Re: Re: Suggestion for new section in SBML
15 Feb '06 10:58
ginkel> Well yes sorry, *but*: now people start touching
ginkel> extended use of SBML, where not all
ginkel> model-variables can be put into the semantic boxes
ginkel> of 'species', 'compartment', 'rate'. And also I
ginkel> present and discuss model representation in SBML
ginkel> and this 'Why is it called parameter, if you use
ginkel> it as a state?' appears to be a FAQ.
Yes, too true.
ginkel> What was the conflict of the name 'variable' as
ginkel> suggested by Herbert (and me)? I searched the
ginkel> forum and the wiki, but couldn't find anything. I
ginkel> remember very vaguely that you had some argument,
ginkel> which I can't remember ...
I'm not sure I was the one with the argument (maybe I was --
just can't remember it), but one point that comes to mind now
is that other things in SBML are variables, like species
concentrations. So if you have a separate "variables"
section, won't that be confusing too? And I don't think
you'd want to call it ListOfOtherVariables...
ginkel> Simplified Ontology: a Variable, flagged
ginkel> constant=true has the meaning of parameter. But
ginkel> parameter constant=false usually doesn't mean a
ginkel> state-variable but rather an input.
Hmm. I do see your point.