Apart from the available sources from http://www.open-systems-pharmacology.org/ on PBPK model building workflow, how can you optimize parameters in a case were simulated data is different from observed data?
Hi Mwila,
I have no experience with PK-Sim, but for "simple" parameter optimization/estimation tasks I like to use Copasi which is intuitive to use and can be used with both timecourse and steady state data (and has a nice user forum + good documentation at http://copasi.org/Support/User_Manual/). If your model is simple enough you can set it up in copasi rather quickly (or import it as SBML).
Alternatively, I recently came across a nice tutorial for using matlab's nlinfit function, which is often good enough for simple tasks: https://matlabgeeks.com/tips-tutorials/modeling-with-odes-in-matlab-part-4a/
Best,
Daniel
Dear Dr. Mulubwa
There are multiple options for optimization. My personal requirement is to minimize or maximize target functions. There are ready to use optimized codes, which include Matlab and R functions. Depending on your approach, we can discuss. I am not a PK-Sim expert, and have never used it.
Sanjay.
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