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Hi Hans,

I can see your point now and agree that the solution I offered is not
suitable. In fact, I wasn't happy with the solution myself, but that was the
best I could come up with with CellML in mind. So, yes, this means that
events are not supported by CellML, unlike in SBML.

Bottom line: you are out of luck with CellML while SBML is what you are
after, at least with regards to events.

Alan

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Dr. Hans Ekkehard Plesser
> Sent: 04 June 2009 13:51
> To: cellml-discussion at cellml.org
> Subject: Re: [cellml-discussion] Using CellML for simplified neuron
models?
> (Alan Garny)
>
>
> Hi Alan!
>
> [Apologies for breaking the thread, I had subscribed to the list in digest
> form.]
>
> Thank you for your example. Unfortunately, fixed time-stepping schemes
> where events (threshold
> crossings and membrane potential resets) can occur only on a fixed time
> grid are one of the big
> no-nos in neuronal network modeling, since they can lead to strong
> synchronization artefacts.
> Indeed, quite a lot of research in recent years has focused on algorithms
> to determine the exact
> time of threshold crossings efficiencly. I'd be happy to send you
reference
> if you are interested.
>
> Thus, if we wanted to use CellML to represent neuron models in a general
> form, we would need a
> possibility to represent instantaneous events in continuous time. I
believe
> SBML events provide
> this, don't they?
>
> Best,
> Hans
>
>
>
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 1 Jun 2009 12:17:54 +0100
> > From: "Alan Garny" <alan.garny at dpag.ox.ac.uk>
> > Subject: Re: [cellml-discussion] Using CellML for simplified neuron
> > models?
> > To: "'CellML Discussion List'" <cellml-discussion at cellml.org>
> > Message-ID: <001001c9e2aa$9beba840$d3c2f8c0$@garny at dpag.ox.ac.uk>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > 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
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> >
> > ------------------------------
> >
> > _______________________________________________
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> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
> >
> >
> > End of cellml-discussion Digest, Vol 59, Issue 1
> > ************************************************
>
> --
> 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
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

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• [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny), Dr. Hans Ekkehard Plesser, 06/05/2009
  • [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny), Alan Garny, 06/05/2009
  • [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny), Poul Nielsen, 06/05/2009
    • [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny), Dr. Hans Ekkehard Plesser, 06/05/2009

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