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

[Dr. Hans Ekkehard Plesser]

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

-- 
Dr. Hans Ekkehard Plesser
Associate Professor

Dept. of Mathematical Sciences and Technology
Norwegian University of Life Sciences

Phone +47 6496 5467
Fax   +47 6496 5401
Email hans.ekkehard.plesser at umb.no
Home  http://arken.umb.no/~plesser