compartment is not being used in the model

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!

Answer 1

[Fulden Buyukozturk]

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

[Fulden Buyukozturk]

Please see attached screenshot.

[Kazutaka Sekiguchi]

thank you for your comment!

i was able to show the parameters after changing the scope

i have a qurstion regarding to the scope

what is the difference between Model Scoped Parameters and Reaction Scoped Parameters?

Thanks,

[Fulden Buyukozturk]

If a parameter is model scoped, the parameter is available to all reactions in the model and the Parent property of the parameter object is SimBiology.Model. This also means you can use these paremeters in other expressions in the model such as assignment rules.

If a parameter is reaction scoped, the parameter is available only to the reaction for which you are using the kinetic law object and the Parent property of the parameter object is SimBiology.KineticLaw.

Hope this helps.

Fulden

[Kazutaka Sekiguchi]

thank you for your comment

I understand the difference between model and reaction scoped parameters

is it possible to set all parameters including ones used for single reaction as model scoped parameters?

or should I set scope of parameters depending on how these parameters used in the model?

[Fulden Buyukozturk]

Yes, you can change SimBiology preferences to set the default scope of parameters as Model.

Go to Preferences on Home tab, choose Model Building, and uncheck "Scope parameters created to the reaction", click apply.

This will ensure that any new parameters you add will be scoped to Model. To change the existing parameter's scope, you need to do the steps outlined above.

Fulden

[Kazutaka Sekiguchi]

Thank you so much!

I appreciate it,

Kazutaka