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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
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>>> ------------------------------
>>>
>>> _______________________________________________
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>>> cellml-discussion at cellml.org
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>>>
>>>
>>> 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

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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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