[cellml-discussion] Looping Cell Cycle Models

[Nicolas Le novère]

Catherine Lloyd wrote:

> However, we now face a different problem...  Although we can easily 
> describe the switches as piece-wise equations, if we define a single 
> variable more than once in a CellML model the simulation tools tell us 
> that the model is over constrained.
> 
> For example in this case we already have a differential equation 
> describing the change in mass over time, and then we have a second 
> equation placing a condition on mass:

No, no. Events are not assignment rules. In SBML as well, you could not 
have a rate rule and an assignment rule on mass. Events are discontinuous 
processes taking place in between simulation iterations. I think this is 
just a missing concept in CellML. It exists in simulators like XPP and 
GENESIS, used for neuronal simulations (e.g. to reset voltage in spiking 
neurons).

(To be absolutely frank, the existence of events as part of the core SBML 
has been challenged many times. But I think we can now see why they are 
needed :-))

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/