Hi Poul! Thanks for the information! I am looking forward to the 1.2 specifications! Do you have an estimate when that would be ready for use?
Best, 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" <[email protected]> >>> Subject: Re: [cellml-discussion] Using CellML for simplified neuron >>> models? >>> To: "'CellML Discussion List'" <[email protected]> >>> Message-ID: <001001c9e2aa$9beba840$d3c2f8...@[email protected]> >>> 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 -------------- >>> A non-text attachment was scrubbed... >>> Name: Test.cellml >>> Type: application/octet-stream >>> Size: 4144 bytes >>> Desc: not available >>> URL: >>> <http://www.cellml.org/pipermail/cellml-discussion/attachments/20090601/4c57e696/attachment.obj >>> >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: Test.png >>> Type: image/png >>> Size: 77437 bytes >>> Desc: not available >>> URL: >>> <http://www.cellml.org/pipermail/cellml-discussion/attachments/20090601/4c57e696/attachment.png >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> cellml-discussion mailing list >>> [email protected] >>> 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 [email protected] >> Home http://arken.umb.no/~plesser >> _______________________________________________ >> cellml-discussion mailing list >> [email protected] >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > _______________________________________________ > cellml-discussion mailing list > [email protected] > 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 [email protected] Home http://arken.umb.no/~plesser _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
