Imperial College/Courses/2009/Synthetic Biology/Computer Modelling Practicals/Practical 1
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Practical 1
Objectives:
 To learn how to use a computational modelling tool for biochemical reaction simulations.
 To build biochemical networks
 To simulate the time evolution of the reactions
 To explore the properties of simple biochemical reactions.
 Examplar: A > B > C model
Part I: Introduction to Computer Modelling
 "All models are wrong, but some of them are useful", George Box.
 Possible Explanation: Modelling = Catching the Trend and Explaining it
 Analysis of a problem identifies the most important process shaping the problem
 The effect of each process is described with some equations (or any tools borrowed from mathematics)
 The combination of all the process is simulated.
 Successful modelling = the outcome to simulation is very close to the outcome in real life
 Modelling is therefore wrong (it is an approximation) but useful!
Part II: Getting to know CellDesigner
 Thanks to Dr V rouilly for the Cell Designer Tutorial!!!
 Read through the tutorial example, and get familiar with CellDesigner features. Official CellDesigner Tutorial
 Please Note: the link redirects you to the 2008 tutorials. Make sure that when you are done you come back to this page!!!
 Open a sample file: File > Open > Samples/...
 Select items, move them around, delete, undo...
Part III: Building Your First Model: A > B > C
 Now is the time to build your first model from scratch with CellDesigner, and to run a simulation.
 The model explored describe a system where a compound 'A' is transformed into a compound 'B', which is consequently transformed into a compound 'C'.
 To start, launch the CellDesigner Application: Double Click on the Icon found on your Desktop.
 Then follow the instructions below to build the model.
Model  CellDesigner Instructions 

Following the Law of Mass action, the dynamic of the system is described as: 

Simulate the dynamical behaviour 

Part IV: Analysis of A > B > C
You are now ready to analyse the behaviour of the biochemical network A > B > C.
The following qustions are to be addressed in Section A of your coursework.
First, let us learn a little bit from the simulations:
 Plot and Describe the evolution with time of the concentrations of A, B and C, using these default parameters?
 Now swap the values of k1 and k2 (k1=10 and k2=1)under the parameters tab
 How does this alter the formation of C?
 How does B change?
 Explain these results
Now, let us place ourselves in the position of an experimentalist.
 If you had real life data showing the accumulation of C for an ABC reaction you could fit the data using this model and two rate constants would be returned. Could you assign these rate constants to k1 or k2 (yes or no)?
 What additional data would you need to assign k1 and k2? (Explain how you would extract k1 and k2)
Part V: Additional Resources
 Law of Mass Action (Wolfram's site)
 Law of Mass Action in Chemistry (Wikipedia site)
 Rate Law (from Wikipedia)