MATLAB: Symbiology new project (Estimating the Bioavailability of a Drug)

SimBiology

Hello, the simbiology project (sbioloadproject('Bioavailability.sbproj','m1')) and the corresponding data (load ondansetron_data) in the new version of matlab (R2015b) is not on the matlab root directory. Can anyone from Matlab please upload this example? this is the link http://www.mathworks.com/help/simbio/ug/_buxe75l.html. Thank you!

Best Answer

Hi,

The files are located under the "examples\simbio" folder of your MATLAB installation. You can open the project in the SimBiology Desktop using the following command:

    simbiology(fullfile(matlabroot, 'examples', 'simbio', 'Bioavailability.sbproj'))

and the data file using the following command:

    load(fullfile(matlabroot, 'examples', 'simbio', 'ondansetron_data.mat'))

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MATLAB: How to convert a .m script to .sbproj file

Hi Colton,

You can use the sbiosaveproject function to save the SimBiology model (and data) to a .sbproj file. For example,

model = sbmlimport ('oscillator.xml');    
simData = sbiosimulate(model);
sbiosaveproject oscillator.sbproj model simData;

Hope it helps, Joe

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

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