Rank: 873 based on 124 downloads (last 30 days) and 6 files submitted
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Sven Mesecke

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MathWorks

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Professional Interests:
Computational/Systems Biology, Bioinformatics, PK/PD, Bioprocess engineering

 

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Files Posted by Sven View all
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07 Feb 2013 Screenshot Renin-Angiotensin-System (RAS) model for SimBiology Provides a SimBiology model implementation of the Renin-Angiotensin-System Author: Sven Mesecke simbiology, pkpd, systems biology, biotech, mechanistic modeling, pathway modeling 12 0
05 Feb 2013 Screenshot Continuous Stirred Tank Bioreactor (CSTR) SimBiology model SimBiology project containing a simple CSTR bioreactor model Author: Sven Mesecke simbiology, simbiology model, biotech, bioprocess engineerin..., metabolic engineering, bioreactor 24 0
04 Feb 2013 Screenshot Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke simbiology, simbiology model, pbpk, pharmacokinetics, drug, bioavailability 38 9
  • 4.5
4.5 | 2 ratings
30 Jan 2013 Convert SimBiology(R) model to COBRA Toolbox model Use SimBiology for dynamic modeling and COBRA Toolbox algorithms for constraint-based modeling. Author: Sven Mesecke simbiology, simbiology export, systems biology, flux balance analysis, metabolic engineering, bioprocess engineerin... 19 0
09 Jan 2013 BerkeleyMadonna model import function for SimBiology Imports ODE models in the BerkeleyMadonna(TM) format into a SimBiology(R) model Author: Sven Mesecke simbiology, simbiology import, systems biology, pharmacodynamics, pharmacokinetics 9 0
Comments and Ratings by Sven View all
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04 Oct 2012 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: 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?

29 Aug 2012 Physiologically-based Pharmacokinetic (PBPK) model for SimBiology Provides a PBPK and a Renin-Angiotensin system model for SimBiology Author: Sven Mesecke

The bare PBPK model that should work with recent releases is available at: http://www.mathworks.de/matlabcentral/fileexchange/37752-generic-simbiology-physiologically-based-pharmacokinetic-pbpk-model
The Renin-Angiotensin-System model can be found here: http://www.mathworks.com/matlabcentral/fileexchange/37759-renin-angiotensin-system-ras-model-for-simbiology

Comments and Ratings on Sven's Files View all
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20 Jun 2014 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke Sven

There might be an error (I have no access to either Matlab or SimBiology anymore), but it would be different from what you suggest.
See the equation in the reference:

dCT/dt = QT/VT * (CAR - (CT * R/ (f * K) )

or just the input into Thymus:

dCT/dt = QT/VT * CAR

so division by input organ volume

the reason for dividing it by the Thymus volume is to account for the different volumes of arterial blood and thymus. The issue I see is that I multiply with VAR which is nowhere to be found in the reference. Can't remember the reason for that and cannot verify now. If you still think there is an issue with your alleged error, please correct it and reupload to the file exchange. Otherwise please contact arthur.goldsipe [at] mathworks.com (sorry Arthur for pulling you into this, I don't have access to these old things anymore).

19 Jun 2014 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke Sebastian

Hey,
well, I'm pretty sure that the model has an error. Here is for example the ode of the model for the change of concentration in thymus:

d(Thymus.Drug)/dt = 1/Thymus*( (1/Thymus*(organismBloodFlowThymus*[Arterial Blood].Drug))*[Arterial Blood] - (1/Thymus*organismBloodFlowThymus*Thymus.Drug*DrugBloodPlasmaRatio/(DrugFractionUnbound*KTissuePartitionThymus*DrugTissueFactor)))*Thymus)

As we can see, the second "1/Thymus" needs to be replaced by "1/[Arterial Blood]", so that it cancels out. This would give "organismBloodFlowThymus*[Arterial Blood].Drug" as the correct input rate in amount/time into thymus (as it is described in the reference).

(Assuming Thymus, [Arterial Blood] are Vol, *.Drug are Conc)

Am I wrong?

17 Jun 2014 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke Sven

Hey Sebastian,
sorry for replying only now, I'm not at MathWorks anymore which is where I build the model. Check the reference for more info on the model, but the reason for the equation, as far as I can remember it, is:

organismBloodFlowTISSUE is in [volume/time]
drug is in [amount/volume]
TISSUE is in [volume]

so the second part of the equation translates concentration per time into amount per time which is then divided by tissue volume to get concentration in tissue changed per unit time. Does that make sense to you?

08 May 2014 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke Sebastian

Hi,
do I miss something or is there an error in the code. Each arterial input (except gut) and the venous input into lung is coded as:
(1/TISSUE*(organismBloodFlowTISSUE*[Arterial Blood].Drug))

(with TISSUE: kindey, heart, bone, etc.)

I would suggest this code:
(1/[Arterial Blood]*(organismBloodFlowTISSUE*[Arterial Blood].Drug))

or am I wrong?

13 Oct 2013 Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. Author: Sven Mesecke Wan Su

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

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