MATLAB: Compartment is not being used in the model

compartment is not being used in the modelSimBiology

i'm replicating the result of the pharmacokinetics of antibacterial drugs in a time-kill curve experiment in the tutorial

when i firstly create the model with simbiology App, i got the message "compartment is not being used in the model" at the top-left of the compartment in the diagram view

how should i manage this message?

And, after setting the kinetic parameter for reaction, hidden parameter was not shown up by "Show All Hidden Blocks and Lines".

How can i show the hidden kinetic parameters?

Thanks!

Best Answer

Hi,

You can ignore the "compartment is not being used in the model" warning. This warning is a benign bug with this version. Sorry about that.

To answer your second question, only model scoped parameters appear on the diagram. By default, the parameters are scoped to the reaction. If you change the scope of the parameter to the model, it should appear on the diagram.

To change the scope, open the reaction on the property editor. Check the scope of the parameter to the left of the parameter name. If it shows reaction, right click on the parameter and choose Change Scope.

Fulden

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MATLAB: Problems with a simbiology model

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.

MATLAB: How to assign values to parameters in simbiology model from a .m file

I'm guessing that some of your parameters are scoped to reactions.

First, some background: In SimBiology, parameters can be "scoped" either to the model or to a specific reaction. A model-scoped parameter can be used in any reaction, rule, or event in the model. A reaction-scoped parameter can only be used in the reaction that it's scoped to, and it "shadows" any model-scoped parameter of the same name. This allows you to use the same parameter name (like "kf") in multiple reactions, even if the reactions have different parameter values.

m1.Parameters only lists model-scoped parameters. To access a reaction-scoped parameter, you normally go through the reaction, for example, m1.Reactions(1).KineticLaw.Parameters(1).

As an alternative that would work for either type of parameter, you can use sbioselect to find your parameters by name. For example, to find all parameters named "kf", you could use kf = sbioselect(m1, 'Name', 'kf', 'Type', 'parameter'). If there's only one parameter named "kf", then you can set it's value with kf.Value = 10.0.

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