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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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• [cellml-discussion] debugging undifined variable in component, hettling, 11/09/2010
  • [cellml-discussion] debugging undifined variable in component, Alan Garny, 11/09/2010
    • [cellml-discussion] debugging undifined variable in component, hettling, 11/09/2010
      • [cellml-discussion] debugging undifined variable in component, Catherine Lloyd, 11/09/2010

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