[cellml-discussion] Looping Cell Cycle Models

[Catherine Lloyd]

Dear All

We are currently curating the cell cycle models in the CellML  
repository:

Chen 2000
Chen 2004
Ciliberto 2000
Ciliberto 2003
Ciliberto 2003b
Hatzimanikatis 1999
Novak 1997
Novak 1998
Novak 2001

Many of these we have fixed such that the CellML model recreates one  
set of peaks from the published graphs - however we can't get the  
beautiful oscillating graphs which are in the original papers - and  
which are also incidentally in the BioModels database!  To achieve  
these oscillations we need to get the models to repeat - or loop - For  
the Novak 1997 model for instance it looks like the cell cycle repeats  
every 140 minutes (http://www.ebi.ac.uk/biomodels-main/publ-model.do?mid=BIOMD0000000007 
) and



Looking at the equations in the papers we can't find any function  
which would cause the models to loop.  Indeed, even where we have  
access to the author's original XPP code, we are struggling to find  
the "loop function" (although, we confess this may be due to our  
misinterpretation of the XPP!).

In SBML is it possible that an event is used to get the model to  
repeat? (My apologies for my ignorance here!).

Finally, we have heard back from one of the cell cycle "experts" and  
she has suggested that we do, at least for certain models, need to  
come up with an artificial loop function.... "to simulate various  
generations you have to artificially loop the various cell cycles".

If anyone has any ideas as to how we can achieve this in CellML I  
would love to hear from you.

Thank you in advance!

Best wishes
Catherine
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