SimBiology Model Analyzer

Analyze QSP, PK/PD, and mechanistic systems biology models

Description

The SimBiology Model Analyzer app lets you analyze models of dynamic systems such as metabolic networks, signaling pathways, quantitative systems pharmacology (QSP) models, and pharmacokinetic/pharmacodynamic (PK/PD) models of drugs. It provides several methods to analyze models and various plots to visualize the results.

Using the app, you can:

• Simulate a model to see its dynamic behavior over time.

• Explore biological variability by simulating alternate scenarios such as virtual patients.

• Estimate model parameters using nonlinear regression and nonlinear mixed-effects methods.

• Perform parameter scans and sensitivity analysis to investigate the influence of model parameters and initial conditions on model behavior.

• Specify units and let the app automatically convert the matching physical quantities to one consistent unit system.

• Explore various dosing regimens.

• Perform noncompartmental analysis (NCA) to compute PK parameters of a drug from its PK data.

• View analysis results in various plots.

Available Plots

The app lets you visualize the analysis results using various plots, including:

• Time course of model quantities

• Sensitivity matrix

• Overlay of estimated results on experimental data

• Plots to measure fit quality, such as confidence interval plots, residuals plots, residual distribution plots, actual-versus-predicted plots, and box plots

• Scatter plot matrix

• Percentile plot

Open the SimBiology Model Analyzer App

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

• MATLAB command prompt: Enter simBiologyModelAnalyzer.

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.

Note

The SimBiology Model Builder and SimBiology Model Analyzer apps support SBPROJ files created in R2012a or later. If you are using sbioloadproject, you can load models from any SBPROJ file.

Examples

• Calculate NCA Parameters and Fit Model to PK/PD Data Using SimBiology Model Analyzer
• Find Important Tumor Growth Parameters with Local Sensitivity Analysis Using SimBiology Model Analyzer
• Find Important Parameters for Receptor Occupancy with Global Sensitivity Analysis Using SimBiology Model Analyzer
• Explore Biological Variability with Virtual Patients Using SimBiology Model Analyzer
• Scan Dosing Regimens Using SimBiology Model Analyzer App
• Perform Unit Conversion on Datasheet Columns Using SimBiology Model Analyzer
• Simulate Groups Using Doses and Variants from Data Set
• Generate Report for SimBiology Program Results
• View and Run Program Code Generated by SimBiology Model Analyzer

Programmatic Use

simBiologyModelAnalyzer opens the SimBiology Model Analyzer app.

simBiologyModelAnalyzer(m1) opens the SimBiology model m1 in the SimBiology Model Analyzer 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.

simBiologyModelAnalyzer(sbprojFile) opens the SimBiology project file sbprojFile in the SimBiology Model Analyzer 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 Builder app open at the same time, both apps share the same project.

Version History

Introduced in R2019b

R2026a: Perform unit conversion and scalar expansion on datasheet columns

The app lets you perform unit conversion on datasheets with tables. You can also specify a scalar value and the value is scalar-expanded to fill the whole column with the same value. For an example, see Perform Unit Conversion on Datasheet Columns Using SimBiology Model Analyzer.

R2026a: SimBiology Model Analyzer will no longer import PKData

You can no longer import PKData in the SimBiology Model Analyzer app. Use groupedData instead.

You can still load your existing PKData objects from MAT-files at the command line but the loaded objects will be read-only. To convert a PKData object, pkd, to groupedData, use the following: gd = groupedData(pkd.DataSet,pkd.GroupLabel,pkd.IndependentVarLabel).

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.