Getting initial estimates for Kp using Calculate partition coefficient function

Hi,

I have constructed a simbiology model and would like to get the intial estimates for Kp values using "calculate partition coefficient" function. Can someone please tell me how to run this function in matlab command window or simbiology model analyser to get the Kp values? Additonally, I also request someone to share any videos/documentation related to this topic that are available in simbiology community.

Thank you!

Answer 1

[Jeremy Huard]

Hi Bhargavi,

I recommend you to have a look at the Generic SimBiology PBPK model and its implementation to see how a MATLAB function can be used to compute partition coefficient.

Typically, this is done with an initial assignment in SimBiology.

Best regards,

Jérémy

[Bhargavi Srija Ramisetty]

Hi Jeremy,

Thank you for answering my question. I already used the above mentioned model. However, I am seeing the following error in simbiology model analyzer when I try to estimate Kp values by data fitting in my model.

"Error evaluating initialAssignment or repeatedAssignment rule (rule rule_3) at t=0.0000. Check MATLAB expressions and user-defined functions for errors."

Can you please help me in solving this issue?

Thank you

[Arthur Goldsipe]

My guess is that the standalone functions (which we call user-defined functions) included with this model are not on your path. Before you run the simulation, make sure either your current directory contains the files calculateParacellularAbsorption.m and calculateTissuePartition.m or that you had added the folder that contains these files to your MATLAB path.

[Bhargavi Srija Ramisetty]

Hi Arthur,

Thank you for your reply. I already added both the files to my current folder. When I verify my simbiology model before proceeding to data fitting I get the following error messages for all the rules having tissue partiton coefficient calculation.

[Source:rule_1

Source Type:Rule

Source Location:PBPK modelMessage:

Cannot perform dimensional analysis for rule 'rule_1' because of the function 'calculateTissuePartition' in the rule. It is recommended that input and output arguments to functions be dimensionless to ensure correct results.]

With respsect to the above error, I double checked my units for all the paramters used in the rule and there are no improperly assigned units.

I might have to get some additional help on this. May I know if I can contact someone direclty?

Thank you in advance,

Bhargavi Srija

[Arthur Goldsipe]

You can safely ignore this warning. It just means that you need to manually check the units, just the way you did.

If you need more help than we can provide here on MATLAB Answers, perhaps Jeremy can advise on next steps. (I'm a SimBiology developer, but Jeremy is an engineer who works directly with customers.) You can also always reach out to our Technical Support, and they should be able to put you in touch with the right people.

[Bhargavi Srija Ramisetty]

Thank you for your help, Arthur