Re: [cellml-discussion] 'Model' has pure virtual functions

2009-07-24 Thread Lucian Smith
* Andrew Miller ak.mil...@auckland.ac.nz [2009-07-24 01:55] writes: Model is an interface, not a concrete class. The way the API works is that you always work with interfaces, but you never directly create them directly. Instead, you need to use one of the bootstrap methods to get access

[cellml-discussion] The CellML library basics

2009-07-27 Thread Lucian Smith
(Thanks for the link to the CellML2C source; that was very helpful.) (Also, I'm more than willing to move this to some other forum if it's better suited there.) So, I feel like I'm missing something pretty fundamental here, because I can't figure out how to set the name of a model. The

Re: [cellml-discussion] The CellML library basics

2009-07-27 Thread Lucian Smith
* Justin Marsh j.ma...@auckland.ac.nz [2009-07-28 00:31] writes: Hi Lucian, The basic C++ should have two functions for each member attribute, named after the attribute; one with no arguments, which returns the value of the attribute, and one with one argument which sets the value of

[cellml-discussion] Modules and Components

2009-07-29 Thread Lucian Smith
the issue will be raised again in the future.) Thanks! -Lucian Smith ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

Re: [cellml-discussion] Lucian's questions

2010-02-23 Thread Lucian Smith
anyone else would like to comment. I can at least put the answers I got; here they are: Begin forwarded message: From: Lucian Smith lpsm...@spod-central.org -Currently, I must run my program from the directory with the 'components/' subdirectory. Is there a way I can set things up

[cellml-discussion] Leftover thoughts from the CellML workshop

2010-02-26 Thread Lucian Smith
Thanks to all of you who were at the workshop for letting me attend remotely. I found it quite valuable, and hope you didn't mind me asking you all to repeat the questions too often. And special thanks to Catherine for being the driving force behind getting it all set up! I had a couple

Re: [cellml-discussion] Leftover thoughts from the CellML workshop

2010-03-16 Thread Lucian Smith
(Whoops, I meant to send this to the list, but replied directly to Poul instead...) - Forwarded message from Lucian Smith lpsm...@spod-central.org - A couple follow-up thoughts: * Poul Nielsen p.niel...@auckland.ac.nz [2010-03-11 03:28] writes: Dear Lucian Many thanks for your

[cellml-discussion] CellML models in Antimony format

2010-04-23 Thread Lucian Smith
Thanks to the help of many of you on this list, I now have a working CellML-to-Antimony translator, and have used it to translate all the models at models.cellml.org into the Antimony format. The results are at: http://antimony.sourceforge.net/antimony-cellml.html along with SBML versions of

Re: [cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]

2010-06-03 Thread Lucian Smith
My only comment is that lines 6 and 9 ('is it valid?' and 'is it simulatable?') are the ones I'd be looking at/for the most, so if those bit of the glyphs were emphasized or at least easy to pick out, that'd be great. -Lucian * Catherine Lloyd c.ll...@auckland.ac.nz [2010-06-03 13:27] writes:

Re: [cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]

2010-06-03 Thread Lucian Smith
* Catherine Lloyd c.ll...@auckland.ac.nz [2010-06-03 20:55] writes: Hi Lucian Adding to that, I'll emphasise again that this list forms the bare minimum and we will be happy to expand on the list in the future. validity and simulation could be two areas which we choose to expand on

Re: [cellml-discussion] ABI CellML Meeting Minutes, 8th December 2010

2010-12-09 Thread Lucian Smith
* Dougal Cowan dj.co...@auckland.ac.nz [2010-12-09 22:12] writes: I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2010/12.08 Woo, I made the minutes! Thanks, guys. For what it's worth, xulrunner is not actually the only problem I am

Re: [cellml-discussion] Unofficial draft CellML specification - backwards compatibility, type attributes on variables

2011-02-01 Thread Lucian Smith
* Andrew Miller ak.mil...@auckland.ac.nz [2011-02-02 03:27] writes: Hi all, I've just put up an unofficial draft CellML specification up at http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml to prototype what some of the new features could look

Re: [cellml-discussion] ABI CellML Meeting Minutes, 25th May 2011

2011-05-26 Thread Lucian Smith
For what it's worth, it's 'Darren', not 'Darryl' (the SBML 'distrib' package guy). -Lucian * Dougal Cowan dj.co...@auckland.ac.nz [2011-05-26 22:32] writes: I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2011/05.25 Cheers, Dougal

Re: [cellml-discussion] ABI CellML Meeting Minutes, 14th September 2011

2011-09-16 Thread Lucian Smith
I should also mention that I've used the Windows Visual Studio 10 SDK with no problems at all (well, with no errors--there are about 15 bajillion warnings, but no errors). This is a tremendous relief, so thanks! (Still haven't gotten back to check the Red Hat issues I had--will report back

[cellml-discussion] New release of Antimony v2.0 and v2.1-beta

2011-09-22 Thread Lucian Smith
) will probably require the development of a brand-new infix parser. If it does, we may consider donating this code to libsbml on the theory that others may find it useful as well. Watch this space! Who is to blame? Antimony was developed by Lucian Smith from

Re: [cellml-discussion] nested components in CellML

2011-10-21 Thread Lucian Smith
* Maxwell Neal mn...@u.washington.edu [2011-10-21 22:03] writes: Hi all, I was wondering - can CellML models have nested components? That is, are there instances where some model component is a component in another model component? Thanks, Yes--this is covered by the concept of

[cellml-discussion] Independent variables, and delay

2011-12-16 Thread Lucian Smith
A couple questions. One: is there a defined way in CellML to find the independent variables? The spec says (about 'initial_value'): This attribute provides a convenient means for specifying the value of a scalar real variable when all independent variables in the model have a value of

Re: [cellml-discussion] Improved CellML support in latest version of JSim

2011-12-19 Thread Lucian Smith
Thanks for the notice, Andre! I want to note that if anyone finds some aspect of their favorite model doesn't survive the new translation, be sure to email me, and I'll see what I can do. I downloaded 1055 models from the repository as my test bed for this project, and got 884 of them working

[cellml-discussion] (forw) JSim 2.06 released

2012-02-02 Thread Lucian Smith
...@auckland.ac.nz, Bart Jardine bar...@u.washington.edu, Gary Raymond ga...@u.washington.edu, Dr. James Bassingthwaighte j...@u.washington.edu, Lucian Smith lpsm...@u.washington.edu, Rebecca Rowe rebika...@gmail.com, Dash, Ranjan rd...@mcw.edu, Richard Ward ward

Re: [cellml-discussion] [sbml-distrib] New draft secondary specification: Uncertainty

2012-05-29 Thread Lucian Smith
* Andrew Miller ak.mil...@auckland.ac.nz [2012-05-29 10:52] writes: On 29/05/12 20:17, Michael Clerx wrote: Dear all, I'm glad to see uncertainty being taken into acount in cell models. Perhaps it would be worthwhile to add the scenario where no assumptions are made about the