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

[James Lawson]

Dear Hans,

Further to Alan's email, I thought I'd refer you to some models we have 
in the CellML Model Repository. Have a look at some of Dr Richard 
Bertram's models at http://www.cellml.org/models - most of these are 
models of bursting in pancreatic beta cells, but there are a couple of 
neuronal models there too. You can find them under 'Bertram' in the 
repository listing.

If your simple conditional statements can be covered by piecewise 
equations, it can be done in CellML.

You might do well to look at some of the electrophysiological models of 
heart cells that we've coded up - 
http://www.cellml.org/models/beeler_reuter_1977_version08 is a fairly 
simple model with a piecewise-based stimulus protocol added.

Please let me know if you need any help accessing the models in the 
repository.

Best of luck!

Kind regards,
James Lawson

Dr. Hans Ekkehard Plesser wrote:
> Hi!
>
> 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
>
> Best regards,
> Hans
>
>   

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