Is volume capacity required to fit PK data in simbiology?
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I have several time-concentration data obtained from rat plasma and wish to fit a standard 2-compartment model using simbiology. Do I need to specify the compartment capcacity (peripheral and central)? or can I let the default values of 1 liter (which of course do not reflect the actual compartment volumes in rats).
In case a good fit requires the capacities be included, where I could get such data?
Arthur Goldsipe on 9 Nov 2021
Let me first make sure I understand your question. I think you want to estimate the volume of peripheral and central compartment volumes in a 2-compartment model (presumably along with other kinetic parameters). And you want to know whether you can use initial estimates of 1 liter, or whether you need to specify "better" initial estimates.
If that's the case, then in general it is best to use reasonable (that is, physiologically realistic) values for your initial estimates. Depending on your data and the specific optimization method you pick, you may still be able to successfully estimate parameters when your initial estimates are far off. But even is such cases, the optimization will typically take longer than if you start with reasonable estimates.
I think you should be able to get some idea of physiological relevant volumes by searching the literature or even just a general internet search. (I quickly found a couple of rate volumes listed in the 0.05 to 0.15 milliliter range.)
In this particular case, you also only need to estimate a few parameters, so you may be able to determine reasonable initial parameter values my manually exploring the effect of parameter values on simulation results. You can do this easily in the SimBiology Analysis App by adding sliders. This approach is illustrated in a tutorial that you might find useful (at around 2:40 time mark).