Chronological Thread 

< Chronological >      < Thread >

---

Hi Hannes

If you give me a couple of hours I can work on the model for you. As
the CellML curator it's my job and I am also interested in getting
these models working.

If you want to take me up on this offer please email the latest copy
of the model to me and I can get back to you - hopefully with
something which is working or close to working!

Best wishes
Catherine


On 9/11/2010, at 8:19 AM, hettling wrote:

> 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
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> cellml-discussion mailing list
>> cellml-discussion at cellml.org
>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-discussion

---

• [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

---

Archive powered by MHonArc 2.6.18.