From dj.cowan at auckland.ac.nz Thu Apr 2 10:36:15 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 02 Apr 2009 09:36:15 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-04-01 Message-ID: <20090402093615.6zdp82uhw480444o@webmail.bioeng.auckland.ac.nz> I have put the minutes from yesterday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-01 Dougal ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From c.lloyd at auckland.ac.nz Fri Apr 3 14:41:16 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Fri, 3 Apr 2009 14:41:16 +1300 Subject: [cellml-discussion] Friendfeed for CellML "et al." Workshop Message-ID: Dear All Just to inform you that a friendfeed room for the CellML SBGN SBO BioPAX MIASE Workshop (5th-9th April) has been created: http://friendfeed.com/rooms/cellml-sbgn-sbo-biopax-miase-2009. Anyone who is attending the meeting is welcome to contribute their thoughts - and for those of you who are unable to be there in person, we hope that this will allow you to follow the discussions. Thank you Abhishek!!! Best wishes Catherine -------------- next part -------------- An HTML attachment was scrubbed... URL: From dj.cowan at auckland.ac.nz Fri Apr 17 07:05:57 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 17 Apr 2009 07:05:57 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-04-15 Message-ID: <20090417070557.yvxybwg5c4sgw8gg@webmail.bioeng.auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-15 Dougal ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ak.miller at auckland.ac.nz Wed Apr 22 12:19:58 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 22 Apr 2009 12:19:58 +1200 Subject: [cellml-discussion] Using a functional programming language to express models Message-ID: <49EE62AE.3090700@auckland.ac.nz> Hi all, I have created a tracker item to discuss the possibility of using a functional programming language to express models. Please see my description of how it could be done, add any comments you have on the idea there. Best wishes, Andrew From alan.garny at dpag.ox.ac.uk Wed Apr 22 12:21:28 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Wed, 22 Apr 2009 12:21:28 +1200 Subject: [cellml-discussion] Using a functional programming language to express models In-Reply-To: <49EE62AE.3090700@auckland.ac.nz> References: <49EE62AE.3090700@auckland.ac.nz> Message-ID: <00fe01c9c2e0$4de78090$e9b681b0$@garny@dpag.ox.ac.uk> What's the tracker item number? A link would be even better, Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Andrew Miller > Sent: 22 April 2009 12:20 > To: For those interested in contributing to the development of CellML. > Subject: [cellml-discussion] Using a functional programming language to > express models > > Hi all, > > I have created a tracker item to discuss the possibility of using a > functional programming language to express models. Please see my > description of how it could be done, add any comments you have on the > idea there. > > Best wishes, > Andrew > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From ak.miller at auckland.ac.nz Wed Apr 22 12:34:11 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 22 Apr 2009 12:34:11 +1200 Subject: [cellml-discussion] Using a functional programming language to express models In-Reply-To: <49EE62AE.3090700@auckland.ac.nz> References: <49EE62AE.3090700@auckland.ac.nz> Message-ID: <49EE6603.80606@auckland.ac.nz> Andrew Miller wrote: > Hi all, > > I have created a tracker item to discuss the possibility of using a > functional programming language to express models. Please see my > description of how it could be done, add any comments you have on the > idea there. My apologies, I missed out the tracker item link. The relevant tracker item is tracker item 1727, at https://tracker.physiomeproject.org/show_bug.cgi?id=1727 > > Best wishes, > Andrew > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From ak.miller at auckland.ac.nz Wed Apr 22 13:07:26 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 22 Apr 2009 13:07:26 +1200 Subject: [cellml-discussion] Proposal to re-structure CellML mailing lists Message-ID: <49EE6DCE.60106@auckland.ac.nz> Hi all, I have created a tracker item for the proposal to restructure the CellML mailing lists, as the current structure of team and cellml-discussion (originally intended to avoid conflating technical and non-technical issues on the same list) isn't necessarily working as well as we would hope it would, as discussed in the tracker item. The new proposal, to replace team and cellml-discussion with 4 lists is discussed at: https://tracker.physiomeproject.org/show_bug.cgi?id=1728 Please add any comments you may have to that tracker item. Best wishes, Andrew From dj.cowan at auckland.ac.nz Fri Apr 24 09:14:10 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 24 Apr 2009 09:14:10 +1200 Subject: [cellml-discussion] ABI Meeting minutes 2009-04-22 Message-ID: <20090424091410.ncz9htfa1c808kog@webmail.bioeng.auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-22/ Dougal ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From alan.garny at dpag.ox.ac.uk Fri Apr 24 17:03:06 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Fri, 24 Apr 2009 17:03:06 +1200 Subject: [cellml-discussion] CellML - MathML e-notation issue Message-ID: <000901c9c499$f6ea7250$e4bf56f0$@garny@dpag.ox.ac.uk> Dear all, Quick Summary: The current CellML Repository uses incorrect MathML for e-notation. This will be repaired across the entire repository when the models are migrated over to PMR2 (the new version of the repository) by the end of May. CellML software tool developers may, therefore, need to modify their software to handle the correct notation. Details: At our latest CellML meeting (of which the minutes can be found at http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-22/), we discussed an issue that we believe should be of direct interest to you, developers of CellML tools (http://www.cellml.org/tools/). The issue is related to the MathML e-notation, which none of the models in the CellML repository (http://www.cellml.org/models/) currently represent correctly. Indeed, say that you have a model that uses 1.23e45 as a constant. At the moment, this constant will be represented as follows: 1.23e45 However, according to the MathML specifications (http://www.w3.org/TR/MathML2/chapter4.html#contm.typeattrib), this is plain wrong and should, instead, be represented as: 1.2345 This is clearly an oversight on our end and we do apologise for it. This must, however, be fixed and we do intend to do it as part of the staging of PMR2 (the next version of the CellML model repository - it will support CellML 1.1, version control, etc.; for more information, please see the presentation given by Tommy Yu at the recent CellML SBGN SBO BioPAX MIASE Workshop: http://www.cellml.org/workshop/workshop2009/presentations/yu_pmr2.pdf and http://www.cellml.org/workshop/workshop2009/audio-files/2009-04-06-tommy.mp3 for the audio). So, this message should be taken as an advance warning that by the end of May 2009, i.e. the time by which PMR2 will be up and running, all of the models in PMR2 will use the correct MathML e-notation formulation. In this context, we would like to suggest that you update and release an updated version of your respective CellML tool(s), and this prior to the staging of PMR2. Sorry again for the inconvenience, but we believe that this should, hopefully, not require too much work on your side. Best regards, Alan. PS: sorry if you have received this more than once, but I wanted to make sure that I didn't miss anyone. Dr Alan Garny University of Oxford, Department of Physiology, Anatomy & Genetics Sherrington Building, Parks Road, Oxford, OX1 3PT, England http://noble.physiol.ox.ac.uk/people/agarny/ http://cor.physiol.ox.ac.uk/ Note: I am currently in New Zealand and will be back in Oxford on 27 April 2009 -------------- next part -------------- An HTML attachment was scrubbed... URL: