Re: How to " OutputSBML" Matlab ODE model encoded in .m file
03 May '12 01:02
So a matlab ode file will have the following function definition
function xdot = some_func(time, x_values)
where xdot and x_values are arrays
followed by code that tells you what the values of xdot are when the
function is called with no arguments and when it is called with arguments.
Yes it is possible to determine how many variables you have and what the
rate of change of each of those variables is. Although given this is a
text file and can have other things in as well (such as other function
definitions used in this file) it is not completely guaranteed. There is
no definitive structure to the m file and since you would be parsing
text it would be error prone.
You *could* turn that into an SBML file that involved parameters and
rateRules; but there would be no biological association at all.
A user could interact with the process and say which variables were
species and it would then be possible (maybe) to determine reactions and
corresponding kineticLaws; but that is getting more tricky.