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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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Error: Model is unsuitably constrained (i.e. there were still some variables
left to be computed, and some unusable equations left over).
At the time of the error, the following variables were found:
* Defined: time in component environment in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: ATP in component ATP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Undefined: v_CK in component v_CK in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Undefined: G_AK in component G_AK in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Undefined: v_AK in component v_AK in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Undefined: G_H in component G_H in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: H_ATP in component H_ATP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: D_ATP in component diffusion_constants in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: R_ATP in component ATP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: Lm in component ATP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: ATPi in component ATPi in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: ADP in component ADP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: ADPi in component ADPi in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: D_ADP in component diffusion_constants in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: R_ADP in component ADP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: Lm in component ADP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: AMP in component AMP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Undefined: AMPi in component AMP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: D_AMP in component diffusion_constants in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: R_AMP in component AMP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: Lm in component AMP in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: PCr in component PCr in model
file:///home/hettling/projects/sloppy_ck_paper/revision_1/vendelin_model/vendelin_kongas_saks_2000-a1a238c25ea7/vendelin_kongas_saks_2000_V5.cellml
* Defined: D_PCr in component diffusion_constants in
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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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