First Steps

This section guides you to your first project with MoBi® and familiarizes yourself with the software's user interface. If you are already familiar with MoBi® and want to learn about the modularization concept, please refer to Modularization concept.

First, the window structure of MoBi®and the basic steps for setting up a new MoBi® project are described, followed by a description on how to set up and carry out a simulation. Additionally, the import of a PK-Sim® simulation is explained. However, more sophisticated applications can be performed in MoBi®, and you are referred to the following chapters for a more detailed description.

To create your first MoBi® project, simply follow the steps described in the sections below.

MoBi® - Window Overview‌

In this section, we give a brief overview of the MoBi® window architecture and introduce some nomenclature.

A typical MoBi® window looks like screenshot below. The window contains different subviews; although some of them are visible only after creating a project, we describe them right here in a comprehensive way.

• The tabs File, Modeling, Parameter Identification & Sensitivity, Working Journal, Import/Export, Utilities, and Views with the Ribbon Bar. Additional tabs may appear depending on the context, e.g. when editing a building block or a simulation.

• The Modules Explorer in the upper left section, which gives access to all modules and their building blocks, the individuals, expression profiles, and observed data of the current project,

• The Simulation Explorer in the bottom left section, which lists all Simulations, Parameter Identifications, Sensitivity Analyses, and Results (comparisons) views defined in the current project,

• The History Manager at the bottom that shows the history of model development,

• The Building Block Editor with a building block specific layout. Generally, it consists of a List, Tree, or Diagram Area of all elements of the building block and a Properties Editor where you can edit the properties of the selected Element.

You can rearrange the window by different actions:

• Click to hide the ribbon bar or to show it,

• Click to auto hide the Building Block Explorer, the Simulation Explorer or the History Manager or to dock it,

• Click to close these views or click the corresponding symbol in the Views group in the Utilities ribbon bar to open it,

• Furthermore, you can drag these views and dock them to a different location. To do so, click on the title bar of the view, drag it around and drop it on one of the icons like

In the following we describe some details of the different subviews.

The ribbon bar offers access to the various functionalities of the application.

The Modules Explorer shows all modules with their building blocks Spatial Structures, Molecules, Reactions, Passive Transports, Observers, Events, Parameter Values, Initial Conditions, and the building blocks for Individuals and Expression Profiles that are located outside of the modules. Additionally, you may find imported observed data in the modules explorer. More information on the concept of modules can be found in Modularization concept. The different building blocks are explained in The Building Block Concept.

A detailed introduction on how to develop models in MoBi® is given in Model Building and Model Components. An in-depth explanation on how to create simulations from the modules can be found in Setting up a Simulation.

Once you have defined the simulations in the current project, the Simulations Explorer lists all of them. For details, see Simulation Results.

The History Manager lists all modeling steps and gives the opportunity to look at earlier versions and thus at the modeling history of the project. For details, see History Manager and History Reporting‌.

Import PBPK Models from PK-Sim®‌

To develop a model in MoBi®, you can either create it from scratch or import a PBPK model from PK-Sim® and extend it. To import a PBPK model, proceed as follows:

1. In PK-Sim®, create a simulation with the desired compound and individual.

2. Save the simulation as *.pkml file (see Export To MoBi®).

3. Start MoBi®.

4. Open the *.pkml file using the File menu and choose the Open Simulation command.

The simulation is loaded into MoBi® as a separate PK-Sim module. Additionally, an Individual and a set of Expression Profiles are created in the Modules Explorer. Furthermore, observed data are imported if they were part of the PK-Sim® simulation.

To add extensions to the PK-Sim® module, create an Extension Module. To do this, right-click the Modules folder in the Modules Explorer, and select Create Module... from the context menu. A new window titled "New Module" will open. Enter a name for the new module (e.g., "Cimetidine Extension"), select the building blocks that should be created in the module, select the merge behavior (see Modularization concept for details), and click OK. The new module will appear in the Modules Explorer.

Create a Project‌ from scratch‌

Alternatively, you can create a new project from scratch. The first step to start working with MoBi® is to create a new project. To do this, click on New in the File menu. You can either work with amount or concentration based reaction networks which needs to be specified when creating a new project.

Create a new module, and create all building blocks in it by selecting them in the "New Module" window. See description of the building blocks on how to populate them with the required information.

Create and Run a Simulation‌

With a model imported from PK-Sim® or created from scratch, you can now create and run a simulation. To do this, follow the steps below:

1. In the ribbon tab Modeling, click the Simulation. The simulation creation wizard allows you to enter simulation name, select the modules to combine, and choose the individual and expression profiles.

2. Enter the simulation name.

3. Select the modules to combine (e.g., the PK-Sim® module and the extension module you created earlier).

1. Click "Next >".

2. Select the individual and the expression profiles you want to use for the simulation.

1. Click "OK".

2. Click the orange arrow ribbon button to run the simulation, or alternatively press the F5 key.

After the computation is done, the simulated results are displayed in the Results tab. On the right, a vertical Chart Editor panel is visible.

The Chart Editor allows you to select the data to be displayed in the chart, and to customize the chart appearance. See Chart Component for details.