SimBiology Desktop Overview

The SimBiology® desktop is a graphical user interface containing a set of integrated tools that are designed to facilitate building, simulating and analyzing models of dynamic systems with a focus on Systems Biology and Pharmacokinetics. Tasks are graphical interfaces that configure simulation and analysis settings used to investigate model behavior. One such task is parameter estimation that calibrates a model against imported data. Tasks produce results that can be further analyzed within the desktop. The models, tasks, imported data and task results are saved in a SimBiology project.

SimBiology also provides a set of libraries. These libraries provide built-in elements for defining kinetic laws, graphical blocks, and units that can be used when building a model. A library of plots provides commonly used visualizations for task results. These libraries can be extended with custom elements.

Opening the Desktop

Open the desktop by typing the following at the MATLAB® command line.

simbiology

Alternatively, select SimBiology from the Apps tab.

Main Desktop Window

The main SimBiology desktop window provides tools for building models, importing and exploring data, visualizing task results, and extending SimBiology libraries. Tasks are defined and executed using the Task Editor.

Home TabAllows you to open and save projects, add models, tasks, and data to a project.
ToolstripDisplays the tabs specific to the open panel.
Content buttonAllows you to quickly access the project files, built-in libraries, and recent files.
Info ButtonShows you the context sensitive help when you hover over it.
Action ButtonContains additional functionality related to the open panel.
Address BarShows the name of the panel that is open.

Additional Tools

You can access additional tools such as the MATLAB Code Capture Tool by selecting Home > Layout > MATLAB Code Capture Tool.

Models

A SimBiology model is composed of species, compartments, parameters, reactions, rules, and events. Species, compartments, and parameters are categorized as model quantities. Reactions, rules, and events are categorized as model expressions. The dynamics of the model are governed by these expressions.

A SimBiology model can also have modifiers associated with it. There are two types of modifiers, variants and doses. Variants allow you to store alternative quantity values that can be applied to a model during analysis. Doses allow you to increase the amount of a species during a simulation.

Adding a Model

Select Home > Add Model to add a model to a project. You can create a new model, load a model from a SimBiology project, or import a SBML file. In addition, you can add commonly used PK models from the PK library.

When a model is open in the main desktop window, the toolstrip will add tabs for working with the model. One of those tabs is the Model tab. It contains buttons for editing the model in tabular or diagram form, and creating tasks.

Data

Data can be imported for use with tasks such as parameter fitting. Once the data is imported you can visualize and perform preliminary data processing.

Adding Data

To add data, select Home > Add Data. You can import data from:

  • CVS formatted files

  • Microsoft® Excel® files

  • SimBiology project files

  • MATLAB MAT files

  • SAS® XPORT formatted files

  • The MATLAB workspace

When data is open in the main desktop window, you can classify data columns and assign units. The toolstrip will add tabs for working with the data. One of those tabs is the Define Plot tab which is used to create plots. Another tab is the Explore Data tab. It allows you to:

  • Exclude data rows – You can exclude data rows manually or using MALAB expressions. Excluded data is ignored when running tasks.

  • Add new data columns – You can add new data columns by using MATLAB expressions on other existing data columns. You can use the new columns when running tasks.

Tasks

Tasks are analyses that can be performed on a model. There are several built-in tasks such as simulation, estimation, and sensitivity analysis. In addition, custom tasks can be created using the MATLAB language.

Adding a Task

Select Home > Add Task to add a task to a project. Alternatively, you can select Model > Add Task when a model is open in the main desktop window.

A task is opened in a separate window called the Task Editor. The editor consists of three section: general task setup, interactive task setup, and live visualization of results. The general setup is used to define settings such as simulation stop time, and variants and doses applied during task execution. The interactive task setup provides sliders for exploring model behavior. The sliders and live visualization plots can be configured using the tools on the Explorer tab.

For example, a simulation task appears as follows.

Layout SectionAllows you to configure the open sections of the Task Editor.
Info ButtonShows you the context sensitive help when you hover over it.
Run SectionPress the Run button to execute the task.
Task Results SectionAllows you to manage results generated from executing the task.

Task Results

Task results generated at the completion of a task run are stored as Last Run. These results are overwritten every time the task is executed. To avoid overwriting a particular set of results, use the Save button in the Task Results section.

A list of all saved results can be accessed from the Task Results section. The Go To button will open the selected results. When task results are open in the main desktop window, the toolstrip will add tabs for working with the results. One of those tabs is the Define Plot tab. There you can visualize results, create additional plots, and export results to the MATLAB workspace.

Related Examples

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