Overview of Simulation and Analysis :: Simulation and Analysis (SimBiology®)

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Contents

Index

• Getting Started Guide

• User's Guide

• Structural Analysis

• Simulation and Analysis

• Overview of Simulation and Analysis

Typical Workflow

• Simulating Models

Simulating a Model

Plotting Simulation Results

Interpreting Simulation Results

Configuring Stop Time and Other Simulation Settings

Choosing a Simulation Solver

SUNDIALS Solvers

Stochastic Solvers

• Example - Simulating a Model and Viewing Results

Loading the Example Model

Configuring Simulation Settings

Simulating the Model

Plotting Simulation Results

Extracting Data for Analysis

• Calculating Sensitivities

About Calculating Sensitivities

Model Requirements for Calculating Sensitivities

Setting SolverOptions Properties for Calculating Sensitivities

Calculating Sensitivities of a Model and Viewing Results

• Example - Calculating Sensitivities

Loading and Configuring the Model for Sensitivity Analysis

Performing Sensitivity Analysis

Extracting and Plotting Sensitivity Data

Perform Parameter Scan

• Estimating Parameters

About Parameter Estimation

Estimating Parameters of a Model

Specifying Solver Type and Options for Parameter Estimation

About Individual and Population Fitting

• Example - Estimating Parameters

Loading the Example Model

Defining Experimental Data

Simulating the G Protein Model

Estimating the kGd Parameter in the G Protein Model

Simulating and Plotting Results Using the Estimated Parameter

Estimating Other Parameters in the G Protein Model

• Accelerating Model Simulations and Analyses

What Is Acceleration?

What Simulations and Analyses Can Be Accelerated?

When to Accelerate Simulations and Analyses

Prerequisites for Accelerating Simulations and Analyses

Accelerating a Simulation or Analysis

Troubleshooting Accelerated Simulations and Analyses

• Pharmacokinetic Modeling

Required and Recommended Software for Pharmacokinetic Modeling

How SimBiology Supports Pharmacokinetic Modeling

Using the Command Line Versus the SimBiology Desktop

Accessing a Pharmacokinetic Modeling Demo

Acknowledgements: Tobramycin Data Set

Supported Files and Data Types

Support for Importing NONMEM Formatted Files

Creating a Data File with SimBiology Definitions

Importing Data From Files

Importing Data From NONMEM Formatted Files

Other Resources for Importing Data

Ways to Create or Import a Pharmacokinetic Model

How SimBiology Models Represent Pharmacokinetic Models

Creating a Pharmacokinetic Model Using the Command Line

About Dosing Types

About Elimination Types

About Intercompartmental Clearance

Unit Conversion for Imported Data

Data Fitting Functionality

Prerequisites for Data Fitting

Prerequisites for Using Custom SimBiology Models in Data Fitting

Data Fitting Workflow

Specifying and Classifying the Data to Fit

Specifying Solver Type and Options for Fitting

Setting Initial Estimates

Specifying a Nonlinear, Mixed-Effects Model

Specifying a Covariate Model

Specifying the Covariance Pattern of Random Effects

Specifying an Error Model

Specifying Parameter Transformations

Performing Population Fitting

Performing Individual Fitting

• Creating Reaction Rates

Definition of Mass Action Kinetics

Zero-Order Reactions

First-Order Reactions

Second-Order Reactions

Reversible Mass Action

Simple Model for Single Substrate Catalyzed Reactions

Enzyme Reactions with Differential Rate Equations

Enzyme Reactions with Mass Action Kinetics

Enzyme Reactions with Irreversible Henri-Michaelis-Menten Kinetics

• Creating Rate Rules

• Models Used in Examples

Goldbeter Model

SimBiology Model with Rate Rules

SimBiology Model with Reactions

Background on G Protein Cycles

Modeling a G Protein Cycle

M-Phase Control Model

M-Phase Control Equations

SimBiology Model with Rate and Algebraic Rules

SimBiology Model with Reactions and Algebraic Rules

• Method Reference

Constructing (Creating) Objects

Using Object Methods

Help for Objects, Methods, and Properties

• Property Reference

Entering Property Values

Retrieving Property Values

Help for Objects, Methods, and Properties

• Release Notes

Overview of Simulation and Analysis

On this page…

Typical Workflow

After creating models in SimBiology, you can simulate and analyze them.

Typical Workflow

To simulate a model, SimBiology:

Converts the model expressions and quantities to a system of differential equations.
Uses deterministic or stochastic solvers to numerically solve these equations.
Determines the changes in species amounts and parameter values over time.

SimBiology also lets you analyze models. These analyses include a basic simulation of the model as well as additional evaluations such as:

Calculate sensitivities
Estimate parameters

See Also

There are demos that show you how to use the command line to simulate and analyze:

To access demos included with the software, see SimBiology Demos.
To access demos on the Web, see SimBiology Demos and Webinars.

Simulation and Analysis

Simulation and Analysis

Simulating Models

Simulating Models

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