How to simulate biological pathways? I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using differential equations or any other formalism. 

For example I would like to try to simulate this KEGG pathway map. Is there something more recent than this work from 2005?

For example to simulate Petri networks?
In matlab this can be done using the SimBiology toolbox.
In mathematica this can be done using the SystemModeler.
In python there are multiple packages, e.g. (in no particular order) PySB, Tellurium, PySD