1. This course will address some of the important issues associated with the mod elling and simulation of processes taking place on or inside a biological cell. The following topics will be covered:
   • A brief introduction to important aspects of Molecular Cellular Biology.
   • How noise arises in cellular processes.
   • Intrinsic and Extrinsic noise.
   • Discrete stochastic modelling and simulation through Markov processes.
   • Continuous stochastic modelling and simulation through stochastic differential equations.
   • Trajectorial simulations versus probability density calculations.
   • The role of delays in genetic regulation.
   • Spatial modelling: granular transport versus reaction diffusion equations.
   • Towards multiscale simulation.
2. Many of these issues will be discussed in the light of a number of case studies.
   • The Hes1 gene as a molecular clock.
   • Cascading reactions: Michaelis-Menten and MAPK.
   • Stochastic switches.
   • Insulin/glucose dynamics.
3. All simulations to be done in MATLAB.
4. Additional reading:
   • Computational Cell Biology (Eds. Fall et al.)
   • An introduction to Stochastic Processes with applications to Biology (Linda J.S. Allen)
   • Stochastic Modelling for Systems Biology (D.J. Wilkinson)
5. Final report to be handed in by Tuesday 13 June 2008.