Problems with a simbiology 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

[Arthur Goldsipe]

Hi Omar,

You probably didn't notice, but you already got an answer to Question 1 from your posting in the newsgroup. I'll repeat it below for completeness, but I encourage you to check your original posts before posting again.

-Arthur

Answer 1

[Arthur Goldsipe]

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.

[Omar]

Thanks Arthur! I will send you the crash report.

Concerning question 1, I tried what you told me and it worked. Then, I realized that in the models that I was able to retrieve the rate constants they were declared to have as scope the compartment where the reaction was defined instead of just the reaction. Is this the reason?

Thanks again,

Omar

[Arthur Goldsipe]

Hi Omar,

SimBiology parameters can only be scoped to a model or a reaction. When you view a reaction in the SimBiology Desktop, you should see that parameters are scoped to either the model or the reaction. You will also see species used in the reaction, and those can be scoped to compartments, so perhaps that's what you were looking at.

-Arthur