MoBi and PKSim Guide

This is a step-by-step guide for MoBi and PKSim

22 May 2025 By Wilbert de Witte

In this guide, we'll learn how to conduct a population simulation using PK-Sim and MoBI. The process involves starting with an individual simulation in PK-Sim and then transitioning to a population simulation. A key step is modifying parameters like lipophilicity in MoBI to allow variability across a population. We'll explore how to adjust these settings in the building block and update the simulation accordingly. Finally, we'll return to PK-Sim to complete the population simulation, focusing on defining variability and analyzing results.

Let's get started

Okay. Start in PKsim with an individual simulation. Then, use this individual simulation for a population simulation.

Step #1: Right-click on "1. Yuan 2012 - GEN L1" — Right-click on "1. Yuan 2012 - GEN L1"

For parameters that are not yet allowed to vary in a population, such as lipophilicity, you first need to send it to MoBI.

Step #2: Click on "Send to MoBi" — Click on "Send to MoBi"

In MoBI, we can change the settings of a specific parameter to vary it within a population. This involves a checkbox that I will show shortly. Alright, now we are in MoBI, and we can open the same simulation. I'm not sure if we can do it in the simulation or if we need to go to the building block. No, we need to go to the building block because we cannot change it in the simulation directly.

I am now showing it in the building block. Go to the modules, then select molecules, and choose genistein.

Step #6: Double-click on "Genistein" — Double-click on "Genistein"

Parameters are set, and then we search for lipophilicity.

Step #7: Click on "Parameters" — Click on "Parameters"

It's here.

Step #9: Click on "Lipo" — Click on "Lipo"

Now it's a constant, but it can be varied in a population.

Step #11: Click on "Can be varied" — Click on "Can be varied"

You will receive a warning, but that's fine.

Step #12: Click on "Yes" — Click on "Yes"

Okay. Lipophilicity can vary within a population. We need to update the simulation to apply the changes we just made to the building block.

Step #13: Right-click on "1. Yuan 2012 - GEN L1" — Right-click on "1. Yuan 2012 - GEN L1"

Step #14: Click on "Update from building blocks" — Click on "Update from building blocks"

Now, we can send it to PKsim for a population simulation.

Step #15: Click on "1. Yuan 2012 - GEN L1" — Click on "1. Yuan 2012 - GEN L1"

Step #16: Right-click on "1. Yuan 2012 - GEN L1" — Right-click on "1. Yuan 2012 - GEN L1"

Step #17: Click on "Send Simulation to PK - Sim for Population Simulation" — Click on "Send Simulation to PK - Sim for Population Simulation"

We only want to change the number of individuals now to keep it quick and easy.

Step #18: Click on "Only allocate the number of individuals" — Click on "Only allocate the number of individuals"

Step #19: Click on " Only allocate the number of individuals ( typically for Mobi )" — Click on " Only allocate the number of individuals ( typically for Mobi )"

In some cases, it might be better to use one of the other options, but...

Type "3"

Step #21: Click on "Start Import" — Click on "Start Import"

Now we can start the import. I will use three individuals to create a quick example. Okay, it's done.

The import is complete. We are now creating a simulation with user-defined variability.

Step #23: Click on "User Defined Variability" — Click on "User Defined Variability"

We can add compounds' lipophilicity here and define either a mean and a standard deviation on the normal scale or the log-normal scale.

Step #25: Click on "Lipophilicity" — Click on "Lipophilicity"

Step #26: Click on "Genistein L1" — Click on "Genistein L1"

Lipophilicity is already measured on a log scale. so, we need to create a normal distribution.

Let's say we have a deviation of half a log unit.

Type "0.5 + Enter"

Now, let's take a look at the distribution.

Step #32: Click on "Distribution" — Click on "Distribution"

We have only three individuals, so we can't see the distribution clearly. However, we can use these three values to run a simulation.

Here, I select the plasma concentration geometric mean and the 95% interval.

Step #34: Click on "Plasma" — Click on "Plasma"

Step #38: Click on "Next" — Click on "Next"

Okay.

Step #39: Click on "Next" — Click on "Next"

Step #40: Click on "Next" — Click on "Next"

Okay. Do the simulation by first setting up your environment. Ensure all necessary software and tools are installed. Next, configure the parameters according to your project requirements. Once everything is set, run the simulation. Monitor the process to ensure it operates smoothly. If any errors occur, troubleshoot them immediately. After the simulation completes, analyze the results. Compare them with your expected outcomes to evaluate the accuracy. Make adjustments as needed and rerun the simulation if necessary. Finally, document your findings and any changes made during the process for future reference.

Okay. Now we have some added variability. In the simulation, you can still check... You can create a scatter plot to visualize how different values vary.

Step #42: Click on "Distribution" — Click on "Distribution"