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Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model


4.5 | 2 ratings Rate this file 33 Downloads (last 30 days) File Size: 181 KB File ID: #37752
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Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model



29 Aug 2012 (Updated )

SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies.

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SimBiology project file and some associated MATLAB files that contain a generic and adaptable PBPK model. Human fasted, Human fed and Rat (new!) physiologies are included as variants.

Tested on R2012a and R2011b and should work with earlier releases as well. Does not contain tasks or the Renin-Angiotensin model as used in the June 2012 webinar. Please see for the project used in that webinar.


Model Structure:
Peters, S. A. (2008). Evaluation of a generic physiologically based pharmacokinetic model for lineshape analysis. Clinical pharmacokinetics, 47(4), 261-75.

Tissue Partition Coefficients:
Rodgers, T., & Rowland, M. (2006). Physiologically Based Pharmacokinetic Modelling 2 : Predicting the Tissue Distribution of Acids , Very Weak Bases , Neutrals and Zwitterions. Journal of pharmaceutical sciences, 95(6), 1238-1257.

Rodgers, T., Leahy, D., & Rowland, M. (2005). Physiologically based pharmacokinetic modeling 1: predicting the tissue distribution of moderate-to-strong bases. Journal of pharmaceutical sciences, 94(6), 1259-76.


Physiologically Based Pharmacokinetic (Pbpk) Model For Sim Biology inspired this file.

Required Products SimBiology
MATLAB release MATLAB 7.14 (R2012a)
Other requirements Requires a C Compiler for acceleration of model simulation.
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Comments and Ratings (5)
13 Oct 2013 Wan Su

Oh! Sorry. There were answers already. It's working well now. Thank you.

13 Oct 2013 Wan Su

When I run this model file, there were 14 errors. Belows are error messages.

"The name 'calculateParacellularAbsorption' in rule 'Paracellular Absorption' does not refer to any in-scope species, parameters, or compartments",
"The name 'calculateTissuePartition' in rule 'Adipose Tissue Partition Coefficient' does not refer to any in-scope species, parameters, or compartments."
and same message for bone, brain, gut, heart, liver, lung, muscle, pancreas, skin, thymus, spleen. What should I do?

05 Oct 2012 Raj

Duh ! As a long time user I should have figured that one out !!! Many thanks for reminding me !!

04 Oct 2012 Sven Mesecke

Hi Raj,
the first warning should not concern you, everything will work fine.
The error message is also slightly misleading. The download file contains two additional files (calculate...). These must be on the MATLAB path as they are called by SimBiology when you try to run the model. Either add the folder to the MATLAB path or navigate in the MATLAB Desktop to the folder. Does this solve your problems?

04 Oct 2012 Raj

This is an excellent tool but doesn't work in my 2012a version. Upon opening the project file, Simbiology complains as follows:

"The SB project version being loaded is newer than the SB version being run. Some features of the project may not be supported in this version"

Also, the additional rules don't work ("does not refer to any in-scope species, parameters or compartment").

Any ideas?

04 Feb 2013

Updated Screenshot

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