Imperial College/Courses/2009/Synthetic Biology/Computer Modelling Practicals/Practical 1

   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.



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 A-B-C 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)

