Re: SBML L2v2 specification vote #4: References to controlled vocabularies
05 Jan '06 01:44
Michael Hucka wrote:
> Hmm. I think if one used user-defined functions, the
> substitution problem would be avoided.
Yes! specifying the SBO with a mapping to user-functions would
be nice I (still) think.
For those who understand math, the SBO-kinetic-lib is in the
SBML. But the mapping of speciesrefs and params into the
kinetic law is explicit in the math of the kinetic law and
any "precompiled-function-tool" can read and write the mapping
directly into the 'real' kinetic law.
Having the standardized function lib in the file also avoids
the SBO-online problem.
It is just a problem for tools that can't substitute functions,
but I think this could be a service-function in libsmbl as well
as an external tool for conversion/expansion.
> I thought I had already posted the whitepaper on this, but
> apparently not (or I can't find it now). It must have
> gotten wrapped up in the stochastic/discrete vs continuous/
> deterministic proposal we were discussing off-line last
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