MATLAB Code
This code runs only in MATLAB version 6.5 (R13) and later
Download all five code files as a zip file here MATLABCode_v1.zip
You need the
following file in your path to run the m-files below:
dde15.m was written by Dr. Lawrence F. Shampine (Southern Methodist University, Dallas, TX) specifically for our project, to take care of the “stiffness” of the delay differential equations. Stiffness refers to rapid changes in certain variables that cause solvers to converge very slowly.
To run the m-files please type their name on the MATLAB command window as usual (after changing to the directory where you saved these files). dde15s.m needs to be in the MATLAB path or in the same directory as the files you choose to run. To download the files you will need to Right-Click on the links below and choose “Save Target As” in Microsoft Internet Explorer or “Save Link As” or “Download Link As” in Netscape/Mozilla/Safari/Opera.
Dynamics
(This code takes about 10-20
seconds to run. It takes 10 seconds on an Intel Pentium 1.8 GHz, 512 MB Windows
XP Personal Computer)
avrB_v1.m System dynamics of wild type and mutant plants responding to bacteria carrying avrB.
avrRpt2_v1.m System dynamics of wild type and mutant plants responding to bacteria carrying avrB.
Parameter Sensitivity
(The effect of varying individual parameters ten-fold up and down on the system
dynamics)
(This code takes about 90-150
minutes to complete running depending on your computer. It will generate MATLAB
.fig files, corresponding .tif image files (at 150 dpi) and the data files as
.txt files in case you want to plot the data in your favorite software )
avrB_parameters_v1.m Wild type plants responding to bacteria carrying avrB.
You may download all the pre-generated figures as follows:
avrRpt2_parameters_v1.m Wild type plants responding to bacteria carrying avrRpt2.
You may download all the pre-generated figures as follows: