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[cellml-discussion] debugging undifined variable in component


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  • From: hannes.hettling at gmail.com (hettling)
  • Subject: [cellml-discussion] debugging undifined variable in component
  • Date: Mon, 08 Nov 2010 20:19:00 +0100
Dear Alan,

thanks a lot for your help and the quick reply!
I checked out COR, but all these connection related error let me realize
that it is best to remove all <connection> tags from the file and redo
them by hand. I do that with OpenCell and it seems to work quite well...
I still have bugs but at least I am past the undefined variables (i
hope).

Cheers,

Hannes


On Mon, 2010-11-08 at 15:28 +0000, Alan Garny wrote:
> Hi Hannes,
>
> First, I would recommend using the latest version of PCEnv (which,
> incidentally, is now known as OpenCell), which is 0.8
> (http://www.opencell.org/). Secondly, I had a quick look at the model using
> COR (http://cor.physiol.ox.ac.uk/; note: that software is not being
> developed further, but it might still provide you with a better way of
> debugging that model. It requires Windows though...), and it did indeed
> report some mapping issues. Basically, there were two occurrences of two
> components being mapped twice (check the Diff.html which highlights what I
> am talking about using the COR 'format' for clarity). I have corrected
> those (see the attached revised CellML file), but now there are tens of
> other errors and well... I shall leave them to you to fix...
>
> Alan
>
> > -----Original Message-----
> > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> > bounces at cellml.org] On Behalf Of hettling
> > Sent: 08 November 2010 15:12
> > To: cellml-discussion at cellml.org
> > Subject: [cellml-discussion] debugging undifined variable in component
> >
> > Dear all,
> >
> > I am having quite some trouble to debug a model from the CellML model
> > repository, I hope this is the right place to pose a question (I'm quite
> > new to
> > CellMl).
> >
> > I want to simulate the model from Vendelin, Kongas, Saks, 2000. Since the
> > model included spatial diffusion using partial differential equations,
> > which is
> > to my knowledge not supported by any simulating environment, I substituted
> > the equations containing PDEs with different equations according to the
> > paper of Vendelin, to get rid of the spacial diffusion, since it is not so
> > important for my analysis.
> >
> > I am using PCenv 0.6 to try to run the model and I get a couple of error
> > messages, I think they are mainly about connecting different model
> > components.
> >
> > I get for example the messages:
> >
> > * Undefined: v_CK in component v_CK in model
> > file:///home/hettling/vendelin_kongas_saks_2000_V5.cellml
> > * Undefined: G_AK in component G_AK in model
> > file:///home/hettling/vendelin_kongas_saks_2000_V5.cellml
> >
> > which I do not understand, since v_CK is defined in the component v_CK and
> > G_AK in G_AK.
> > For variable ATP, which is defined in the component ATP, I do not get an
> > error.
> > I attached the model file and a file containing all error messages.
> >
> > Could someone give me a hint on what could be the problem? I am new to
> > CellML, so I must have overlooked something important.
> > I would very appreciate any help,
> >
> > many thanks in advance,
> >
> > Hannes
> >
> >
> >
> >
> >
>
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