing the rate. Play with the relationship between the concentrations for the substrate and for the enzyme.
   Note: Follow the link to download the continuous quantitative model ma1.spcontped.

6. Download the stochastic version of the MA1 enzymatic model from here. Explore the behaviour of this model on Snoopy.
   
   • Play with the relationship between the concentrations for the substrate and for the enzyme.
   • Try increasing the number of runs.
   • Try increasing the levels of the substrate and enzyme.
   • Explore the relationship between the number of runs and the number of levels.

7. Have a look at the behaviour of the Kholodenko model of the MAPK pathway - it is a 3 stage model, and is supposed to produce oscillating behaviour. Can you make it do this?:-
   Qualitative model (would you ever detect oscillations?)
   Continuous model
   Stochastic model

8. Go to the biomodels.org website, which is hosted by the European Bioinformatics Institute.
   • Search for Schoeberl, who has made models of the EGF MAPK cascade.
   • Select the first curated model, Schoeberl2002.
   • Download the model, as SBML L2 V1 [level2 version 1]. You can also try the curated version L2 V4.
   • Use the file->import function of Snoopy to read the file in as a Continuous Petri net, using the default layout option (it is a large model).
     Click all 3 boxes in the dialogue: Highlight reversible reactions; Create reverse reactions; Create boundary conditions.
     Note: this automatic layout is unlikely to result in a recognisable 'standard' diagram of the MAPK pathway.
   • Explore the model by simulating it - start off with 100 time steps -- but you may need to extend the time longer.
   • Try to just display ERK-PP (doubly phosphorylated ERK) - you will need to deselect all the species, then select the one(s) that you want.
   • How does ERK-PP behave? Is this what you would expect?

9. Some SBML models for the MAPK cascade that you may wish to explore are in MAPK_SBMLmodels:
   • MAPK_SBMLmodels/Kholodenko1999.xml>Kholodenko1999
   • MAPK_SBMLmodels/Levchenko2000.xml>Levchenko2000
   • MAPK_SBMLmodels/Schoeberl2002.xml>Schoeberl2002
   • MAPK_SBMLmodels/Brown2004.xml>Brown2004

10. Further work: modifying models Modify the enzymatic reaction model MA1 to
    • include an additional substrate C, so that the reaction now takes A and C as substrates to make B as the product (which will be some kind of complex between A and C), as the final product, catalysed by the enzyme E.
      A + C + E --> A|C|E --> B + E
      You can do this for the qualitative model, or continuous model, or both.
    • include an additional product D, so that the reaction now takes A as the substrate to make B and D as the two final products, catalysed by the enzyme E.
      A + E --> A|E --> B + D + E
      You can do this for the qualitative model, or continuous model, or both.
    • include both an additional substrate C and also an additional product D, so that the reaction now takes A and C as the substrates to make B and D as the two final products, catalysed by the enzyme E.
      A + C + E --> A|C|E --> B + D + E
      You can do this for the qualitative model, or continuous model, or both.