SimBiology

Build PK/PD and mechanistic systems biology models interactively

Description

The SimBiology app lets you build models of dynamic systems such as quantitative systems pharmacology (QSP), pharmacokinetic/pharmacodynamic (PK/PD) and systems biology models interactively. It provides a block diagram editor to build the model reaction schematic by using built-in blocks.

Using the app, you can:

  • Build a variety of dynamic systems such as metabolic networks, signaling pathways, QSP, PBPK, and PK/PD models.

  • Create standard compartmental PK models from the built-in library.

  • View your model in the form of mathematical equations using the Equations View, or view the graphical representation using the Diagram view.

  • Use variants to store a set of parameter values or initial conditions that are different from the base model configuration.

  • Create an array of doses to explore different dosing regimens.

  • Import or export SimBiology models to and from the MATLAB® workspace or from a Systems Biology Markup Language (SBML) file.

Open the SimBiology App

  • MATLAB toolstrip: On the Apps tab, under Computational Biology, click the app icon.

  • MATLAB command prompt: Enter simbiology.

Programmatic Use

expand all

simbiology opens the SimBiology desktop.

simbiology(model) opens the app with a SimBiology model. You can make changes to the model in the app or in the command line. Because both the command line and the app point to the same model object, changes you make to the model in the app are reflected in the command line or vice versa. If you have the SimBiology Model Analyzer app open at the same time, the model changes are reflected in there also.

simbiology(file) opens the project file specified by file in the app. file is a string or character vector specifying a file name or path and file name of a SimBiology project sbproj file. If you specify only a file name, the file must be on the MATLAB search path or in the current folder.

Introduced in R2019b