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?
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).
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?
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?
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:
(with TISSUE: kindey, heart, bone, etc.)
I would suggest this code:
(1/[Arterial Blood]*(organismBloodFlowTISSUE*[Arterial Blood].Drug))
or am I wrong?