To reproduce the figures from the paper:

Copy all the files to a directory on your computer
Add the directory to your path in matlab. 
At the matlab prompt, type: M = PhosphoPaper_050412('filename'); where 'filename' is 
the name of file you want to save the results in.


This will return a 'Model' object called 'M'. 

To list the species and their initial conditions, type: M.Species
To list the parameters and their values, type: M.Parameter
To list the compartments and their sizes, type: M.Compartment
To list the reactions, type: M.Reaction

New simulations can be run with various parameter values and initial conditions by 
following the format within 'PhosphoPaper_050412.m'. Additional help is available
with each function by typing 'help [function name]'.
