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Hello Stefan, All,

On Tue, Sep 8, 2009 at 12:22 PM, shoops<shoops@vbi.vt.edu> wrote:
> You have several species in the same compartment thus having a
> compartment entity facilitates normalization. Your alternative would
> require manual synchronization of the compartment size for all species
> in the same compartment.

You can use a parameter. Also, if species are just pools of
anything, compartments may not have well-defined sizes anyway.

> I did not say at all that the way MIRIAM annoation is implemented in
> SBML is good. In fact I am one of the harshes critics. However any
> grouping mechanism will require the group to be annotated with MIRIAM
> information to identify the group in a MIRIAM complian way. We all know
> that names are not an option. Thus MIRIAM annotation will be part of the
> final solution. Improving the capabilities of providing MIRIAM compliant
> annotation is another problem.

I agree annotation is important. I'm just saying that it is not a
substitute for species type, as you seem to imply.

> The above is a logically wrong statement. How can two indistinguishable
> things be distinguishable. It seems that my attempt to remove confusion
> was not sufficient though you claim that there is no need for this ;)

Now you are causing a new confusion. Obviously, the objects in the
pools are indistinguishable, but the pools are not. But the pools are
uniquely related.

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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