Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
16 Jan '06 11:57
> This is in my opinion an attempt through the back door to make the
> sboTerm authoritative by just omitting the Math element in the kinetic
No, it is not. It is an issue independant of sboTerm. It is larger than that.
> But let me come to the other pro optional argument given by Mike. The
> kinetic law itself is optional, i.e., we already have the ability to
> store models which are not 'fully fleshed out'. Since we know already
> the list of substrates, products and modifiers, from the reaction
But not the local parameters! So far SBML has been tied to ODE-type
models. But there is an increasing pressure to make it accept other kind
The ability to store local parameters without a kineticLaw is a desirable
feature for some quantitative descriptions that are not kinetics models
per se (particularly if the parameters are properly annotated ...).
SBML is the Systems Biology Markup Language, not ODE-ML. It was very
clever to restrict its use to one kind of model initially. It was
certainly seminal in its adoption. But it is a fact that SBML is now used
by a much wider community.
In the current situation, the user has the choice between a representaiton
that one can instantiate in a time-serie simulation (with kineticLaw), and
a completely qualitative representation (without kineticLaw). There is
maybe a middle-way.
We are not advocating for a wild explosion of SBML elements here. But on
the contrary for simpler SBML models. Even COPASI could read such models,
even it they would be undetermined. A user would have to complete them to
run simulations. But this is already the case if he/she import a model
from Reactome or KEGG.
The problem is that an empty MathML returns "0". It is not undefined. One
can decide that the following return "0"
while <math /> returns undefined.
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