Re: Suggestion for new section in SBML
10 Feb '06 04:51
Herbert Sauro wrote:
> This model has a rateRule for a quantity called p3. However the rateRule
> is function of one of the species, it is therefore strictly a state
> variable just like a floating species. The trouble is, there is nowhere
> sensible to declare such a variable. It is obviously not a parameter and
> as some have noted, it is also not a species, so where should it go?
> Given that it is a state variable, and a rateRule at that, it should
> have an initial condition, so where does this go, into the list of
> global parameters? In fact, in the SBML p3 is initialized in the list of
> parameters even though it is not a parameter. Now I understand the
> confusion because where ever one puts it there would be disagreement.
Do you remember, that we discussed this before?
Yes, the so-called 'parameters' can be intermediately assigned variables
(assignmentrule), dynamic state (rate rule) or algebraic state
(determined by algebraic rule) in SBML.
And I completely aggree: It would be better to call them differently and
define 'parameter' to be something, that is not changed by the model
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