MATLAB: Unable to add an event block to a reaction rate in SimBiology

SimBiology

I'm unable to add an event block to a reaction rate block (ke) in SimBiology diagram view (taken from the help page "Model Views in SimBiology App") – please see attached file. When I connect the two blocks the event block for the reaction rate block is still undefined.

Best Answer

Hi Jacopo,

The parameter you are adding the event function to, ke, is currently "reaction-scoped". If you change the scope of your parameter ke to be "model-scoped" you will be able to add the event function to ke. Note that you will have to change your EventFunction to from reaction2.ke = ... to ke = ....

This behavior is rooted in SBML standards but it would be helpful for us to understand why you want ke to be reaction-scped as opposed to model-scoped. Is there a particular reason why you want ke to be reaction-scoped?

Let me know if that helps.

Best,

Sietse

Related Solutions

MATLAB: Simbiology Desktop: Why the parameter is not recognized in the EventFcns (I would like to change its value at a precise timepoint)

Hi Raphaelle,

SimBiology allows you to create 2 kinds of parameters: model-scoped and reaction-scoped. Reaction-scoped parameters can only be used inside of the reaction they're associated with. Therefore, if you want to modify a parameter using an event, the parameter must be model-scoped. You can easily change the scope of a parameter in the SimBiology Desktop by right-clicking on it and selecting the "Change Scope" option.

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.

Best Answer

Related Solutions

MATLAB: Simbiology Desktop: Why the parameter is not recognized in the EventFcns (I would like to change its value at a precise timepoint)

MATLAB: Problems with a simbiology model

Related Question