From j.marsh at auckland.ac.nz Mon Aug 3 09:54:48 2009 From: j.marsh at auckland.ac.nz (Justin Marsh) Date: Mon, 03 Aug 2009 09:54:48 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Message-ID: <4A760B28.2000808@auckland.ac.nz> Dear CellML community, The ABI CellML team meeting minutes for 2009-07-22 are belatedly available at: http://www.cellml.org/community/meeting/minutes/2009/07.22 Kind Regards, Justin Marsh. From p.hunter at auckland.ac.nz Mon Aug 3 17:29:09 2009 From: p.hunter at auckland.ac.nz (Peter Hunter) Date: Mon, 3 Aug 2009 17:29:09 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Message-ID: Hi Justin, Some agenda items for the next CellML mtg: 1. I noticed a bug on the new website where the 'home page' reverts to the models top page instead of the CellML home page. 2. A plea from users for implementation of more session files. In particular the Iribe et al model needs to be setup for OpenCell. 3. Has the implementation of the SBML API been discussed for OpenCell? 4. A number of comments from people who attended the IUPS workshop about the great job you guys did. Cheers, Peter -------------------------- Sent using BlackBerry ----- Original Message ----- From: cellml-discussion-bounces at cellml.org To: CellML Discussion List Sent: Mon Aug 03 09:54:48 2009 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Dear CellML community, The ABI CellML team meeting minutes for 2009-07-22 are belatedly available at: http://www.cellml.org/community/meeting/minutes/2009/07.22 Kind Regards, Justin Marsh. _______________________________________________ cellml-discussion mailing list cellml-discussion at cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion From c.lloyd at auckland.ac.nz Mon Aug 3 19:59:13 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Mon, 3 Aug 2009 19:59:13 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 In-Reply-To: References: Message-ID: <58297DAD-539F-427A-A69F-9EC7BF6B4D4F@auckland.ac.nz> Hi Peter With regards to item 2, according to the model status comment James has already created a PCEnv session file for Iribe et al: http://models.cellml.org/exposure/62724a9b65d81c479e484513aa32e9d3 It looks like this already has a session file - but without an embedded SVG diagram (I make that comment based on the fact there is no image for this model in the repository). Pulasthi/Linda - would you please be able to create a diagram for this model, load it into the repository in the correct folder, and update the documentation to link to it please? The paper is attached. Unfortunately there is no schematic in the paper - it's going to be a case of creating one from scratch based on the list of currents, etc. in the appendix. Andre and James will be back from Japan next week and they will be able to check your diagram for you (sorry to volunteer you Andre and James in your absence - but I thought you wouldn't mind!!!) Also, related to number 2 in general - Peter, I know that James is reluctant to create a whole lot of OpenCell session files right now - there is a valid reason for this - either relating to OpenCell or PMR2 - he can update you himself. But creating one-off session files that have been requested, for the time being, is fine. Best wishes Catherine -------------- next part -------------- A non-text attachment was scrubbed... Name: Iribe_2006.pdf Type: application/pdf Size: 765054 bytes Desc: not available URL: -------------- next part -------------- On 3/08/2009, at 5:29 PM, Peter Hunter wrote: > Hi Justin, > > Some agenda items for the next CellML mtg: > 1. I noticed a bug on the new website where the 'home page' reverts > to the models top page instead of the CellML home page. > 2. A plea from users for implementation of more session files. In > particular the Iribe et al model needs to be setup for OpenCell. > 3. Has the implementation of the SBML API been discussed for OpenCell? > 4. A number of comments from people who attended the IUPS workshop > about the great job you guys did. > > Cheers, > Peter > -------------------------- > Sent using BlackBerry > > > ----- Original Message ----- > From: cellml-discussion-bounces at cellml.org > > To: CellML Discussion List > Sent: Mon Aug 03 09:54:48 2009 > Subject: [cellml-discussion] ABI CellML team meeting minutes > 2009-07-22 > > Dear CellML community, > > The ABI CellML team meeting minutes for 2009-07-22 are belatedly > available at: > http://www.cellml.org/community/meeting/minutes/2009/07.22 > > Kind Regards, > Justin Marsh. > _______________________________________________ > 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 p.hunter at auckland.ac.nz Mon Aug 3 21:01:29 2009 From: p.hunter at auckland.ac.nz (Peter Hunter) Date: Mon, 3 Aug 2009 21:01:29 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Message-ID: Hi Catherine, The link on the Iribe model page did let me load OpenCell with the session file, but gave error messages. I take your point re session files in general - we do need to make it easier to create them as the difference between models with (including SVG files) & without them is day & night for new users. Cheers, Peter -------------------------- Sent using BlackBerry ----- Original Message ----- From: cellml-discussion-bounces at cellml.org To: CellML Discussion List Cc: lfen034 lfen034 ; Pulasthi Mithraratne Sent: Mon Aug 03 19:59:13 2009 Subject: Re: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Hi Peter With regards to item 2, according to the model status comment James has already created a PCEnv session file for Iribe et al: http://models.cellml.org/exposure/62724a9b65d81c479e484513aa32e9d3 It looks like this already has a session file - but without an embedded SVG diagram (I make that comment based on the fact there is no image for this model in the repository). Pulasthi/Linda - would you please be able to create a diagram for this model, load it into the repository in the correct folder, and update the documentation to link to it please? The paper is attached. Unfortunately there is no schematic in the paper - it's going to be a case of creating one from scratch based on the list of currents, etc. in the appendix. Andre and James will be back from Japan next week and they will be able to check your diagram for you (sorry to volunteer you Andre and James in your absence - but I thought you wouldn't mind!!!) Also, related to number 2 in general - Peter, I know that James is reluctant to create a whole lot of OpenCell session files right now - there is a valid reason for this - either relating to OpenCell or PMR2 - he can update you himself. But creating one-off session files that have been requested, for the time being, is fine. Best wishes Catherine From dj.cowan at auckland.ac.nz Mon Aug 10 11:17:06 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Mon, 10 Aug 2009 11:17:06 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-08-05 Message-ID: <4A7F58F2.7020000@auckland.ac.nz> I have put the minutes from last Wednesday's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/08.05 Dougal __________ Information from ESET Smart Security, version of virus signature database 4320 (20090809) __________ The message was checked by ESET Smart Security. http://www.eset.com From dj.cowan at auckland.ac.nz Mon Aug 17 08:30:27 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Mon, 17 Aug 2009 08:30:27 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-08-12 Message-ID: <4A886C63.8010500@auckland.ac.nz> I have put the minutes from last Wednesday's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/08.12 Dougal __________ Information from ESET Smart Security, version of virus signature database 4340 (20090816) __________ The message was checked by ESET Smart Security. http://www.eset.com From j.lawson at auckland.ac.nz Mon Aug 17 18:16:48 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 17 Aug 2009 18:16:48 +1200 Subject: [cellml-discussion] CellML and cmgui tutorials Message-ID: <4A88F5D0.5070808@auckland.ac.nz> Dear all, A contingent of the CellML group recently attended the IUPS2009 meeting in Kyoto, where we hosted a workshop-style tutorial on CellML (as well as cmgui*). The resources for the CellML tutorial are available at http://www.cellml.org/community/iups2009. The tutorial was primarily written by Andre Nickerson, and serves as an introduction to the modularity, reuse, and exchange features that are available when developing models in a CellML 1.1 framework. There are two parts to the tutorial. The first is a detailed guide to the modification of an existing "published" model which is available on the internet. The example used is modifying the original Hodgkin & Huxley 1952 squid axon model to produce action potentials closer to those found in the Noble 1962 model of cardiac cells. The second part applies the same techniques to a more realistic scenario, namely that of modifying the stimulus protocol being applied to a human cardiac myocyte model. The OpenCell software package is used in this tutorial. If you have any questions or feedback, please contact myself or any member of the CellML group (see http://www.cellml.org/community/team for contact details.) Thanks very much, I hope you find this useful, and please feel free to forward it to anyone you know whom it might interest. Kind regards, James Lawson *The cmgui (http://www.cmiss.org/cmgui) introductory tutorial is available from Dougal Cowan - email him at dj.cowan at auckland.ac.nz if you'd like a copy. -------------- 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 Mon Aug 31 14:07:32 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 31 Aug 2009 14:07:32 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-09-26 Message-ID: <4A9B3064.8090808@auckland.ac.nz> Dear CellML community, The minutes for last week's Auckland CellML team meeting are now up at: http://www.cellml.org/community/meeting/minutes/08.26 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: