SimBiology Apps

Interactive apps to facilitate building, simulating, and analyzing dynamic systems

SimBiology provides a set of integrated apps that are designed to facilitate building, simulating, and analyzing models of dynamic systems such as quantitative systems pharmacology (QSP), pharmacokinetic/pharmacodynamic (PK/PD) and systems biology models.

The SimBiology Model Builder app lets you build dynamic models interactively using various modeling elements. For instance, you can model a variety of biological systems such as signaling pathways, metabolic networks, PBPK, QSP, and PK/PD models. It also lets you model biological variability and different dosing regimens to investigate various experimental conditions and dosing strategies.
The SimBiology Model Analyzer app lets you perform analyses on models of dynamic systems. You can simulate the dynamic behavior of a model using various solvers and estimate model parameters. To investigate system dynamics and guide experimentation, you can perform sensitivity analysis and parameter sweeps.

Apps

SimBiology Model Builder	Build QSP, PK/PD, and mechanistic systems biology models interactively
SimBiology Model Analyzer	Analyze QSP, PK/PD, and mechanistic systems biology models

Functions

`simbiology`	Open SimBiology Model Builder
`simbio.diagram.getBlock`	Get SimBiology diagram block properties
`simbio.diagram.setBlock`	Set SimBiology diagram block properties
`simbio.diagram.getLine`	Get SimBiology diagram line properties
`simbio.diagram.setLine`	Set SimBiology diagram line properties
`simbio.diagram.splitBlock`	Split SimBiology species block in diagram
`simbio.diagram.joinBlock`	Combine copies of SimBiology species block in diagram

Topics

Build Models

Create Model of Receptor-Ligand Kinetics
Create and simulate a simple receptor-ligand kinetics model using SimBiology apps.
Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder
Update a glucose-insulin model to integrate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound.
Copy SimBiology Blocks
Copy and paste SimBiology blocks while building models in the Diagram.
SimBiology Model Component Libraries
The SimBiology^® libraries are collections of built-in components that you can use to build and analyze models.
Message Indicator Icons in SimBiology Model Builder
The SimBiology Model Builder app uses contextual icons to provide more information about model components in the browser tables and blocks in the Diagram tab.
Undo and Redo Model Changes in SimBiology
You can undo and redo actions related to model building and configuring block properties.
Keyboard Shortcuts for SimBiology Model Builder
The SimBiology Model Builder app provides keyboard shortcuts for various modeling actions.
Generate SimBiology Model Report
Generate reports containing model information.
View and Run Generated Code by SimBiology Model Builder
View and run generated MATLAB code for model building actions in the Model Builder app.
Import and Export Variants and Doses from Excel to SimBiology Model Builder
Import and export variant and dosing information saved in an Excel file to the Model Builder app.

Analyze Models and Data

Calculate NCA Parameters and Fit Model to PK/PD Data Using SimBiology Model Analyzer
Calibrate model parameters by performing noncompartmental analysis and fitting to experimental PKPD data using nonlinear regression.
Find Important Tumor Growth Parameters with Local Sensitivity Analysis Using SimBiology Model Analyzer
Perform local sensitivity analysis to find important parameters for tumor growth.
Find Important Parameters for Receptor Occupancy with Global Sensitivity Analysis Using SimBiology Model Analyzer
Perform GSA analyses, such as Sobol indices, elementary effects, and multiparametric GSA, to find important model parameters in a target-mediated drug disposition model.
Explore Biological Variability with Virtual Patients Using SimBiology Model Analyzer
Generate sample values for model parameters to represent virtual patients, simulate to explore tumor growth variability, and investigate the effects of dosing regimens on tumor size.
Scan Dosing Regimens Using SimBiology Model Analyzer App
Explore multiple dosing amounts that meet efficacy and toxicity thresholds.
Simulate Groups Using Doses and Variants from Data Set
Perform group simulation using the group-specific doses and variants from a data set.
Generate Report for SimBiology Program Results
Generate reports containing analysis results from programs.
View and Run Program Code Generated by SimBiology Model Analyzer
View and run generated program code at the command line.
Percentile Plot
Visualize experimental data and simulation statistics using percentile plot.
Keyboard Shortcuts for SimBiology Model Analyzer
The SimBiology Model Analyzer app provides keyboard shortcuts for various analysis actions.