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Martin Ginkel


Posts: 26
Registered:
September 2003
Re: Re: Suggestion for new section in SBML 15 Feb '06 02:10 Go to previous messageGo to previous message

Hi Michael,

Michael Hucka wrote:
> Right, and as you pointed out in your other message, this
> name issue has been a perennial topic and every couple of
> years the same question is asked all over again :-(.

Well yes sorry, *but*: now people start touching extended use of SBML,
where not all model-variables can be put into the semantic boxes
of 'species', 'compartment', 'rate'. And also I present and
discuss model representation in SBML and this
'Why is it called parameter, if you use it as a state?'
appears to be a FAQ.

> The fundamental reason it's called "parameter" in SBML is
> that no one has offered an alternative name "X" that is
> applicable to all of these roles and doesn't conflict with
> someone's preconception of what an "X" is.

What was the conflict of the name 'variable' as suggested by Herbert
(and me)?
I searched the forum and the wiki, but couldn't find anything.
I remember very vaguely that you had some argument, which I can't
remember ...

Simplified Ontology: a Variable, flagged constant=true has the meaning
of parameter.
But parameter constant=false usually doesn't mean a state-variable but
rather an input.

CU
Martin

--
+-[Martin Ginkel]-------------[mailto:mginkel(at)mpi-magdeburg.mpg.de]-+
| MPI Magdeburg, Zi S2.09 Sandtorstr. 1, D-39106 Magdeburg, Germany |
| In the beginning the universe was created. This is considered a bad |
| idea and has made many people unhappy. Douglas A. |
+-[tel/fax: +49 391 6110 482/529]----[http://www.mpi-magdeburg.mpg.de]-+

      

SubjectPosterDate
Read Message   Suggestion for new section in SBML Herbert Sauro09 Feb '06 23:51
Read Message   Re: Suggestion for new section in SBML Rainer Machne10 Feb '06 04:46
Read Message   Re: Suggestion for new section in SBML Martin Ginkel10 Feb '06 04:51
Read Message   RE: Suggestion for new section in SBML rphair10 Feb '06 12:31
Read Message   RE: Suggestion for new section in SBML Nicolas Le Novere11 Feb '06 17:14
Read Message   Re: Suggestion for new section in SBML Jordan Atlas11 Feb '06 11:37
Read Message   Re: Re: Suggestion for new section in SBML Martin Ginkel13 Feb '06 00:39
Read Message   Re: Re: Suggestion for new section in SBML Mike Hucka14 Feb '06 19:31
Read Message   Re: Re: Suggestion for new section in SBML  Martin Ginkel15 Feb '06 02:10
Read Message   Re: Re: Suggestion for new section in SBML Mike Hucka15 Feb '06 10:58
Read Message   Re: [sbml-discuss]Suggestion for new section in SB... Martin Ginkel15 Feb '06 23:51
Read Message   Re: Suggestion for new section in SBML bshapiro11 Feb '06 19:52
Read Message   Re: Suggestion for new section in SBML Mike Hucka14 Feb '06 19:23
Read Message   RE: Suggestion for new section in SBML Andrew Finney17 Feb '06 00:53
Read Message   RE: Suggestion for new section in SBML Nicolas Le Novere19 Feb '06 11:05
Read Message   RE: Suggestion for new section in SBML Andrew Finney19 Feb '06 13:49
Read Message   RE: Suggestion for new section in SBML Nicolas Le Novere19 Feb '06 16:05
Read Message   RE: Suggestion for new section in SBML Herbert Sauro20 Feb '06 12:57
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