TissuePartition Function Inclusion into SimBiology PBPK

I am trying to incorporate the functions described here:

https://www.mathworks.com/matlabcentral/fileexchange/37752-generic-simbiology-physiologically-based-pharmacokinetic-pbpk-model

In particular the tissue partition coefficients - how do I load that matlab code?

Answer 1

[Sietse Braakman]

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.