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: [email protected] [mailto:cellml-discussion- > [email protected]] 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" <[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 _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
