>
> I have a chemical reaction:
> e.g. : a => b
> with one parameter:
> kinetic_constant=value_1
>
> I want to describe an event like this:
> at a defined time (e.g. t=12 s): kinetic_constant=value_2
>
> Is it possible to describe events like this with SBML?
There are at least two ways to do this, you should choose according to
what features your software supports.
In any case you will have to define a global parameter for the
kinetic_constant (not a local parameter in the reaction).
Then you could use an event. The event can be triggered by a condition
like "time>=12" and then assign a new value to the kinetic constant
(see the paraphs about events in the specification).
Alternatively you can define an assignment rule for the kinetic
parameter using a piecewise defined function like "if time<12 then
value_1 else value_2". see the paragraphs about assignment rules and
the paragraph about mathML for how to write the piecewise function in
mathml.
Sven
Dr. Sven Sahle
Abteilung Modellierung biologischer Prozesse
Universität Heidelberg, BIOQUANT/Zoologie
| 
07 May '09 10:52
