MATLAB: Problems with a simbiology model

SimBiologysimbiology model

Dear friends,
I have a simbiology model with 27 reactions, most of them reversible, that is giving me trouble:
1- When trying to retrieve parameters of the model object from the MatLab desktop with get(modelobj1,'Parameters') just 7 parameters are listed all of them unitless. The 43 rate constants are not listed. While this fails, other model properties like 'Reactions' are displayed complete (get(modelobj1,'Reactions')).
2- A reproducible crash each time I run a deterministic simulation.
None of the other simbiology models I'm dealing with have any of these problems.
Have any of you experienced similar problems with a simbiology model?
Thanks in advance,
Omar

Best Answer

Question 1: First, a little background. In SimBiology, parameters can be associated either with a model (sometimes called "model-scoped parameters") or with a kinetic law of a reaction ("reaction-scoped parameters"). A model-scoped parameter is visible throughout the model and can be used in any reaction, event, or rule. A reaction-scoped parameter can only be used in the rate of the reaction that it's associated with.
get(modelObj1,'Parameters'), or equivalently modelObj1.Parameters, only lists model-scoped parameters. You can get the parameters associated with a particular reaction with code like modelObj1.Reactions(1).KineticLaw.Parameters, or the equivalent
reactionObjs = get(modelObj1, 'Reactions')
kineticLawObj = get(reactionObjs(1), 'KineticLaw')
parameterObjs = get(kineticLawObj, 'Parameters')
If you'd like a simple way to get all the parameters used in a model, you can use use sbioselect function as follows:
allParameterObjs = sbioselect(modelObj, 'Type', 'parameter')
Question 2: I'm a developer on the SimBiology team, and I would need to know more details to assist you with diagnosing a crash. For example, what version of MATLAB are you using? What operating system? Can you provide the crash log? Can you provide reproduction steps? I will try to contact you to obtain this information.
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