RE: Multiple kineticLaw Sections Per Reaction
10 Mar '06 18:01
I also think there is a real problem, how would one know that a given
rate law in an SBML model is valid for a stochastic model? As far as I
know, and I please correct me if I am wrong, there are only a very small
number of rate laws that have been shown to be usable for stochastic
simulations. I can't blindly read a SBML file, Level 1 or 2 (and we use
level 2), and just plug all the equations into a, say, Gillespie
simulator. I think this is what the SBO idea will solve?
From: Stefan Hoops [mailto:firstname.lastname@example.org]
Sent: Friday, March 10, 2006 3:05 PM
Subject: Re: [sbml-discuss] Multiple kineticLaw Sections Per Reaction
On Fri, 10 Mar 2006 21:51:42 +0000 (GMT) Darren Wilkinson
> --- Herbert Sauro <Herbert_Sauro@kgi.edu> wrote:
> > Seems to make sense to me. I would agree that there is a real
> > problem with representing stoachstic models in the current SBML, we
> > are confronted with this problem almost every week.
> Actually, there is no problem representing stochastic models in SBML
> Level 2.
I am not sure about that. Actually I think it is impossible if we
interpret what is said in the kinetic law section strictly :( The
kinetic law section states in paragraph 3:
The expression in math may refer to species identifiers; in that case,
as discussed in Section 3.6.3, the units of each species reference are
those of concentration.
However section 3.6.3 somewhat contradicts that and says that it may
also be substance units depending on the species definition.
The minimum we need to do is to correct the paragraph 3 in 4.9.7 and add
this to the errata.
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics
Facility I Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606