[cellml-discussion] Looping Cell Cycle Models

[Catherine Lloyd]

Sorry - clearly after 5 days away my brain has died - or at least it  
is not in gear yet!

Actually, having since read some of the other cell cycle papers, it  
seems that there are similar descriptions in their figure legends.

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:

(When UbE becomes inferior or equal to 0.1
  immediately      kp = 2 * kp
                   Mass = Mass / 2)

However - this now becomes an issue for the tool developers - so I  
will refer the problem to them instead!

Thanks again.

Best wishes
Catherine




On 29/12/2008, at 10:45 AM, Nicolas Le novère wrote:

> Catherine Lloyd wrote:
>
>> I thought that this might have been the case.  I believe we can  
>> mimic your events as you describe them below in CellML by using  
>> piecewise equations.
>> Just out of interest, where did you get these descriptions from?   
>> The original paper?  Correspondence with the authors?  Or did you  
>> come up with them yourselves?
>
> As I said:
>
>>> For Novak and Tyson 1997, they are described in Table 1, in the  
>>> section "switches".
>
> :-)
>
> -- 
> 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
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>
>
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