From c.lloyd at auckland.ac.nz Mon Nov 2 09:33:32 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Mon, 2 Nov 2009 09:33:32 +1300 Subject: [cellml-discussion] Registration for the 2010 CellML workshop is now open Message-ID: <9A2F9D91-1572-485F-8669-4C0B5E3E32F4@auckland.ac.nz> If you are interested in attending the 2010 CellMl workshop registration is now open. The registration form and more information about the event can be found on the CellML website: http://www.cellml.org/community/events/workshop/2010 Best wishes Catherine From dj.cowan at auckland.ac.nz Thu Nov 5 13:38:28 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 05 Nov 2009 13:38:28 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-11-04 Message-ID: <4AF21E84.2000503@auckland.ac.nz> I have put the minutes from yesterday's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/11.04 Dougal __________ Information from ESET Smart Security, version of virus signature database 4574 (20091104) __________ The message was checked by ESET Smart Security. http://www.eset.com From hans.ekkehard.plesser at umb.no Fri Nov 6 22:14:41 2009 From: hans.ekkehard.plesser at umb.no (Dr. Hans Ekkehard Plesser) Date: Fri, 6 Nov 2009 10:14:41 +0100 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: <4AF3E901.8070100@umb.no> 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" >>> 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 r.britten at auckland.ac.nz Mon Nov 9 16:36:24 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Mon, 9 Nov 2009 16:36:24 +1300 Subject: [cellml-discussion] Using CellML for simplified neuron models? (Alan Garny) In-Reply-To: <4AF3E901.8070100@umb.no> References: <4A27C333.9090102@umb.no> <1D70655A-C23B-4959-8D83-ADB2E523F925@auckland.ac.nz> <4AF3E901.8070100@umb.no> Message-ID: <004501ca60ed$cff73200$6fe59600$@britten@auckland.ac.nz> 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: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] 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" > >>> 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 > > > > _______________________________________________ > > 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 > _______________________________________________ > 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 Nov 13 07:37:53 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 13 Nov 2009 07:37:53 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-11-11 Message-ID: <4AFC5601.7060309@auckland.ac.nz> I have put the minutes from this Wednesday's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/11.11 Dougal From j.lawson at auckland.ac.nz Thu Nov 19 13:08:33 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Thu, 19 Nov 2009 13:08:33 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 Message-ID: <4B048C81.9000805@auckland.ac.nz> Dear all, The minutes for this week's ABI CellML team meeting are now available at: http://www.cellml.org/community/meeting/minutes/2009/11.18 Kind regards, James -------------- 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 Thu Nov 19 23:28:44 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 19 Nov 2009 10:28:44 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 In-Reply-To: <4B048C81.9000805@auckland.ac.nz> References: <4B048C81.9000805@auckland.ac.nz> Message-ID: <001c01ca6903$1265a4b0$3730ee10$@garny@dpag.ox.ac.uk> Dear all, First, thanks to the Auckland team for sending the minutes within 24 hours. I, personally, certainly very much appreciate it! Second, a couple of comments regarding the minutes: - Point 3.5 ("It was noted that the syntax is slightly different from the COR language"): it's true that the syntax of the "COR language" in OpenCell is slightly different to that in COR itself. It (unfortunately?) had to be done for several reasons, e.g. the use of piecewise statements in OpenCell is broader than in COR (hence the need for a rather different syntax indeed!), OpenCell (through the CellML API) supports CellML 1.1 while COR doesn't, OpenCell allows for most elements to have parameters associated with them (class, style, id, xref and href), something that COR doesn't. At the end of the day, it is worth remembering that OpenCell aims at supporting every tiny aspect of the CellML language while COR is a bit more loose in that respect. There are clearly advantages and disadvantages to both, e.g. OpenCell can really handle any CellML model while the "COR language" in COR is somewhat simpler than that in OpenCell. - Point 5.1 ("Dougal has put up a page with CellML logos in various sizees and formats for publication purposes "): apart from a type ("sizes" rather than "sizees"), I noticed that if you click on the CellML logos link (http://www.cellml.org/community/about/cellmllogos), you do get a page with the logos (a welcome addition by the way!), the "Community" tab is highlighted while I believe the "About CellML" one should be. Also, if I go one level up (i.e. to the "About CellML" page), I can't see any mention of the CellML Logos page. I tried the different sub-pages (i.e. "Contact us", "Current development", etc.), but to no avail. So, this makes me wonder whether all the different web pages on the CellML website are linked to in some way or another, as opposed to having to know the exact link to get to a particular page (as seems to be the case with the logos page). Best regards, Alan. > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of James Lawson > Sent: 19 November 2009 00:09 > To: CellML Discussion List > Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 > > Dear all, > > The minutes for this week's ABI CellML team meeting are now available > at: > http://www.cellml.org/community/meeting/minutes/2009/11.18 > > Kind regards, > James From dj.cowan at auckland.ac.nz Fri Nov 20 07:17:55 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 20 Nov 2009 07:17:55 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 In-Reply-To: <001c01ca6903$1265a4b0$3730ee10$@garny@dpag.ox.ac.uk> References: <4B048C81.9000805@auckland.ac.nz> <001c01ca6903$1265a4b0$3730ee10$@garny@dpag.ox.ac.uk> Message-ID: <4B058BD3.7020108@auckland.ac.nz> Alan Garny wrote: > - Point 5.1 ("Dougal has put up a page with CellML logos in various sizees > and formats for publication purposes "): apart from a type ("sizes" rather > than "sizees"), I noticed that if you click on the CellML logos link > (http://www.cellml.org/community/about/cellmllogos), you do get a page with > the logos (a welcome addition by the way!), the "Community" tab is > highlighted while I believe the "About CellML" one should be. Also, if I go > one level up (i.e. to the "About CellML" page), I can't see any mention of > the CellML Logos page. I tried the different sub-pages (i.e. "Contact us", > "Current development", etc.), but to no avail. So, this makes me wonder > whether all the different web pages on the CellML website are linked to in > some way or another, as opposed to having to know the exact link to get to a > particular page (as seems to be the case with the logos page). I suspect that the word "community" has been spuriously added to the URL in the minutes. Unfortunately Plone does strange automatic things with incorrect URLs which mean that they work. Try the following sequence to get to the logos: * Go to www.cellml.org * Navigate to the "About" section through the nav-bar at the top * Click on "CellML logos" in the "Navigation" sidebar This should get you to the logos page with the About tab highlighted. I'm not sure that the logos page needs to be more visible than this - I suspect most people looking for logos will use the search function. But one certainly should be able to easily navigate to the page without using search. Dougal __________ Information from ESET Smart Security, version of virus signature database 4622 (20091119) __________ The message was checked by ESET Smart Security. http://www.eset.com From alan.garny at dpag.ox.ac.uk Fri Nov 20 07:27:19 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 19 Nov 2009 18:27:19 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 In-Reply-To: <4B058BD3.7020108@auckland.ac.nz> References: <4B048C81.9000805@auckland.ac.nz> <001c01ca6903$1265a4b0$3730ee10$@garny@dpag.ox.ac.uk> <4B058BD3.7020108@auckland.ac.nz> Message-ID: <000b01ca6945$ed877d60$c8967820$@dpag.ox.ac.uk> > > - Point 5.1 ("Dougal has put up a page with CellML logos in various > > sizees and formats for publication purposes "): apart from a type > > ("sizes" rather than "sizees"), I noticed that if you click on the > > CellML logos link (http://www.cellml.org/community/about/cellmllogos), > > you do get a page with the logos (a welcome addition by the way!), the > > "Community" tab is highlighted while I believe the "About CellML" one > > should be. Also, if I go one level up (i.e. to the "About CellML" > > page), I can't see any mention of the CellML Logos page. I tried the > > different sub-pages (i.e. "Contact us", "Current development", etc.), > > but to no avail. So, this makes me wonder whether all the different > > web pages on the CellML website are linked to in some way or another, > > as opposed to having to know the exact link to get to a particular page (as > seems to be the case with the logos page). > > I suspect that the word "community" has been spuriously added to the URL > in the minutes. Unfortunately Plone does strange automatic things with > incorrect URLs which mean that they work. Try the following sequence to get > to the logos: > > * Go to www.cellml.org > * Navigate to the "About" section through the nav-bar at the top > * Click on "CellML logos" in the "Navigation" sidebar > > This should get you to the logos page with the About tab highlighted. > I'm not sure that the logos page needs to be more visible than this - I suspect > most people looking for logos will use the search function. But one certainly > should be able to easily navigate to the page without using search. Hi Dougal, Thanks for the steps. It did get me to the right place, so that's all good and sufficient indeed. I certainly didn't notice the Plone redirection. As for the "Navigation" sidebar, I had noticed it, but somehow assumed that it was there to remind me of recently visited pages (I guess that the word "Navigation" is what confused me here), and since I had indeed recently visited logos... Alan From dj.cowan at auckland.ac.nz Fri Nov 20 07:43:12 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 20 Nov 2009 07:43:12 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 20091118 In-Reply-To: <000b01ca6945$ed877d60$c8967820$@dpag.ox.ac.uk> References: <4B048C81.9000805@auckland.ac.nz> <001c01ca6903$1265a4b0$3730ee10$@garny@dpag.ox.ac.uk> <4B058BD3.7020108@auckland.ac.nz> <000b01ca6945$ed877d60$c8967820$@dpag.ox.ac.uk> Message-ID: <4B0591C0.7030405@auckland.ac.nz> Alan Garny wrote: > Thanks for the steps. It did get me to the right place, so that's all good > and sufficient indeed. > > I certainly didn't notice the Plone redirection. As for the "Navigation" > sidebar, I had noticed it, but somehow assumed that it was there to remind > me of recently visited pages (I guess that the word "Navigation" is what > confused me here), and since I had indeed recently visited logos... The Navigation sidebar is a per-section navigational element that provides "random-access" to items within the current section. This might not be obvious, and could perhaps do with some kind of clarification. As for Plone redirects, one can really get quite silly with them. For example; http://www.cellml.org/tools/tools/index/index/getting-started/specifications/index/community/tools/about/cellmllogos I feel this is actually quite unhelpful, and it breaks the navbar, as we have seen! Comments on the usability of the site are always welcome, as we are still actively working on it and we do want to make it as useful as possible. Dougal __________ Information from ESET Smart Security, version of virus signature database 4622 (20091119) __________ The message was checked by ESET Smart Security. http://www.eset.com From dj.cowan at auckland.ac.nz Fri Nov 27 07:30:11 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 27 Nov 2009 07:30:11 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-11-25 Message-ID: <4B0EC933.6090904@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/11.25 Dougal From alan.garny at dpag.ox.ac.uk Fri Nov 27 23:46:16 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Fri, 27 Nov 2009 10:46:16 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-11-25 In-Reply-To: <4B0EC933.6090904@auckland.ac.nz> References: <4B0EC933.6090904@auckland.ac.nz> Message-ID: <000301ca6f4e$d9716520$8c542f60$@dpag.ox.ac.uk> Hi, A comment about item #1 of this week's agenda (terms of use for CellML models and associated content hosted on models.cellml.org). I don't know enough about licensing to suggest one over another. The only thing I do know, however, is that it is important to ensure that the license that is to be chosen doesn't come under the law of a particular country, state, etc. and/or doesn't conflict with the law under which someone's University comes. The reason I am saying this is that for COR, I was at the time told by OSS Watch (an Open Source organisation here in the UK; www.oss-watch.ac.uk) that the best license for COR would be MPL 1.1. However, that license is governed by Californian law and because of that the University didn't agree to COR being released under MPL 1.1 (since the University comes under English law). The University offered me another license, but it was so restrictive (for the end user mainly and me a bit) that, in the end, I had no choice but to decline the offer. Eventually, all parties involved (University, OSS and myself) agreed that the best course of action was for me to release the executable and give the source code only to those who would request it from me. In other words, the University is not responsible for anything, and this is the reason COR is not and never will be open source (not that it matters now!). Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dougal Cowan > Sent: 26 November 2009 18:30 > To: cellml-discussion at cellml.org > Subject: [cellml-discussion] ABI CellML meeting minutes 2009-11-25 > > I have put the minutes from this week's meeting up at: > > http://www.cellml.org/community/meeting/minutes/2009/11.25 > > > Dougal > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: