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Jordan Atlas wrote:
>> It is obviously not a parameter and as some have noted, it is also
>> not a species, so where should it go?
>
> Herbert,
>
> Can you explain in more detail why it is not a parameter (where a
> parameter is a quantity with a symbolic name)?

The usual semantics AFAIK from Systems Theory, that a
parameter is a quantity (somehow external), which is not part of
the mathematical models state.
Sometimes time-dependent external variables are called inputs,
distinguished from time-independent (constant) parameters.
If you just perform time-course simulation, a parameter
remains constant.

I know, that it's stated differently in the SBML spec. And I also know,
that SBML has the constant-flag to mark species, compartments as well as
'other variables' called parameters to be 'time-constant symbolic
quantities'.

But it is still difficult to explain newbies to SBML, that parameters
can be used to describe anything that does not fit into the semantics
of 'species', 'rate' and 'compartment'.

CU
Martin
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