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: [email protected] [mailto:cellml-discussion- > [email protected]] On Behalf Of Dr. Hans Ekkehard Plesser > Sent: 04 June 2009 13:51 > To: [email protected] > 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" <[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
