Forums

--- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> However, we have still a problem here. The way a kinetic law
> is meant to
> be interpreted is stated as:
> Rate expressions in SBML are expressed in terms of
> substance/time,
>
> Here we have two problems at once :(
>
> 1) "Rate expression" vs. "reaction propensities"
> 2) "substance per time" vs. "events per time"

In both cases these are entirely comparable. What you call
"events per time" is essentially "molecules per time", and that
_is_ "substance per time". Similarly, reaction propensities
_are_ rate expressions, measured in directly comparable units.
Of course, the precise units are usually different, but SBML has
a (too?!) sophisticated system for dealing with units. I
maintain that a continuous deterministic simulator with a good
understanding of SBML (including SBML units) could take any SBML
model intended for discrete stochastic simulation and simulate
directly from the continuous deterministic approximation
correctly without any external "help" at all. Moving in the
other direction (continuous to discrete) is more problematic
however...

> I know that it is often possible to convert between them.
> Especially,
> for mass action kinetics we probably can agree on the rules
> guiding the
> conversion. But in general these are fundamental different
> things and as
> long as we try to put them into the same object, we will run
> into
> difficulties.

I disagree. They are not fundamentally different things. They
are exactly the same thing, measured in directly comparable
units. Treating them as different things when they are
essentially the same will lead to a needless divergence. One of
the strengths of SBML is that is captures the essentials of the
dynamics of a biochemical network without being explicitly
linked to a particular chemical kinetic theory. Let's not invent
a split where none exists.

Cheers,


--
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/