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[cellml-discussion] embedded stimulus currents in CellML models


Chronological Thread 
  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] embedded stimulus currents in CellML models
  • Date: Tue, 17 Jul 2007 13:53:18 +0800

[I'm splitting this discussion to the mailing list]

From Alan Garny (following some discussion on stimulus currents with
the Auckland group):

> CellML models that require a stimulus protocol to generate an action
> potential currently implement one in the CellML model itself (Noble 98 is
> one such example indeed). Still, I don't think such a protocol should be
> part of the model. The only reason Penny Noble did it that way in the first
> place is that we had no other choice in COR (she was waiting for me to
> implement my concept of COR project).
>
> Still, what happens if I want to use that model in a multi-cellular
> environment? Ideally I would, in that environment and at some point, specify
> the different cellular models that I want to use by selecting different
> CellML files. Now, if those CellML files contain a hard-coded stimulus
> protocol in them, this will obviously cause problems.
>
> We may therefore want to think of another way of incorporating a stimulus
> protocol, not to mention that one could come up with a different protocol
> and still get an action potential (granted, the underlying physiology will
> likely be different, but that's another debate). What about, therefore,
> making the stimulus protocol(s?) available in some metadata? From there, the
> modelling software could extract that protocol and use it, if and only if
> the user wants it.
>
> I would imagine you guys have already discussed this before, in which case I
> would appreciate any conclusion that has been drawn about this.

While I think that we have discussed this before, but perhaps not
officially, I'll kick it off here :-)

I think the current use of an embedded stimulus current is due to the
repository being limited to CellML 1.0 models. The "correct" way to
approach this problem is this: (1) define the mathematical model
independent of parameter values and boundary/initial conditions; (2)
(this is an optional step) import the mathematical model into a model
which defines the common parameters and boundary conditions; (3) then
import this model into any simulation specific models - it is at this
level you define the particular stimulus protocol or other simulation
specific parameter values and/or boundary conditions.

For the case of a tissue/multi-cellular simulation, you'd probably use
either (1) or (2) depending on the requirements of the tissue model and
then connect the diffusive "stimulus" current to the single cell model
stimulus current.

While people (including myself) often point out the stimulus current as
a special case, it is not really. Any extra or modified current being
added to a model can be handled in the same way. For example, the way a
(potassium) stimulus current is handled should not be any different to
the case where you add the K(ATP) current to a model which does not
already have one.


David.




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