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Remove paragraph on calculating specific intestinal permeability from experimentally measured values #120

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AndreDlm opened this issue Jan 14, 2021 · 4 comments

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@AndreDlm
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In this section, the paragraph pasted below on calculating specific intestinal permeability from experimentally measured values, e.g. from Caco-2-cell permeability assays, should be removed from the documentation. This is not part of PK-Sim and may lead to misunderstandings (as in Open-Systems-Pharmacology/Forum#668).

In addition to the calculated specific intestinal permeability, experimentally determined permeabilities, e.g. from Caco-2-cell permeability assays can be used. However, due to the large inter-laboratory variability in Caco-2 permeations, a proper calibration of the measured in vitro values and the calculated in silico permeabilities for a defined set of compounds is necessary. If experimentally determined values for intestinal permeabilities are available and the customized calibration method has been implemented in PK-Sim®, this option is then available in the drop-down menu in the Calculation methods window.

@Yuri05
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Yuri05 commented Jan 15, 2021

I would rather enable calibration as user input (not much to do for this: Open-Systems-Pharmacology/PK-Sim#1631) and rewrite this paragraph correspondingly.

@StephanSchaller
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I agree with Yuri, the paragraph is not wrong per see, it might just need a bit of more detail / be more specific and a minor correction:

The "calculation methods" window it refers to is actually the "Parameter Alternative" list in the Compound settings when you CREATE or CONFIGURE your simulations:
image

@AndreDlm
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Also fine for me, but then I would suggest to add a description for the user on how to conduct the correlation and come up with meaningful values for the calibration parameters...

@msevestre
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suggestions on what to write here @AndreDlm ?

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