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Hi Hans

Our progress on this is that we have an interim format for representing
reset-rules/events, and are now prototyping the handling of this in
software.

Please see https://tracker.physiomeproject.org/show_bug.cgi?id=1543, where
we will post updates on progress. (If you create a login for yourself on
our tracker, you can "CC" yourself to that tracker item, and get e-mails
regarding progress updates, or add comments and suggestions.)

Regards,
Randall

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Dr. Hans Ekkehard Plesser
> Sent: Friday, 6 November 2009 10:15 p.m.
> To: CellML Discussion List
> Subject: Re: [cellml-discussion] Using CellML for simplified neuron
models?
> (Alan Garny)
>
>
> Hi Poul,
>
> I was just wondering how the work on CellML 1.2 is coming along,
especially
> with respect to
> events. I couldn't find anything about events on the "differences between
> 1.1 and 1.2" page
>
(http://www.cellml.org/specifications/proposed-differences-between-the-1-1-
> and-1-2-CellML-specifications).
>
> Best regards,
> Hans
>
> Poul Nielsen wrote:
> > Dear Hans
> >
> > Thank you for raising this. It s, in fact, one of the issues discussed
> > at the recent combined CellML SBGN-SBO BioPAX MIASE Workshop held this
> > April on Waiheke Island. There is a clear need to be able to specify
> > discontinuous processes and events, such as you have described.
> > However, both CellML and SBML use a declarative specification of
> > models, described with content MathML. Event handling fits more
> > naturally with imperative descriptions of models so there is currently
> > no clean way of describing events using content MathML. SBML, which
> > also uses content MathML as its underlying mathematical description
> > language, has addressed this problem by augmenting the language with
> > events and reset rules. After some discussion at the recent workshop,
> > the consensus was that the next iteration of CellML (1.2) would
> > include facilities for specifying events and applying reset rules in a
> > way that is consistent with SBML. There are several reasons for taking
> > this approach: it is a method that fits reasonably naturally with
> > modellers' notion of describing such models; the solution has been
> > tested by the SBML community; the construct will be straightforward to
> > handle when translating between SBML and CellML. We are currently
> > working on the CellML 1.2 specification and plan to have a draft
> > released shortly with the addition of events and reset rules to handle
> > problems such as you have described.
> >
> > Best wishes
> > Poul
> >
> > On 2009-06-05, at 00:50, Dr. Hans Ekkehard Plesser wrote:
> >
> >> 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
> >>> -------------- next part --------------
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> >>> URL: <http://www.cellml.org/pipermail/cellml-
> discussion/attachments/20090601/4c57e696/attachment.png
> >>> ------------------------------
> >>>
> >>> _______________________________________________
> >>> cellml-discussion mailing list
> >>> 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
> >
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> --
> 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, 11/06/2009
  • [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny), Randall Britten, 11/09/2009

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