Forums

--- 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. There was with Level 1, but most of us have moved
on from that now. The problem is in flipping between an SBML
model designed with continuous deterministic simulation in mind
and one designed with discrete stochastic simulation in mind.
However, even this is not hopeless. So, for examples of SBML
models correctly encoded for discrete stochastic simulation,
please take a look at the "discrete stochastic models test
suite":

http://www.calibayes.ncl.ac.uk/Resources/dsmts/

I gave a talk about it at the SBML Forum in Boston, and you can
get the slides from:

http://sbml.org/workshops/tenth/presentations/wilkinson-dsmts.pdf

And at the risk of spamming the list with a self-promoting book
advert, my forthcoming book "Stochastic modelling for systems
biology", has an extensive discussion of the issues involved in
using SBML for encoding discrete stochastic models. The web site
is at:

http://www.staff.ncl.ac.uk/d.j.wilkinson/smfsb/

Note that there are several SBML models on this web site
encoding discrete stochastic models.

Yours,


--
Darren Wilkinson
email: darrenjwilkinson@btinternet.com
home www: http://www.darrenjwilkinson.btinternet.co.uk/
work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/