Forums

--- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > On Tue, 17 Jan 2006, Stefan Hoops wrote:

> > > Any kind of local parameter is associated with a
> mathematical
> > > expression, be it for 'traditional ODE' modelling,
> stochastic
> > > modelling, or flux balance analysis.
> >
> > I'm not sure for logical modelling or petri net. Also, you
> can
>
> I am not sure either but not being sure is bad reason either
> way :).

Clearly you both need to read my book! ;-)

I'm certainly not aware of any modelling framework where a rate
parameter makes sense completely independently of any rate law.
There are frameworks where rates and rate laws are not used at
all, but then kinetic laws are not required, so we are all
happy. There are also frameworks where there is a
_default_assumption_ about the nature of the rate law (such as
for stochastic petri nets and discrete stochastic modelling more
generally) - namely that unless otherwise stated, irreversible
mass-action stochastic kinetics is assumed. But in this case it
is clear what the rate law is, so there is no problem for tools
to include it when they write the SBML, and there is nothing to
stop tools from ignoring it when they read it. So I must admit
that I am a bit puzzled as to why it is such a big deal to make
the math optional. What is the harm in including it for
completeness?

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/