[sbml-discuss] Multiple kineticLaw Sections Per Reaction

Stefan Hoops shoops at vbi.vt.edu
Fri Mar 10 18:04:35 PST 2006


Hello Darren,

On Fri, 10 Mar 2006 21:51:42 +0000 (GMT)
Darren Wilkinson <darrenjwilkinson at btinternet.com> wrote:

> --- Herbert Sauro <Herbert_Sauro at 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.


Thanks,
Stefan



-- 
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
Email: shoops at vbi.vt.edu


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