I think what we see here is again the problem that SBML originally was
only developed fro ODE based modelling. We all know that we have moved
far beyond that however one crucial component of SBML has not kept
This component in my opinion is the way we specify the kinetic laws. A
kinetic law for a stochastic model is different from the kinetic law for
an ODE model. This discussion makes that clear again.
I suggest that we start a discussion on how to deal with this issue.
My propose to create a new object "kinetic law". The real contend will
be in subclasses derived from this. Two subclasses come immediately into
my mind these are "ODE kinetic law" and "stochastic kinetic law". The
ODE kinetic law is what we currently understand under kinetic law. The
stochastic kinetic law could have a forward and a backward probability.
Additional subclasses can be envisioned and added.
A reaction may have only one entity of each subclass of the kinetic law.
The reason for this restriction is that each tool now easily can decide
which law to use dependent on the type of simulation/analysis intended.
In addition allowing multiple different subclasses of "kinetic law"
would allow us to store a stochastic and an "equivalent" ODE model in
the same file.
What are your thoughts on this?
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility I
Blacksburg, Va 24061, USA