the model is underconstrained (i.e. some variables need to be initialised or computed).

[Luciana Carota]

Hello,

for my model I have the runtime error in object just for simulation: 

Runtime: invalid.

Error: the model is underconstrained (i.e. some variables need to be initialised or computed).

How can I look for the variables to be initialised or computed using OpenCOR?

Cheers

Luciana 

[Nima Afshar Ghotli]

Hi there

When you are using an ODE for a specific parameter, that specific parameter needs to have an initial value (e.g. in ode(x,t): variable "x" needs to be initialised). 

If you do not find it you can also run your model in OpenCell. It usually shows you where the errors come from. 

Warmly,

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Dr Nima Afshar

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Auckland Bioengineering Institute

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[Alan Garny]

Hi Luciana,

 

Short answer: I am afraid that you will have to look for that variable yourself. Not great, I know, although we are currently working on improving OpenCOR’s error reporting.

 

Long(er) answer: OpenCOR currently relies on the CellML API to handle CellML files. OpenCell uses the same API, but an older version of it. Unfortunately, the two versions don’t report the exact same errors (!!) (see here for example). Yet, we can’t use the old version because it contains some critical bugs that have been fixed in the current version. Also, the CellML API is not being worked on anymore. Instead, we are now focussing our efforts on a new API: libCellML. That new API is long overdue, but we are hoping to make use of it in OpenCOR in the next few months. It provides the kind of reporting you are after (see here, here, here and here for example), which will result in OpenCOR providing better error reporting.

 

Otherwise, please keep in mind that OpenCell is neither being developed nor maintained anymore. So, if you are on your own if you ever decide to use it.

 

Alan

 

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