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How to monitor total urinary process rates #666

Closed Mitmischer closed 3 years ago

Mitmischer commented 3 years ago

Hello,

I set up urinary clearance via tubular secretion in PK-Sim and exported the model to Mobi. I have ~20 metabolites in the system and for ~each 10, I need to monitor the total secretion rate. Plotting would be nice to have, but availability in the R Toolbox would be fine.

In the passive transports tab, I found the Renal Clearances for each metabolite. I checked the "Create ... parameter on each" for each of them and I verified that those are plausible. They are located in the neighborhood between kidney plasma und urine:

grafik

Finally, I defined two custom parameters that add the process rate parameters. One of them looks like this: grafik

However, this does not work. If I plot UrinaryRate_Deconj, it will be a constant 10 (which leads me to the conclustion that each n_i is just 1 and not updated. That confuses me as the rates themselves are plausible and not 1 during the whole simulation. Am I doing something the wrong way or is that a bug?

StephanSchaller commented 3 years ago

The approach should be correct.

On first glance, you are missing an "n" in the formula:

image

likely the clearance rates are quite small (<< 1) and thus you don't see the change on top of the static "10" that is currently added in the formula.

Hope that helps, Stephan

Mitmischer commented 3 years ago

Well, that's embarassing - you're right! Thanks a lot :)

StephanSchaller commented 3 years ago

No worries, it happens to the best ;-)