[cellml-discussion] Using CellML for simplified neuron models?

[Alan Garny]

Hi Hans,

> We are looking for a good way to describe and share neuron models, and
> CellML appears a good
> candidate. The neuron models we are interested in consist mostly of a
> single compartment,
> possibly of a small number of compartments.
> 
> As far as I can see, CellML appears well suited to describe the so-called
> subthreshold dynamics
> of model neurons. But I am wondering if CellML can also capture (or be
> extended to capture) the
> threshold operation present in most simplified neuron models. Briefly, the
> model dynamics are
> integrated according to a set of differential equations. When the membrane
> potential of the
> neuron crosses a certain threshold, the neuron is said to "fire": the
> membrane potential is
> reset to a certain value instantaneuously, and often clamped at that value
> for a certain period
> of time afterwards (refractory period); also, an output signal is
generated.
> In simple
> pseudocode, this would look like:
> 
> while ( simulation time not up )
> 
>   process input
>   update dynamics according to ODE
> 
>   if ( neuron is refractory )
>     V_m = V_reset
>     count down "refractoriness"
> 
>   if ( V_m > Threshold )
>     V_m = V_reset
>     emit output signal
> 
>   count up time

I believe this could easily be done, as long as you are OK with the
following:
 - this would require integrating the model using an integration technique
that relies on a fixed time step. In my experience, anything will make your
resetting of Vm difficult.
 - your output signal (Vm?) will always be generated.

Attached is a very simple CellML file (based on the van der Pol model) that
illustrates the kind of thing I think you are after. You want to plot the x
and y parameters (see attached screenshot).

Alan
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Test.cellml
Type: application/octet-stream
Size: 4144 bytes
Desc: not available
URL: <http://www.cellml.org/pipermail/cellml-discussion/attachments/20090601/4c57e696/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Test.png
Type: image/png
Size: 77437 bytes
Desc: not available
URL: <http://www.cellml.org/pipermail/cellml-discussion/attachments/20090601/4c57e696/attachment-0001.png>