SBML is the "Systems Biology Markup Language", not the "Biochemical
Markup Language". Systems Biology is scale-free. As far as the same
rate-law can describe the behaviour of a population of molecules, a
population of cells, or a population of individuals, I don't see the
problem. Lotka-Volterra is a good example.
Now, I think what ultimately define the scope is the usage. It was
mainly metabolic analysis. More and more it moves to signal
transduction and gene regulatory network. I would not been surprise to
see other usage in the future.
Besides, a lot of soft are supporting more or less correctly SBML. I'm
not sure it would be a good idea to restart the whole process again
and again. Wait and see.
On Tue, 26 Apr 2005, Michael Hucka wrote:
> lenov> Just to throw a bit of oil on the furnace: I
> lenov> actualy hope that SBML is bit more than just a way
> lenov> to represent biochemical network models:
> To some extent, I have to disagree. The model you showed is
> more appropriate for something like CellML. I don't think
> it is wortwhile to call an entire cell an SBML "species".
> At this stage in our collective understanding of biology and
> modeling, I think it is not practical to have one language
> attempt to cover an excessively broad range of spatial
> scales and biological phenomena. Yes, you *can* go ahead
> and start using SBML to represent tissues and organs and so
> on, and perhaps if you write software that interprets it as
> you designed it, then it might work for you. But as we've
> seen from the rest of this discussion thread, it is hard
> enough to get agreement between different people on even
> basic matters limited to the scope of SBML's original
> design. Imagine now trying to widen that scope.
> I personally feel we will see the evolution of a patchwork
> of languages, each of which is suited to a different subset
> of needs, stiched together into a larger fabric for covering
> an ever-increasing range of phenomena. These languages will
> evolve as people settle on accepted ways of handling each
> different subset of needs and find that stretching the
> existing languages is impractical.
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 AIM screen name: nlenovere