Stochastic Modelling and Simulation of Biological Processes [C]:  2008-2009

Synopsis

This course will address some of the important issues associated with the modelling 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.

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.

All simulations to be done in MATLAB.

Reading list

• 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)

Related research

Taking our courses

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Other matriculated University of Oxford students who are interested in taking this, or other, courses in the Department of Computer Science, must complete this online form by 17.00 on Friday of 0th week of term in which the course is taught. Late requests, and requests sent by email, will not be considered. All requests must be approved by the relevant Computer Science departmental committee and can only be submitted using this form.