From alan.garny at dpag.ox.ac.uk Mon Jun 1 23:17:54 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Mon, 1 Jun 2009 12:17:54 +0100 Subject: [cellml-discussion] Using CellML for simplified neuron models? In-Reply-To: <4A1FF0FB.8070601@umb.no> References: <4A1FF0FB.8070601@umb.no> Message-ID: <001001c9e2aa$9beba840$d3c2f8c0$@garny@dpag.ox.ac.uk> 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Test.png Type: image/png Size: 77437 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Tue Jun 2 12:17:51 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Tue, 02 Jun 2009 12:17:51 +1200 Subject: [cellml-discussion] [cellmlteam] Contributing CellML models to Wolfram Alpha In-Reply-To: <000f01c9e2a7$217dfb10$6479f130$@garny@dpag.ox.ac.uk> References: <20090530103438.g63sfb9lwwgk4c00@webmail.bioeng.auckland.ac.nz> <000f01c9e2a7$217dfb10$6479f130$@garny@dpag.ox.ac.uk> Message-ID: <4A246FAF.1090705@auckland.ac.nz> To be honest I'm not really so impressed with WA yet, but that's probably because I haven't learned to use it properly. Can anyone explain/speculate to me how submitting to WA would help our goals of a.) increasing uptake of CellML, b.) model distribution [this one is obvious,] c.) model reuse, d.) model mix/match/cut/paste/remix/mashup, e.) model reparameterisation, f.) merging of data sets....? Simulation and graphing is nice - I guess this fits partly under distribution? Actually Abhishek, this suggest echoes that request by the BestGRID project for CellML input... (see http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-05-20/) but potentially more accessible. Kind regards, James Alan Garny wrote: >> From: team-bounces at cellml.org [mailto:team-bounces at cellml.org] On Behalf >> > Of > >> Abhishek Tiwari >> By now you must have heard about computational engine Wolfram|Alpha, >> if not you can try here http://www.wolframalpha.com/. I am curious if >> anyone have thoughts about contributing cellml models to Wolfram|Alpha >> engine, currently they are accepting contributed structured data, >> models and algorithms >> (http://www18.wolframalpha.com/participate/algorithms.html). Alpha >> does lot of fantastic things, simulation and graphing is one of them. >> > > That seems like an interesting idea, but hopefully this wouldn't mean giving > them CellML files as such, but rather them making use of the CellML > Repository?... > > Alan > > _______________________________________________ > team mailing list > team at cellml.org > http://www.cellml.org/mailman/listinfo/team > -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From j.lawson at auckland.ac.nz Tue Jun 2 12:25:19 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Tue, 02 Jun 2009 12:25:19 +1200 Subject: [cellml-discussion] Using CellML for simplified neuron models? In-Reply-To: <4A1FF0FB.8070601@umb.no> References: <4A1FF0FB.8070601@umb.no> Message-ID: <4A24716F.3080003@auckland.ac.nz> Dear Hans, Further to Alan's email, I thought I'd refer you to some models we have in the CellML Model Repository. Have a look at some of Dr Richard Bertram's models at http://www.cellml.org/models - most of these are models of bursting in pancreatic beta cells, but there are a couple of neuronal models there too. You can find them under 'Bertram' in the repository listing. If your simple conditional statements can be covered by piecewise equations, it can be done in CellML. You might do well to look at some of the electrophysiological models of heart cells that we've coded up - http://www.cellml.org/models/beeler_reuter_1977_version08 is a fairly simple model with a piecewise-based stimulus protocol added. Please let me know if you need any help accessing the models in the repository. Best of luck! Kind regards, James Lawson Dr. Hans Ekkehard Plesser wrote: > Hi! > > 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 > > Best regards, > Hans > > -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From alan.garny at dpag.ox.ac.uk Tue Jun 2 21:17:23 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Tue, 2 Jun 2009 10:17:23 +0100 Subject: [cellml-discussion] [cellmlteam] Contributing CellML models to Wolfram Alpha In-Reply-To: <4A246FAF.1090705@auckland.ac.nz> References: <20090530103438.g63sfb9lwwgk4c00@webmail.bioeng.auckland.ac.nz> <000f01c9e2a7$217dfb10$6479f130$@garny@dpag.ox.ac.uk> <4A246FAF.1090705@auckland.ac.nz> Message-ID: <007d01c9e362$f04195e0$d0c4c1a0$@garny@dpag.ox.ac.uk> > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of James Lawson > > To be honest I'm not really so impressed with WA yet, but that's > probably because I haven't learned to use it properly. I must confess that I am not particularly impressed with it either. I did 'play' with it quite a bit when it got released and, yes, it's fun/cool if you stick to the kind of stuff shown in Wolfram's demo, but otherwise... it's basically 'useless'. This put aside, I like the concept and no doubt that it's going to take time to make it worthwhile. > Can anyone explain/speculate to me how submitting to WA would help our > goals of a.) increasing uptake of CellML, b.) model distribution [this > one is obvious,] c.) model reuse, d.) model > mix/match/cut/paste/remix/mashup, e.) model reparameterisation, f.) > merging of data sets....? a) and c) I would imagine it's pretty obvious. The sole fact that CellML models would become 'available' through WA means that people would get to know about CellML and, from there, might be interested in finding more about it, etc. As for your other points, I don't know for certain, but I don't think it matters: anything that can help people use CellML is a good thing (as long as it fits the maximum output for minimum input paradigm... :)) Alan From e.crampin at auckland.ac.nz Wed Jun 3 08:33:33 2009 From: e.crampin at auckland.ac.nz (Edmund J. Crampin) Date: Wed, 3 Jun 2009 08:33:33 +1200 Subject: [cellml-discussion] [cellmlteam] Contributing CellML models to Wolfram Alpha In-Reply-To: <007d01c9e362$f04195e0$d0c4c1a0$@garny@dpag.ox.ac.uk> References: <20090530103438.g63sfb9lwwgk4c00@webmail.bioeng.auckland.ac.nz> <000f01c9e2a7$217dfb10$6479f130$@garny@dpag.ox.ac.uk> <4A246FAF.1090705@auckland.ac.nz> <007d01c9e362$f04195e0$d0c4c1a0$@garny@dpag.ox.ac.uk> Message-ID: <8BDA70BA-2ACD-4A95-856A-4BA30E41A1CD@auckland.ac.nz> I think this is a good suggestion from Abhishek, which was also raised earlier by Richard Simpson (our Business Development Manager) in a broader context than just CellML. I wonder if Abhishek is willing to explore this a little further? Edmund Dr Edmund J. Crampin Systems Biology Group Leader Associate Director Postgraduate Auckland Bioengineering Institute and Senior Lecturer Department of Engineering Science The University of Auckland New Zealand On 2/06/2009, at 9:17 PM, Alan Garny wrote: >> -----Original Message----- >> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- >> bounces at cellml.org] On Behalf Of James Lawson >> >> To be honest I'm not really so impressed with WA yet, but that's >> probably because I haven't learned to use it properly. > > I must confess that I am not particularly impressed with it either. > I did > 'play' with it quite a bit when it got released and, yes, it's fun/ > cool if > you stick to the kind of stuff shown in Wolfram's demo, but > otherwise... > it's basically 'useless'. This put aside, I like the concept and no > doubt > that it's going to take time to make it worthwhile. > >> Can anyone explain/speculate to me how submitting to WA would help >> our >> goals of a.) increasing uptake of CellML, b.) model distribution >> [this >> one is obvious,] c.) model reuse, d.) model >> mix/match/cut/paste/remix/mashup, e.) model reparameterisation, f.) >> merging of data sets....? > > a) and c) I would imagine it's pretty obvious. The sole fact that > CellML > models would become 'available' through WA means that people would > get to > know about CellML and, from there, might be interested in finding > more about > it, etc. > > As for your other points, I don't know for certain, but I don't > think it > matters: anything that can help people use CellML is a good thing > (as long > as it fits the maximum output for minimum input paradigm... :)) > > Alan > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From hans.ekkehard.plesser at umb.no Fri Jun 5 00:50:59 2009 From: hans.ekkehard.plesser at umb.no (Dr. Hans Ekkehard Plesser) Date: Thu, 4 Jun 2009 14:50:59 +0200 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) In-Reply-To: References: Message-ID: <4A27C333.9090102@umb.no> 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" > Subject: Re: [cellml-discussion] Using CellML for simplified neuron > models? > To: "'CellML Discussion List'" > 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 -------------- > A non-text attachment was scrubbed... > Name: Test.cellml > Type: application/octet-stream > Size: 4144 bytes > Desc: not available > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Test.png > Type: image/png > Size: 77437 bytes > Desc: not available > URL: > > ------------------------------ > > _______________________________________________ > 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 From alan.garny at dpag.ox.ac.uk Fri Jun 5 01:02:23 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 4 Jun 2009 14:02:23 +0100 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) In-Reply-To: <4A27C333.9090102@umb.no> References: <4A27C333.9090102@umb.no> Message-ID: <007601c9e514$b40b8410$1c228c30$@garny@dpag.ox.ac.uk> 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: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dr. Hans Ekkehard Plesser > Sent: 04 June 2009 13:51 > To: cellml-discussion at cellml.org > 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" > > Subject: Re: [cellml-discussion] Using CellML for simplified neuron > > models? > > To: "'CellML Discussion List'" > > 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 -------------- > > A non-text attachment was scrubbed... > > Name: Test.cellml > > Type: application/octet-stream > > Size: 4144 bytes > > Desc: not available > > URL: 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: 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 From p.nielsen at auckland.ac.nz Fri Jun 5 09:22:23 2009 From: p.nielsen at auckland.ac.nz (Poul Nielsen) Date: Fri, 5 Jun 2009 09:22:23 +1200 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) In-Reply-To: <4A27C333.9090102@umb.no> References: <4A27C333.9090102@umb.no> Message-ID: <1D70655A-C23B-4959-8D83-ADB2E523F925@auckland.ac.nz> 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" >> Subject: Re: [cellml-discussion] Using CellML for simplified neuron >> models? >> To: "'CellML Discussion List'" >> 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 -------------- >> A non-text attachment was scrubbed... >> Name: Test.cellml >> Type: application/octet-stream >> Size: 4144 bytes >> Desc: not available >> URL: > > >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Test.png >> Type: image/png >> Size: 77437 bytes >> Desc: not available >> URL: > > >> >> ------------------------------ >> >> _______________________________________________ >> 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 From dj.cowan at auckland.ac.nz Fri Jun 5 15:06:53 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 05 Jun 2009 15:06:53 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-03 Message-ID: <4A288BCD.40306@auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-03 Dougal From p.hunter at auckland.ac.nz Fri Jun 5 17:51:14 2009 From: p.hunter at auckland.ac.nz (Peter Hunter) Date: Fri, 5 Jun 2009 17:51:14 +1200 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) Message-ID: Thanks Poul. -------------------------- Sent using BlackBerry ----- Original Message ----- From: cellml-discussion-bounces at cellml.org To: CellML Discussion List Sent: Fri Jun 05 09:22:23 2009 Subject: Re: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) 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" >> Subject: Re: [cellml-discussion] Using CellML for simplified neuron >> models? >> To: "'CellML Discussion List'" >> 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 -------------- >> A non-text attachment was scrubbed... >> Name: Test.cellml >> Type: application/octet-stream >> Size: 4144 bytes >> Desc: not available >> URL: > > >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Test.png >> Type: image/png >> Size: 77437 bytes >> Desc: not available >> URL: > > >> >> ------------------------------ >> >> _______________________________________________ >> 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 From hans.ekkehard.plesser at umb.no Fri Jun 5 21:26:59 2009 From: hans.ekkehard.plesser at umb.no (Dr. Hans Ekkehard Plesser) Date: Fri, 5 Jun 2009 11:26:59 +0200 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) In-Reply-To: <1D70655A-C23B-4959-8D83-ADB2E523F925@auckland.ac.nz> References: <4A27C333.9090102@umb.no> <1D70655A-C23B-4959-8D83-ADB2E523F925@auckland.ac.nz> Message-ID: <4A28E4E3.3060204@umb.no> 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" >>> Subject: Re: [cellml-discussion] Using CellML for simplified neuron >>> models? >>> To: "'CellML Discussion List'" >>> 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 -------------- >>> A non-text attachment was scrubbed... >>> Name: Test.cellml >>> Type: application/octet-stream >>> Size: 4144 bytes >>> Desc: not available >>> URL: >> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: Test.png >>> Type: image/png >>> Size: 77437 bytes >>> Desc: not available >>> URL: >> ------------------------------ >>> >>> _______________________________________________ >>> 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 From j.lawson at auckland.ac.nz Tue Jun 9 16:24:37 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Tue, 09 Jun 2009 16:24:37 +1200 Subject: [cellml-discussion] IUPS2009 CellML Workshop Announcement Message-ID: <4A2DE405.204@auckland.ac.nz> Dear CellML community, The IUPS2009 meeting will take place in Kyoto from 28th July until August 1st, 2009. Attendees from the CellML project have organised a workshop-style tutorial at this event to provide an introduction to CellML, its usage, and tools for working with CellML models. This workshop will take place on the second day of the conference, *29th July 2009, from 14:15-16:45hrs, in Room K* of the conference complex. The workshop will consist of a short introductory presentation, followed by a period of hands-on tuition supervised by senior members of the CellML community. Computers and internet connections will be available, although attendees would be advised to bring a notebook computer if possible. If you are planning on attending this conference, please come join us and participate in the workshop. Further information on this workshop will be released as the details are finalised. Kind regards, James Lawson -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From dj.cowan at auckland.ac.nz Fri Jun 12 08:09:05 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 12 Jun 2009 08:09:05 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 Message-ID: <4A316461.9060306@auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-10/ Dougal From r.britten at auckland.ac.nz Fri Jun 12 12:33:03 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Fri, 12 Jun 2009 12:33:03 +1200 Subject: [cellml-discussion] CellML model repository: phasing in PMR2 Message-ID: <002801c9eaf5$58d040e0$0a70c2a0$@britten@auckland.ac.nz> Hi all As you may know, deployment of PMR2, the new software that will run the CellML repository, is imminent. As of now, the old repository has been placed into a "read-only" state. Some final testing of the new PMR2 instance is in progress, and the switch over is expected to take place on Monday 15 June. Old URL's for CellML models will be preserved, and the plan is that most users will find the transition seamless. We will send a follow up e-mail once this is done. Regards, Randall Britten ___________________________ Leader of the Bioengineering Software Development Group Auckland Bioengineering Institute Auckland University Auckland, New Zealand -------------- next part -------------- An HTML attachment was scrubbed... URL: From alan.garny at dpag.ox.ac.uk Fri Jun 12 19:28:37 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Fri, 12 Jun 2009 08:28:37 +0100 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 In-Reply-To: <4A316461.9060306@auckland.ac.nz> References: <4A316461.9060306@auckland.ac.nz> Message-ID: <008d01c9eb2f$666ba250$3342e6f0$@garny@dpag.ox.ac.uk> Regarding item #9, i.e. OpenCell update and the COR-like view in particular: I think one should think of the COR-like view as offering a different kind of serialisation for the CellML file. We have the XML view which indeed offers the raw serialisation and therefore keeps everything in the order in which they are in the CellML file (+/- some spaces / blank lines maybe). The COR-like view is the same, except that it makes the serialisation prettier and more user friendly (hopefully!). The bottom line is that for this type of views, it makes sense to keep things in the order in which they are in the CellML file. Think of it in terms of opening a file in a text editor. The text editor is not going to rearrange things... Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dougal Cowan > Sent: 11 June 2009 21:09 > To: cellml-discussion at cellml.org > Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 > > I have put the minutes from Wednesday's meeting up at: > > http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06- > 10/ > > Dougal > > > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From r.britten at auckland.ac.nz Sat Jun 13 15:00:41 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Sat, 13 Jun 2009 15:00:41 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 In-Reply-To: <008d01c9eb2f$666ba250$3342e6f0$@garny@dpag.ox.ac.uk> References: <4A316461.9060306@auckland.ac.nz> <008d01c9eb2f$666ba250$3342e6f0$@garny@dpag.ox.ac.uk> Message-ID: <000301c9ebd3$235c05f0$6a1411d0$@britten@auckland.ac.nz> Hi Please continue the discussion of this COR text "sequencing" issue on the tracker. I've put references to other mailings on the relevant tracker item: https://tracker.physiomeproject.org/show_bug.cgi?id=152 Regards, Randall > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Alan Garny > Sent: Friday, 12 June 2009 7:29 p.m. > To: 'CellML Discussion List' > Subject: Re: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 > > Regarding item #9, i.e. OpenCell update and the COR-like view in particular: > I think one should think of the COR-like view as offering a different kind > of serialisation for the CellML file. We have the XML view which indeed > offers the raw serialisation and therefore keeps everything in the order in > which they are in the CellML file (+/- some spaces / blank lines maybe). The > COR-like view is the same, except that it makes the serialisation prettier > and more user friendly (hopefully!). The bottom line is that for this type > of views, it makes sense to keep things in the order in which they are in > the CellML file. Think of it in terms of opening a file in a text editor. > The text editor is not going to rearrange things... > > Alan > > > -----Original Message----- > > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > > bounces at cellml.org] On Behalf Of Dougal Cowan > > Sent: 11 June 2009 21:09 > > To: cellml-discussion at cellml.org > > Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-10 > > > > I have put the minutes from Wednesday's meeting up at: > > > > http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06- > > 10/ > > > > Dougal > > > > > > > > > > _______________________________________________ > > 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 From r.britten at auckland.ac.nz Mon Jun 15 14:16:04 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Mon, 15 Jun 2009 14:16:04 +1200 Subject: [cellml-discussion] CellML model repository: phasing in PMR2 In-Reply-To: <002801c9eaf5$58d040e0$0a70c2a0$@britten@auckland.ac.nz> References: <002801c9eaf5$58d040e0$0a70c2a0$@britten@auckland.ac.nz> Message-ID: <008401c9ed5f$3c0e0e80$b42a2b80$@britten@auckland.ac.nz> Due to some issues with model listings, we will defer this to Wednesday at the soonest. From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-bounces at cellml.org] On Behalf Of Randall Britten Sent: Friday, 12 June 2009 12:33 p.m. To: cellml-discussion at cellml.org Subject: [cellml-discussion] CellML model repository: phasing in PMR2 Hi all As you may know, deployment of PMR2, the new software that will run the CellML repository, is imminent. As of now, the old repository has been placed into a "read-only" state. Some final testing of the new PMR2 instance is in progress, and the switch over is expected to take place on Monday 15 June. Old URL's for CellML models will be preserved, and the plan is that most users will find the transition seamless. We will send a follow up e-mail once this is done. Regards, Randall Britten ___________________________ Leader of the Bioengineering Software Development Group Auckland Bioengineering Institute Auckland University Auckland, New Zealand -------------- next part -------------- An HTML attachment was scrubbed... URL: From chenli at ebi.ac.uk Wed Jun 17 01:48:40 2009 From: chenli at ebi.ac.uk (Chen Li) Date: Tue, 16 Jun 2009 14:48:40 +0100 Subject: [cellml-discussion] [BioModels Database] 14th release Message-ID: <4A37A2B8.30303@ebi.ac.uk> Hinxton, Wednesday 16th June 2009 Dear colleagues, We are pleased to announce the fourteenth release of BioModels Database. In this release, 5 new models have gained entry to the curated branch. The public version of BioModels Database now contains 216 models in the curated and 196 in the non-curated branch. Together these 412 models comprise 28901 species and 36264 reactions. Some of the existing models have been slightly changed for correction and to enhance reusability. Also the annotations of some existing models have been updated. The database now features around 14611 cross-references. Out of the 196 models that are in the non-curated branch, 92 models are imported from the CellML repository (http://www.cellml.org/), which would subsequently be moved to the curated branch in future. After the last release, the BioModels Database software has been enhanced to alter some new features. Some features concerning public users are: * Submission of models now accepts models encoded in SBML Level 2 Version 4 * On the homepage, besides "Search", there is another button "Go to the model". After giving the model's name or ID, user could directly go the model presentation page. * Subversion is adopted for models revision control. When a model is submitted or replaced, a copy of the model will be go into SVN repository. * In model's presentation page, there is a new tab called Curation, in which, user can find curation result and all revisions of the model. Authorized user also could download the past revisions or choose different revisions and compare them. * On the top left of model presentation page, there are links for downloading models in different versions of SBML level 2. The link of curated version is highlighted with bold font. Other versions are automatically generated by using libsbml. * BioModels Database now stores more complete information of Taxonomy terms to help improving the search result. * Along with the release, there are also some bugs fixed. For more details, please check: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_16June2009 BioModels Database is being developed by the Computational Neurobiology group (EMBL-European Bioinformatics Institute, United-Kingdom) and the SBML Team (California Institute of Technology, USA). Collaborators include the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML team (Auckland Bioengineering Institute, NZ). BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Neurobiology group), the Biotechnology and Biological Sciences Research Council (Computational Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thank you to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they provide and develop. The BioModels Database Team http://www.ebi.ac.uk/biomodels From dj.cowan at auckland.ac.nz Fri Jun 19 13:57:16 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 19 Jun 2009 13:57:16 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-17 Message-ID: <4A3AF07C.5050906@auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-17 Dougal From alan.garny at dpag.ox.ac.uk Fri Jun 19 21:35:48 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Fri, 19 Jun 2009 10:35:48 +0100 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-17 In-Reply-To: <4A3AF07C.5050906@auckland.ac.nz> References: <4A3AF07C.5050906@auckland.ac.nz> Message-ID: <000f01c9f0c1$53f4db40$fbde91c0$@garny@dpag.ox.ac.uk> For what it is worth: - 7.2: it is CellML to COR-like code that is working, not the other way around; - 7.3: regarding the metadata, it should be easy to keep track of them, so that when we go from COR-like code to CellML they get 'reinserted'. This is the way COR works for instance. Also, even though metadata are not currently handled in the COR-like format, it doesn't mean that they couldn't. We could, for example, have a generic way of representing metadata, as well as a specific way of representing metadata that we know about, can recognise. Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dougal Cowan > Sent: 19 June 2009 02:57 > To: cellml-discussion at cellml.org > Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-17 > > I have put the minutes from Wednesday's meeting up at: > > http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-17 > > Dougal > > > > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From tommy.yu at auckland.ac.nz Mon Jun 22 13:28:15 2009 From: tommy.yu at auckland.ac.nz (Tommy Yu) Date: Mon, 22 Jun 2009 13:28:15 +1200 Subject: [cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2 v0.1) Message-ID: <4A3EDE2F.6080902@auckland.ac.nz> Greetings, Team CellML is pleased to announce the immediate availability of the new CellML Model Repository running on PMR2 v0.1 at http://models.cellml.org/. All CellML models which were hosted within PMR1 (which was at http://www.cellml.org/models) have been migrated into PMR2. In addition to the data migration, every URI within PMR1 will remain valid and will redirect to their respective URI in PMR2 (i.e. all links in existing publications will not be broken). Also, PMR2, or Physiome Model Repository 2 v0.1 has been released. This is a complete rewrite compared to PMR1, and will now handle CellML 1.1 imports and full version control has been implemented using Mercurial. If you would like access to the entire history of any particular model in PMR2, please install a Mercurial client (Download link at http://www.selenic.com/mercurial/wiki/BinaryPackages). Please report any bugs or issues you find in PMR2 at the Physiome Tracker (https://tracker.physiomeproject.org/), to this mailing list, or directly to tommy.yu at auckland.ac.nz. Kind Regards, Tommy. From alan.garny at dpag.ox.ac.uk Mon Jun 22 21:29:55 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Mon, 22 Jun 2009 10:29:55 +0100 Subject: [cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2 v0.1) In-Reply-To: <4A3EDE2F.6080902@auckland.ac.nz> References: <4A3EDE2F.6080902@auckland.ac.nz> Message-ID: <003801c9f31c$011cfa80$0356ef80$@garny@dpag.ox.ac.uk> Hi Tommy, Well done on getting PMR2 out into the open! A few things: - Is there any documentation/tutorial that I could read so that I can learn more about the differences between PMR1 and PMR2, as well as learn the basics about PMR2 (e.g. what is an exposure?, what is a workspace?, what is Mercurial?)? - Full model listing: by clicking on the full model listing, I can see that 'only' the first 100 models are listed. Is there no way to really get the full listing? It might also be nice to have anchors that would allow us to go straight to the first model where the first author's name starts with an "A", "B", "C", etc. Also, though I like the list of categories of models in the homepage, I think it would be nice, in the full model listing, to have fields on which to sort the list. E.g. one could sort by name (as is currently the case), year, model type (i.e. the category mentioned on the front page), type with a given category (e.g. in cardiac electrophysiology, it could be ventricular, atrial, purkinje fibre, etc.). - Access a model via "Solve using OpenCell": I have PCEnv (not OpenCell, since it will only be called that as of the next official release) installed on my system (Windows XP) and clicked on the link, but all that did was to offer me to save the file (I have tried using both Opera and Firefox). I have just tried under Linux using Firefox, and same story. Otherwise, the URL contains "pcenv" while I would have expected "opencell", if anything... - Generation of procedural code for a particular model: it might be useful to mention the version of the CellML API that was used to generate the code? In the past, people have often assumed that PMR1 used the latest version when I understand it wasn't the case. It might now be the case with PMR2 (I don't know!), but in any case it would help to know the version used. Anyway, those are just a few quick thoughts... for having had a very quick look at PMR2... :) Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Tommy Yu > Sent: 22 June 2009 02:28 > To: CellML Discussion Group > Subject: [cellml-discussion] Announcement of the new CellML Model > Repository (and release of PMR2 v0.1) > > Greetings, > > Team CellML is pleased to announce the immediate availability of the new > CellML Model Repository running on PMR2 v0.1 at http://models.cellml.org/. > All CellML models which were hosted within PMR1 (which was at > http://www.cellml.org/models) have been migrated into PMR2. In addition to > the data migration, every URI within PMR1 will remain valid and will > redirect to their respective URI in PMR2 (i.e. all links in existing > publications will not be broken). > > Also, PMR2, or Physiome Model Repository 2 v0.1 has been released. This is > a complete rewrite compared to PMR1, and will now handle CellML 1.1 imports > and full version control has been implemented using Mercurial. If you > would like access to the entire history of any particular model in PMR2, > please install a Mercurial client (Download link at > http://www.selenic.com/mercurial/wiki/BinaryPackages). > > Please report any bugs or issues you find in PMR2 at the Physiome Tracker > (https://tracker.physiomeproject.org/), to this mailing list, or directly > to tommy.yu at auckland.ac.nz. > > Kind Regards, > Tommy. > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From tommy.yu at auckland.ac.nz Tue Jun 23 11:39:33 2009 From: tommy.yu at auckland.ac.nz (Tommy Yu) Date: Tue, 23 Jun 2009 11:39:33 +1200 Subject: [cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2 v0.1) In-Reply-To: <003801c9f31c$011cfa80$0356ef80$@garny@dpag.ox.ac.uk> References: <4A3EDE2F.6080902@auckland.ac.nz> <003801c9f31c$011cfa80$0356ef80$@garny@dpag.ox.ac.uk> Message-ID: <4A401635.5040400@auckland.ac.nz> Alan Garny wrote: > Hi Tommy, > > Well done on getting PMR2 out into the open! > Hi Alan, Thank you. > A few things: > - Is there any documentation/tutorial that I could read so that I can learn > more about the differences between PMR1 and PMR2, as well as learn the > basics about PMR2 (e.g. what is an exposure?, what is a workspace?, what is > Mercurial?)? It will be written soon. > - Full model listing: by clicking on the full model listing, I can see that > 'only' the first 100 models are listed. Is there no way to really get the > full listing? It might also be nice to have anchors that would allow us to The 100 model listing limit was put into place to decrease loading time. If you would like to see the full listing, you will need to login, then select 'folder contents', and scroll to the bottom, select 'Show all items'. You can sort by name or other fields that are present. > go straight to the first model where the first author's name starts with an > "A", "B", "C", etc. Also, though I like the list of categories of models in > the homepage, I think it would be nice, in the full model listing, to have > fields on which to sort the list. E.g. one could sort by name (as is > currently the case), year, model type (i.e. the category mentioned on the > front page), type with a given category (e.g. in cardiac electrophysiology, > it could be ventricular, atrial, purkinje fibre, etc.). Sorting by category will be difficult because most models have multiple categories (which are actually keywords associated with the model). > - Access a model via "Solve using OpenCell": I have PCEnv (not OpenCell, > since it will only be called that as of the next official release) installed > on my system (Windows XP) and clicked on the link, but all that did was to > offer me to save the file (I have tried using both Opera and Firefox). I > have just tried under Linux using Firefox, and same story. Otherwise, the > URL contains "pcenv" while I would have expected "opencell", if anything... You need to manually get your browser to associate that link with PCEnv/OpenCell, as it is sent via a custom mime-type. > - Generation of procedural code for a particular model: it might be useful > to mention the version of the CellML API that was used to generate the code? > In the past, people have often assumed that PMR1 used the latest version > when I understand it wasn't the case. It might now be the case with PMR2 (I > don't know!), but in any case it would help to know the version used. > Yes, good point. Currently CellML API 1.6 is used to generate the code. > Anyway, those are just a few quick thoughts... for having had a very quick > look at PMR2... :) > Thank you for your observations. Regards, Tommy. > Alan > >> -----Original Message----- >> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- >> bounces at cellml.org] On Behalf Of Tommy Yu >> Sent: 22 June 2009 02:28 >> To: CellML Discussion Group >> Subject: [cellml-discussion] Announcement of the new CellML Model >> Repository (and release of PMR2 v0.1) >> >> Greetings, >> >> Team CellML is pleased to announce the immediate availability of the new >> CellML Model Repository running on PMR2 v0.1 at http://models.cellml.org/. >> All CellML models which were hosted within PMR1 (which was at >> http://www.cellml.org/models) have been migrated into PMR2. In addition > to >> the data migration, every URI within PMR1 will remain valid and will >> redirect to their respective URI in PMR2 (i.e. all links in existing >> publications will not be broken). >> >> Also, PMR2, or Physiome Model Repository 2 v0.1 has been released. This > is >> a complete rewrite compared to PMR1, and will now handle CellML 1.1 > imports >> and full version control has been implemented using Mercurial. If you >> would like access to the entire history of any particular model in PMR2, >> please install a Mercurial client (Download link at >> http://www.selenic.com/mercurial/wiki/BinaryPackages). >> >> Please report any bugs or issues you find in PMR2 at the Physiome Tracker >> (https://tracker.physiomeproject.org/), to this mailing list, or directly >> to tommy.yu at auckland.ac.nz. >> >> Kind Regards, >> Tommy. >> _______________________________________________ >> 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 From dj.cowan at auckland.ac.nz Tue Jun 30 14:15:33 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Tue, 30 Jun 2009 14:15:33 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-06-24 Message-ID: <4A497545.4080104@auckland.ac.nz> Firstly, I apologize for the delay this week! I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-cellml-meeting-minutes-2009-06-24 Dougal