Rank: 1113 based on 134 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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(last 30 days)
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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 18 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 30 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 34 5
  • 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... 17 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 12 0
Comments and Ratings by Sven View all
Updated File Comments Rating
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
Updated File Comment by Comments Rating
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.

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

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?

24 Aug 2013 Physiologically-based Pharmacokinetic (PBPK) model for SimBiology Provides a PBPK and a Renin-Angiotensin system model for SimBiology Author: Sven Mesecke Rizwan

excellent submission. Would like to see more like this.

05 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 Raj

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

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 Mesecke, Sven

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?

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