Re: Proposed addition to L3 core
09 Sep '09 04:29
Hello Nicolas, All,
On Tue, Sep 8, 2009 at 6:41 PM, Nicolas Le novère<email@example.com> wrote:
>> Optionally, use a parameter.
> Not that simple: you need to define the dimension of a compartment.
I agree, compartments make life easier. But you could model without
them, if you had to.
> Because the string "phosphorylated_mapk" is just a set of bits that have no
> particular meaning. For instance, you cannot relate it to
> "phosphorylated_cyclin" or "phosphorylated_mapkk".
I agree that having an entity alone does not make you know what
entity it is. But just knowing that two species are the same entity is
worth a lot.
>> No you can not do it with names, because there is no standard for
> And? There is no standard for SpeciesType either.
If you make it part of L3 Core, then it would be a standard we could
rely upon. There may be alternatives, but you would have to propose
them first and get them accepted.
>> It's trivial to redesign SBML to make compartments obsolete.
>> Compartment size is just a little number that can be easily moved
>> somewhere else. You can justify compartments on philosophical grounds,
>> or argue with traditions, but you can not defend them based on
>> mathematical necessity.
> Ah ... OK. I thought we were talking about SBML Level 3. Sorry for my
Sorry if I wasn't clear. My point is, if it can be removed easily,
it can not be essential. It is a hypothetical change of L2 or L3.
> I am very willing to talk about redesigning SBML for
> Level 4. I actually have pretty precise ideas on how to do it for cleanly
> separating model structure, biological semantics and model display. I
> believe we will converge on this actually.
Sounds interesting! I would like to hear that. Feel free to open a
new thread about this.
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
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