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> I think the discussions in this list are starting to convince me that anyone
> who wants to be doing any modeling of biochemical systems should first have
> to pass an "Enzyme Kinetics" course. The concept of modifier is not vague
> at all, it is quite well defined. It seems to me that there are a number of
> people out there that want to define this concept according to whatever
> their software thinks a modifier is.
Just in case you don't know, software developers don't define what
a modifier is. The specification does. And this is very important for
interoperativity. If the specification is ambiguous, then there may be
many different ways to interpret it.

> As someone else already stated in this thread, a modifier is not changed by
> the reaction therefore the only number that could be attributed to its
> stoichiometry is zero.
True for ODE, but not true for discrete Monte Carlo method.

>
> Also, reactions do not need any modifier (eg activator) to proceed. If you
> put NADH in contact with oxygen, it is only a matter of time that you end
> up with NADP+ and water - no enzymes required.
This is because of a reaction with basal rate. It has nothing to do with
enzymatic reaction. And it's not convicing.

>
> Anyway, I am one of the defenders that software should be sufficiently
> user-friendly to allow non-speciallists to carry out simulation. But this
> has always meant to me that they do not need to be speciallists in
> mathematics, numerical analysis, or software engineering. They DO need to
> know biochemistry if they want to model biochemical systems - I'm sorry for
> this lengthy rant, but I am strongly opposed that we should bastardize
> terms that are objective and quite specific (and old) just because some
> software happens to use them in some wrong way.
Old and traditional representation can be ill-defined. If you read the
paper from Hiroaki Kitao (graphical notation for biochemical network), you
would know that.

hiro
>