Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010
>From what I recall, the IDA docs actually suggest that you use a separate method (i.e. non-IDA) to get initial conditions, but I'll check through them, just to see if my recollection is correct. Can I suggest we please discuss this further on tracker item 2516 (https://tracker.physiomeproject.org/show_bug.cgi?id=2516). Regards, Randall > -Original Message- > From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- > boun...@cellml.org] On Behalf Of David Nickerson > Sent: Tuesday, 27 April 2010 8:52 a.m. > To: CellML Discussion List > Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 > > I think what Alan might be getting at, and something that I am also > concerned with, is that rather than letting the "solver do its job", > we are going down the route of replacing the well tested and supported > IDA initial condition solver with something that is perhaps better > suited to the types of models generally expressed in CellML. It would > be good to see the data which supports the decision to go down this > route as well as ensuring that CCGS and CIS can be used with the > default IDA initial condition solver if the user so chooses. > > > Cheers, > Andre. > > On Tue, Apr 27, 2010 at 8:16 AM, Randall Britten > wrote: > > From what I understand, this is exactly what Andrew is setting up. > > > > Regards, > > Randall > > > > On 26/04/2010, at 8:17 PM, "Alan Garny" wrote: > > > >> Then, the approach that I would personally take (and the one that I people > >> take when solving ODE models, though I accept things might be different > >> with > >> DAE models!) is to start from the original ICs and let the solver do its > >> job. Now, I imagine there might be cases where user changes to some of the > >> parameters are such that the original ICs might not be suitable at all? > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010
I think what Alan might be getting at, and something that I am also concerned with, is that rather than letting the "solver do its job", we are going down the route of replacing the well tested and supported IDA initial condition solver with something that is perhaps better suited to the types of models generally expressed in CellML. It would be good to see the data which supports the decision to go down this route as well as ensuring that CCGS and CIS can be used with the default IDA initial condition solver if the user so chooses. Cheers, Andre. On Tue, Apr 27, 2010 at 8:16 AM, Randall Britten wrote: > From what I understand, this is exactly what Andrew is setting up. > > Regards, > Randall > > On 26/04/2010, at 8:17 PM, "Alan Garny" wrote: > >> Then, the approach that I would personally take (and the one that I people >> take when solving ODE models, though I accept things might be different >> with >> DAE models!) is to start from the original ICs and let the solver do its >> job. Now, I imagine there might be cases where user changes to some of the >> parameters are such that the original ICs might not be suitable at all? ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010
From what I understand, this is exactly what Andrew is setting up. Regards, Randall On 26/04/2010, at 8:17 PM, "Alan Garny" wrote: Then, the approach that I would personally take (and the one that I people take when solving ODE models, though I accept things might be different with DAE models!) is to start from the original ICs and let the solver do its job. Now, I imagine there might be cases where user changes to some of the parameters are such that the original ICs might not be suitable at all? Alan -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Randall Britten Sent: 25 April 2010 22:54 To: 'CellML Discussion List' Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 Andrew pointed out some time ago that even if consistent IC's are provided by the model author, one of the things we often do with models is change some of the parameters, or re-use the models in a different context, in which case some assistance from the software in recalculating new consistent IC's is invaluable. Regards, Randall -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml- discussion- boun...@cellml.org] On Behalf Of Alan Garny Sent: Friday, 23 April 2010 11:43 p.m. To: 'CellML Discussion List' Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 But aren't or, rather, shouldn't ICs be provided by the model developer? Or is it the case that you want to be able to determine the ICs, should the model developer not have provided some? Then again, if no ICs have been provided, then this would be a shortcoming of the model, and rather than trying to determine some ICs, we should try to get the ICs from the model author. Just thinking 'aloud', so sorry if I am missing something obvious here (not least because I have never 'played' with DAEs myself). Alan -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Randall Britten Sent: 23 April 2010 12:35 To: CellML Discussion List Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 DAEs are a little more complex, it isn't always obvious which unknowns require initial conditions, or how to ensure ICs are consistent. Regards, Randall On 23/04/2010, at 8:50 PM, "Alan Garny" wrote: Sorry, one more (non-OpenCell) comment: - "... the biggest problem is using IDA's default solver for initial conditions..." -- What is exactly meant by solver for initial conditions? Do you mean that you are trying to use IDA to determine what the initial value of the state variables should (i.e. like those 99 guesses in the original OpenCell DAE solver?)? I would think/hope not (I thought we had 'agreed' to provide the initial conditions to the solver?). Alan -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Dougal Cowan Sent: 22 April 2010 21:19 To: CellML Discussion List Subject: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2010/04.21 Thanks, Dougal ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010
Hi Justin, > - I have not put up a binary version anywhere; I will in the next few days. Thanks, I am looking forward to giving it a try. > - I have not done development for the prototype outside of Linux. > Dependency management under Eclipse can be done in several ways; > supposedly using Maven2 or Ant and the respective plugins for Eclipse is > totally cross platform, but setting up Maven2 or Ant configuration files is > quite time consuming, especially as the dependant projects (jeuclid and > JFreechart) do not seem to have valid Ant or Maven2 configuration files. For > the purpose of the demo, I chose to do this in the 'Eclipse' > way, which it turns out is not really friendly with source control. > Importing a project with dependencies into an Eclipse workspace does not > work nicely unless you either use Maven2 or Ant, or bundle *all* of the jars > under your project, or have *all* of the jars have the same > *absolute* path under all machines, or already have 'projects' in that > workspace that deal with this in one of the ways above which your project is > dependant upon; the 'cascading project' pattern is quite common, but would > require putting the entire thing under version control. I am sure there is > another way that is actually workable (or that the Ant or Maven2 way is > workable) that I just do not know, but I have already exceeded a reasonable > fraction of the total time I had available on this particular problem. I don't see a problem with putting everything under version control (as you might have realised by now, I don't care too much about 'conventions'). In fact, it makes it much easier for anyone who would potentially be interested in contributing, since they wouldn't first have to install a bunch of dependencies before being able to compile the project. If you remember, this is what I did with Qt/C++, though mainly out of time constraint (since I wanted to quickly be able to test things on Windows, Linux and Mac OS X). > If we do > go ahead with using Scala, setting up a dependency handling system so that > this is not something anyone has to deal with again will be one of the first > things I want to do, as otherwise this system fails at one of our hard > requirements (that is, that other people can build and develop for OpenCell > 'easily'). Ideally, one should be able to build it with just the jdk, a scala > compiler, and something like Ant or Maven2. That would be ideal indeed. > - A vanilla Scala application is trivial to deploy; there is a particular jar you can > bundle your application with that allows it to run under the jvm. This bundle > has no native components. Eclipse RCP applications require a few more > platform specific jars bundled with them to run under the respective jvms, > but there is a specific archive available from eclipse.org (the Eclipse Delta > pack) which you just need to take the jars from. I have not attempted to > create a 'launcher' > (which is Eclipse speak for something that looks like a native > application) on any platform other than Linux; it worked under Linux at the > push of a button in Eclipse. I am currently working on a solution that will > work from the command line. Personally, I would first be interested in a Windows and Mac OS X solution. It would be good to be able to compare the different 'versions' of your mockup. Alan ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010
Then, the approach that I would personally take (and the one that I people take when solving ODE models, though I accept things might be different with DAE models!) is to start from the original ICs and let the solver do its job. Now, I imagine there might be cases where user changes to some of the parameters are such that the original ICs might not be suitable at all? Alan > -Original Message- > From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- > boun...@cellml.org] On Behalf Of Randall Britten > Sent: 25 April 2010 22:54 > To: 'CellML Discussion List' > Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010 > > Andrew pointed out some time ago that even if consistent IC's are provided > by the model author, one of the things we often do with models is change > some of the parameters, or re-use the models in a different context, in which > case some assistance from the software in recalculating new consistent IC's is > invaluable. > > Regards, > Randall > > > -Original Message- > > From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- > > boun...@cellml.org] On Behalf Of Alan Garny > > Sent: Friday, 23 April 2010 11:43 p.m. > > To: 'CellML Discussion List' > > Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st > > April > 2010 > > > > But aren't or, rather, shouldn't ICs be provided by the model developer? > Or > > is it the case that you want to be able to determine the ICs, should > > the model developer not have provided some? Then again, if no ICs have > > been provided, then this would be a shortcoming of the model, and > > rather than trying to determine some ICs, we should try to get the ICs > > from the model author. Just thinking 'aloud', so sorry if I am missing > > something obvious here (not least because I have never 'played' with DAEs > myself). > > > > Alan > > > > > -Original Message- > > > From: cellml-discussion-boun...@cellml.org > > > [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Randall > > > Britten > > > Sent: 23 April 2010 12:35 > > > To: CellML Discussion List > > > Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st > > > April > > 2010 > > > > > > DAEs are a little more complex, it isn't always obvious which > > > unknowns require initial conditions, or how to ensure ICs are consistent. > > > > > > Regards, > > > Randall > > > > > > On 23/04/2010, at 8:50 PM, "Alan Garny" > > > wrote: > > > > > > > Sorry, one more (non-OpenCell) comment: > > > > - "... the biggest problem is using IDA's default solver for > > > > initial conditions..." -- What is exactly meant by solver for > > > > initial conditions? Do you mean that you are trying to use IDA to > > > > determine what the initial value of the state variables should > > > > (i.e. like those > > > > 99 guesses in the original OpenCell DAE solver?)? I would > > > > think/hope not (I thought we had 'agreed' to provide the initial > > > > conditions to the solver?). > > > > > > > > Alan > > > > > > > >> -Original Message- > > > >> From: cellml-discussion-boun...@cellml.org > > > >> [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of > > > >> Dougal Cowan > > > >> Sent: 22 April 2010 21:19 > > > >> To: CellML Discussion List > > > >> Subject: [cellml-discussion] ABI CellML Meeting Minutes, 21st > > > >> April > > > >> 2010 > > > >> > > > >> I have put the minutes from this week's meeting up at: > > > >> > > > >> http://www.cellml.org/community/meeting/minutes/2010/04.21 > > > >> > > > >> Thanks, > > > >> Dougal > > > >> > > > >> ___ > > > >> cellml-discussion mailing list > > > >> cellml-discussion@cellml.org > > > >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > > > > > > > ___ > > > > cellml-discussion mailing list > > > > cellml-discussion@cellml.org > > > > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > ___ > > > cellml-discussion mailing list > > > cellml-discussion@cellml.org > > > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > > ___ > > cellml-discussion mailing list > > cellml-discussion@cellml.org > > http://www.cellml.org/mailman/listinfo/cellml-discussion > > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML models in Antimony format
> > little-used CellML constructs such as partial differential equations > > or rates of change with respect to some non-time variable > > Yes - these are a legacy of coding up models in a text editor without any way > of testing them! Partial diffs can be coded up in CellML but there are no > existing tools which will recognise them. There shouldn't be anymore PDE > models added to the repository, I believe they fall under the FieldML domain. I believe PDE models fall under a standard (ModelML?) that has yet to be specified, but like you I am happy to be corrected if I am wrong! Alan ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
