SimBiology Model Builder

Build QSP, PK/PD, and mechanistic systems biology models interactively

Since R2020b

Description

The SimBiology Model Builder app lets you build models of dynamic systems such as quantitative systems pharmacology (QSP) models, pharmacokinetic/pharmacodynamic (PK/PD) models, 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 models, PBPK models, and PK/PD models.

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

• View your model as a graphical representation or as mathematical equations.

• 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.

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Open the SimBiology Model Builder App

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

• MATLAB command prompt: Enter simBiologyModelBuilder.

Warning

SimBiology projects (SBPROJ) are not forward-compatible. Do not load the projects that you created and saved using SimBiology apps from a newer version (such as R2024a) into an older version (such as R2023a) of the apps.

Examples

• Create Model of Receptor-Ligand Kinetics
• Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder
• View Model Expressions in SimBiology Model Builder
• Generate SimBiology Model Report
• View and Run Generated Code by SimBiology Model Builder
• Import and Export Variants and Doses from Excel to SimBiology Model Builder

Programmatic Use

simBiologyModelBuilder

simBiologyModelBuilder opens the app.

simBiologyModelBuilder(m1)

simBiologyModelBuilder(m1) opens the SimBiology model m1 in the SimBiology Model Builder app.

If the SimBiology Model Builder or SimBiology Model Analyzer app is already open, you cannot load a model from the command line. Load the model from the app directly.

simBiologyModelBuilder(sbprojFile)

simBiologyModelBuilder(sbprojFile) opens the SimBiology project file sbprojFile in the SimBiology Model Builder app. sbprojFile 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. If you also have the SimBiology Model Analyzer app open at the same time, both apps share the same project.

Version History

Introduced in R2020b

R2023b: Open a project from the command line when the app is open

You can open a SimBiology project from the MATLAB command line while SimBiology Model Builder or SimBiology Model Analyzer or both apps are already open. If the apps have an unsaved project open, you will be prompted to save it before opening the new project.

R2020b: Loading a project or model from the command line when the app is open is not allowed

If the SimBiology Model Builder or SimBiology Model Analyzer app is open, you cannot load a project or model from the command line using the simBiologyModelBuilder or simBiologyModelAnalyzer functions. Load the project or model from the app directly.