RE: Global vs. local parameters (was: Proposal: simple mechanism forreferencing ratelaws)
22 Jul '05 16:59
Sure, I appreciate the problem you have encountered with dual parameter spaces. Not sure what to do about it, at our end we will move to global parameters.
From: Nicolas Le Novère [mailto:email@example.com]
Sent: Friday, July 22, 2005 2:28 PM
To: SBML Discussion List
Subject: RE: [sbml-discuss] Global vs. local parameters (was: Proposal: simple mechanism forreferencing ratelaws)
> There is a very close
> (unfortunately) relationship between the internals of the simulator
> and SBML. Sure one can have layers of interface code to go between the
> two worlds but it is not so simple.
I agree in general. But I don't think this is really the case for parameters. This is definitively not reciprocal, but a local param can always be transformed in a global one. *This* transformation is a tool problem. Again, my main problem in current SBML is the coexistence of local and global parameters in the *same* file, and the associated problems (such as a local parameter able to overide a species or a compartment). And I am really happy of any discussion dealing with parameter problem. Their frequency is IMHO the surest sign that the current situation is not satisfactory.
Nicolas LE NOVÈRE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676 http://www.ebi.ac.uk/~lenov
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