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[cellml-discussion] Leftover thoughts from the CellML workshop


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  • From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
  • Subject: [cellml-discussion] Leftover thoughts from the CellML workshop
  • Date: Wed, 17 Mar 2010 11:43:09 +1300
Funny - we just realised this ourselves in this morning's CellML
meeting. Lukas is talking with Andrew right now about events - and I
think he wants to talk with Poul about this too... I'm sure you'll
get some more feedback.

Best wishes
Catherine

On 17/03/2010, at 11:02 AM, Lucian Smith wrote:

> (Whoops, I meant to send this to the list, but replied directly to
> Poul
> instead...)
>
> ----- Forwarded message from Lucian Smith <lpsmith at spod-central.org>
> -----
>
> A couple follow-up thoughts:
>
> * Poul Nielsen <p.nielsen at auckland.ac.nz> [2010-03-11 03:28] writes:
>> Dear Lucian
>>
>> Many thanks for your participation in the CellML workshop and
>> subsequent comments.
>>
>> On 2010-02-27, at 08:43, Lucian Smith wrote:
>>
>>> CellML 1.2:
>>> One thing I noticed was the claim that events could be stored in
>>> CellML as piecewise formulas. I'm pretty sure that won't be the
>>> case with
>>> SBML events, which are 'fire once' events instead of 'true while'
>>> events.
>>> Maybe one could come up with a piecewise hack to store SBML
>>> events, but if
>>> a goal is to become more amenable to SBML-translated models, you
>>> might
>>> want to think about how best to translate SBML events. Or maybe
>>> I'm wrong
>>> and there's already a way to do it?
>>> Another thing I noticed was a reluctance to add too many new
>>> features
>>> to the language in the fear that interpreters might not be able or
>>> willing
>>> to handle them. One way to mitigate this would be to allow models
>>> to
>>> claim somewhere in the header whether the model required that
>>> feature or
>>> not--an interpreter could then more cleanly note whether it was
>>> able to
>>> correctly interpret a given model, while still being able to
>>> interpret
>>> other 1.2 models.
>>
>> I don't think the goal is necessarily to become more amenable to
>> SBML-translated models. What we are most strongly motivated by is to
>> come up with simple, powerful generic mechanisms for representing
>> events
>> and behaviours that depend on them. I would value your thoughts on
>> why
>> piecewise representations are insufficient for handling events.
>
> Certainly I don't think SBML translation is *the* goal of CellML
> 1.2, I
> just posited that it might be *a* goal.
>
> Piecewise functions say "while (condition), the following is always
> true".
> SBML events say "when (condition) becomes true, set the following to
> be
> true at that instant, and let it change after that."
>
> Depending on the nature of the condition, these can be very different
> beasts. As an example, you could have a species X controlled by
> various
> reactions, and at regular intervals, it's being injected into the
> system
> (daily feeding, say). An SBML event would just say something like
> 'when
> time is a multiple of 24, X = X+5'. A piecewise function would have
> to
> incorporate that event into all the other things that change X. It
> might
> be possible, but the resulting expression will probably be very
> complicated. And it might be impossible to write any sort of
> automatic
> translator that translated SBML events to CellML.
>
> At the core, SBML events allow you to separate 'the sort of math the
> normally happens to these variables' from 'these things happen every
> so
> often, and the model adjusts accordingly'. If you require those two
> things to be mushed together into piecewise functions, I *think* you
> could
> probably end up with a function that produced the same output (though
> there might be some counter-examples), but it would be complicated.
> I'm
> not saying you definitely should add SBML-style events to CellML,
> but the
> tradeoff is simplicity for interpreters if you leave it as-is vs.
> simplicity for modelers if you add some new construct.
>
> -Lucian
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