|20 Jun 2014||Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies.||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.
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.||Sebastian||
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.||Sven||
organismBloodFlowTISSUE is in [volume/time]
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||Sebastian||
(with TISSUE: kindey, heart, bone, etc.)
I would suggest this code:
or am I wrong?
|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",
|24 Aug 2013||Physiologically-based Pharmacokinetic (PBPK) model for SimBiology Provides a PBPK and a Renin-Angiotensin system model for SimBiology||Rizwan||
excellent submission. Would like to see more like this.
|05 Oct 2012||Raj||
|04 Oct 2012||Sven Mesecke||
|04 Oct 2012||Raj||
"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").
|29 Aug 2012||Physiologically-based Pharmacokinetic (PBPK) model for SimBiology Provides a PBPK and a Renin-Angiotensin system model for SimBiology||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