Chris J. Myers wrote:
> I can think of one way that this proposal could affect simulation.
> Namely, with the entity concept, one could plot the total amount of
> some entity which may be useful. One could also use the total amount
> in rate laws and equations by referring to the entity id. Currently,
> this can be done by creating an artificial total species and using an
> assignment rule, but the entity idea seems a bit cleaner to me.
I do not see why this is "artificial", but I actually agree this is a good
idea. And the group fits that perfectly.
> The problem I see though is what I'm often interested in is not how
> many molecules of a species are in all compartments but rather how
> many molecules are in all forms. For example, the total amount of CI
> is the number of monomers, plus two times the number of dimers, plus
> all the various bound CI molecules. This is not captured by the
> entity concept. R
Exactly! Thanks for pointing that. If I have four species MAPKK, MAPKKP,
MAPK, MAPKP, I want to be able to say "all the MAPK proteins", "all the
phosphorylated proteins", "all the kinases"
group kinases: MAKP, MAPKP, MAPKK, MAPKKP
group MAPK: MAPK, MAPKP
group phosphorylated: MAPKP, MAPKKP
> I'm not sure though how strongly I would push to have such a concept
> in the core. I would not argue against it, since it is useful. If
> this idea is absorbed into the groups package, then I would like to
> see it modified to accept a number which can be interpreted as the
> number molecules in a complex as described above.
Yes, I would very much like that too actually.
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
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