MATLAB: How to view differential equations produced by SimBiology

biologydifferential equationsmodellingSimBiology

I am reproducing a published model and need to view the differential equations produced by the SimBiology functions. I am using a script (rather than the GUI interface) though I can import the model into the SimBiology GUI if the solution requires. Does anybody know how to see the differential equations from a SimBiology model.

Thanks in advance.

Best Answer

You can use the GUI to export model equations.

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MATLAB: Model/Simulation of Drug Release in Graphical SimBio Interface

Hi Greg,

we have released video tutorials which cover different topics including model building:

SimBiology Tutorials for QSP, PBPK, and PK/PD Modeling and Analysis

Using these concepts you will be able to build any model based on ordinary differential equations.

Best regards,

Jérémy

MATLAB: TissuePartition Function Inclusion into SimBiology PBPK

Hi Andrew,

Are you trying to pull out the values of the partition coefficients or the model equations?

In general, SimBiology models are objects (as in object-oriented programming), rather than MATLAB code. As such, you can create MATLAB code to construct a SimBiology model object, but you can't extract MATLAB code from the SimBiology model. What you can do is get the equations or model parameter values from the SimBiology object.

In order to load the model you refer to in your post, you can either open the SimBiology App by typing in the command line:

simbiology

and then clicking on 'Open' and navigating to the folder where the model is.

If you want to load the model object in MATLAB, rather than in the SimBiology App, you can use the function sbioloadproject.

model = sbioloadproject('PBPK.sbproj');
parameters = model.Parameters % shows you all parameters, their model values and units (if present)
equations = getequations(model) % retrieves the equations from the model

Note that the PBPK model relies on a two functions (calculateParacellularAbsorptions.m and calculateTissuePartition.m) that need to be on your MATLAB path or in your current folder in order for the PBPK model to simulate without errors.

I hope that helps.

Best Answer

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MATLAB: Model/Simulation of Drug Release in Graphical SimBio Interface

MATLAB: TissuePartition Function Inclusion into SimBiology PBPK

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