Example Workflows
The following workflows illustrate how to use MoBi in different scenarios.
Modularization use case - adding a tumor to a PBPK model
This workflow illustrates how to add a tumor compartment to a PBPK model in MoBi. The steps are as follows:
Export a simulation from PK-Sim to MoBi. This will create a PK-Sim module.
Image Open the spatial structure of the PK-Sim module, select a tissue organ (e.g., muscle), and export it to pkml, e.g. as "Muscle.pkml".
Image Optionally, select an individual and expression profile(s) to include in the exported organ.
Image Create a new "Tumor" extension module with the "Spatial Structure" and "Initial Conditions" building blocks.
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Image In the "Tumor" extension module: open the spatial structure and load the top container from the previously saved file Muscle.pkml.
{% hint style="note" %} Note that the neighborhoods between muscle and arterial/venous blood are also loaded. {% endhint %}
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Image Rename the "Muscle" container to "Tumor". Be sure to check the "Rename Related Entities" checkbox in the next dialog!.
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Image {% hint style="note" %} After renaming, the neighborhoods have been renamed accordingly. {% endhint %}
- Open the Initial Conditions building block of the Tumor module and click on "Extend".
Image Select molecules to be incorporated into the tumor.
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Image Create a new simulation and select both modules (make sure that the PK-Sim module is on top!).
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In the next step, optionally select an Individual and Expression Profile(s).
The "Tumor" organ will now appear in the simulation.
Image Tumor drug concentrations, etc. can now be plotted in the simulation.
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