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[cellml-discussion] Time delays in CellML models?


Chronological Thread 
  • From: r.britten at auckland.ac.nz (Randall Britten)
  • Subject: [cellml-discussion] Time delays in CellML models?
  • Date: Wed, 15 Jul 2009 10:18:49 +1200
Recent work on addressing issues with the CellML specification have focussed
on reset rules (see
https://tracker.physiomeproject.org/show_bug.cgi?id=1543). Some of the
discussion on reset rules has touched on how delays may need to be
expressed, though this is still unresolved. I have added a comment to
tracker item 70 pointing to tracker item 1543.

Please join these discussions, we would really appreciate your input.

Regards,
Randall

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Dom Layfield
> Sent: Wednesday, 15 July 2009 8:13 a.m.
> To: cellml-discussion at cellml.org
> Subject: [cellml-discussion] Time delays in CellML models?
>
> Is there a recommended/suggested way to add time-delays to a CellML model?
>
> I found this model: "A model of HIV-1 pathogenesis that includes an
> intracellular delay"
> http://models.cellml.org/exposure/a0c93131fa0a4cc2b1740fdc4076ac78
> However, this model will not run in current versions of either PCEnv or
COR.
>
> I also found this tracker item:
> https://tracker.physiomeproject.org/show_bug.cgi?id=70
>
> Everything looks pretty unresolved, with no comments since Feb '08.
> Has there been any progress on this?
>
> If not, are there any suggested workarounds? It seems that I might be
> able to add a variable to a component to provide dynamics that
> approximate a straight delay. But I can't think of how to do it.
>
> As in the model referenced above, there are legions of instances where
> a time delay would be useful: incubation periods, dissolution times,
> transit time etc. In my case, I'm trying to model the passage of food
> through the digestive tract. And unless I incorporate some sort of
> delay, I'll have the problem of material starting to exit the distal
> end of the tract immediately that any enters the proximal end. With
> an organ that is ~8 m long, this doesn't make much physical sense.
>
> Can anyone provide any advice?
>
> Thanks,
>
> -- Dom Layfield
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion



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