MATLAB: How to retrieve specific compartment in Simbiology model by name

compartmentgetindexMATLABsetSimBiology

Given a Simbioloogy 'model' I can access/get a specific compartment object if I know the numerical index, e.g.

model.compartments(2)

shows me the 2nd compartment. I can get/set properties from this indexing. Say this compartment is named 'turtle'. Can I get this compartment object from the Name, instead of by index? Something like model.compartments('turtle'), or model.compartments('Name'=='turtle'). although clearly these won't work.

Best Answer

Hi,

We made the sbioselect function for things like this, and even for more general kinds of searching. In this case, you could do the following:

    sbioselect(model, 'Name', 'turtle', 'Type', 'compartment')

or if you're not worried about other things named 'turtle' you could just do this:

    sbioselect(model, 'Name', 'turtle')

Take a look at the reference page for more examples.

Related Solutions

MATLAB: Condition in which one compartment does not affect the mass balance

Hi Kazutaka,

In the example you are following along with (https://www.mathworks.com/help/simbio/ug/model-views.html), the PK part of the model is determined by a one compartment model with linear clearance (the compartment Central, with species Drug_Central and elimination reaction reaction_1). The biophase of the drug is modeled in a separate compartment: Biophase, with species Drug_Biophase, and creation reaction reaction_3 and elimination reaction reaction_2. The assumption in this model is that the drug concentration in the biophase does not affect the drug concentration in the central compartment and thereby the mass balance. This concept is implemented through reaction_3 : the stoichiometry of the reaction (Drug_Central -> Drug_Central + Drug_Biophase) has Drug_Central on both sides of the arrow, ensuring that Drug_Central is not being 'consumed' by the reaction. In other words: the concentration of Drug_Central is not affected by reaction_3 and reaction_3 doesn't show up in the ODEs for Drug_Central. In the diagram, this is illustrated by the dashed line between Drug_Central and reaction_3.

The assumption that the Biophase compartment does or doesn't affect the mass balance is a modeling decision made by the authors of the paper referenced at the bottom of the example page. As such, there is no condition that I can say your model should comply with in order to say that the compartment doesn't affect mass balance. The example merely states how to implement this.

I hope that helps. Let me know if you have further questions.

Best,

Sietse

MATLAB: Accessing a simbiology class

Hi Omar,

In the code you typed above, "msp" should be a vector of species objects that you can index using "msp(1)", "msp(2)", etc. Here is an example using a demo model included with SimBiology:

>> m1 = sbmlimport('lotka.xml')
     SimBiology Model - lotka 
     Model Components:
       Compartments:      1
       Events:            0
       Parameters:        3
       Reactions:         3
       Rules:             0
       Species:           4
>> s = m1.Species; % equivalent to get(m1, 'Species')
>> s(1)
     SimBiology Species Array
     Index:    Compartment:    Name:    InitialAmount:    InitialAmountUnits:
     1         unnamed         x        1                 
>> s(end)
     SimBiology Species Array
     Index:    Compartment:    Name:    InitialAmount:    InitialAmountUnits:
     1         unnamed         z        0

Best Answer

Related Solutions

MATLAB: Condition in which one compartment does not affect the mass balance

MATLAB: Accessing a simbiology class

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