PIMS IGTC - Mathematical Cell Biology Summer Course UBC 2012
-Local Perturbation Analysis - Bifurcation analysis of Reaction Diffusion Equations
-Bifurcation analysis using Matcont
-Wave pinning and Actin Waves - Models and analysis.
Lecture 1: LPA - Theory and Context
Matlab Codes / Matcont Materials
The following are codes associated with the examples discussed in these notes and videos. In each case, two matlab files are provided. One includes the matlab function file used to encode information about the system in 'Matcont' format. These are compiled by matcton from the information typed in the GUI. A command line driver is also included. All examples performed using the GUI can also be performed from the command line (eg. integration, equilibrium continuation). The driver files show examples of how to do this. The benefit of this approach is it is higher throughput and makes passing data to plotting scrips simpler.
One note about using this software package. It can be a bit tricky for Mac OSX - Lion users. Matcont (and many other matlab packages) need access to a C-compiler to some background files. OSX - Lion no longer comes with built in compilers. So you will need to add them before you can use this program. This is relatively easy and does not require much tech savy. Here are some instructions for how to install a C-compiler and link it to matlab.
LPA and Wave Pinning Assignment