SimBiology - Documentation

Contents

Index

• Getting Started Guide

• Defining Reaction Rates with Mass Action Kinetics

Definition of Mass Action Kinetics

Zero-Order Reactions

First-Order Reactions

Second-Order Reactions

Reversible Mass Action

• Defining Reaction Rates with Enzyme Kinetics

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

• Evaluation of Reaction Rate

Reaction Rate Dimensions

Reactions Spanning Multiple Compartments

• Using Constant Amount and Boundary Condition for Species

Definition of Constant and Boundary Properties

Changing Species Amounts with Reactions or Rules

Keeping Species Amount Unchanged

Constant = NO, Boundary = YES

Constant = YES, Boundary = YES

• Scoping Parameters for Reactions, Rules, and Events

Definition of Parameter Scope

Using a Parameter in Events and Rules

Changing the Scope of a Parameter

• Changing Model Component Values Using Rules

What Is a Rule?

What Is an initialAssignment Rule?

What Is a repeatedAssignment Rule?

What Is an Algebraic Rule?

What Is a Rate Rule?

Typical Uses of Rate Rules

• Changing Model Component Values Using Events

What Is an Event?

How Events Are Evaluated

Evaluation of Simultaneous Events

Evaluation of Multiple Event Functions

When One Event Triggers Another Event

Cyclical Events

• Desktop Example - Changing Species Amounts Using an Event

Adding an Event to the Example Model

Simulating the Modified Model

• Storing and Applying Alternate Model Values Using Variants

What Are Variants?

Applying Multiple Variants in a Model

• Desktop Example - Applying Changes to Parameter Value Using a Variant

Applying Alternate Values Using Variants

Simulation Results for the Model of the Mutant Strain

• Verifying that the Model Has No Warnings or Errors

Verifying the Model in the SimBiology Desktop

Verifying the Model at the Command Line

• Desktop Example - Using User-Defined Functions in Expressions

Creating an M-File Function

Calling the Function in a Rule Expression

• Importing and Exporting Model Component Data

Importing Model Component Data

Exporting Model Component Data

• Performing Simulations

Performing Simulations at the Command Line

Performing Simulations in the SimBiology Desktop

• About Simulation Solvers

How Solvers Work

Stiff Versus Nonstiff Models

Selecting a Solver

• Nonstiff Deterministic Solvers

When to Use Nonstiff Deterministic Solvers

ode45 (Dormand-Prince)

ode23 (Bogacki-Shampine)

• Stiff Deterministic Solvers

When to Use Stiff Deterministic Solvers

ode15s (stiff/NDF)

ode23s (stiff/Mod. Rosenbrock)

ode23t (Mode. stiff/Trapezoidal)

ode23tb (stiff/TR-BDF2)

• Stochastic Solvers

When to Use Stochastic Solvers

Stochastic Simulation Algorithm (SSA)

Explicit Tau-Leaping Algorithm

Implicit Tau-Leaping Algorithm

Ensemble Runs of Stochastic Simulations

Sundials Solvers

• Scanning Analysis

Scanning Overview

Creating a Scan Task

Setting Options to Scan Using User-Defined Values

Options For Monte Carlo Methods

Setting Options to Scan Using Monte Carlo Methods

• Desktop Example - Scanning

Setting Options to Scan with One Parameter

Results of Scanning with One Parameter

Scanning with Multiple Parameters

Results of Scanning with Multiple Parameters

• Sensitivity Analysis

About Sensitivity Analysis

Performing Sensitivity Analysis Using the Command Line

Performing Sensitivity Analysis Using the Desktop

• Desktop Example - Calculating Sensitivities

Setting Options for Sensitivity Analysis

Getting Results for Sensitivity Analysis

• Command-Line Example - Calculating Sensitivities

Loading and Configuring the Model for Sensitivity Analysis

Performing Sensitivity Analysis

Extracting and Plotting Sensitivity Data

• Parameter Estimation

About Parameter Estimation

SimBiology Parameter Estimation

• Command-Line Example - Parameter Estimation

About the Example Model

Importing Target Experimental Data

Simulating the G Protein Model

Estimating a Parameter (kGd) in the G Protein Model

Simulating and Plotting Results Using the Estimated Parameter

Estimating Other Parameters in the G Protein Model

• Moiety Conservation

Introduction to Moiety Conservation

Algorithms for Conserved Cycle Calculations

• Command-Line Examples - Determining Conserved Moieties

G Protein Example

Mitotic Oscillator Example

• Desktop Example - Creating Custom Analysis

About Custom Analysis

Open the Example Project

Setting Up a Custom Task

Parameter Estimation Using Custom Task

• Visualizing Results Using Plot Types

About Plot Types

How Plot Types Work

Summary of Built-In Plot Types

When to Use User-Defined Plot-Types

• Desktop Example - Creating and Using Plot Types

Why Use User-Defined Plot Types?

Creating a User-Defined Plot Type in the Library Explorer

Using the Plot Type in a Task

• Pharmacokinetic Modeling

• Pharmacokinetic Modeling Functionality

Required and Recommended Products

How This Product Supports Pharmacokinetic Modeling

Using the Command Line Versus the SimBiology Desktop

Accessing a Pharmacokinetic Modeling Demo

• Importing Data

Supported Files and Data Types

Importing Data at the Command Line

Data Import in the SimBiology Desktop

Importing Data from the MATLAB Workspace into the SimBiology Desktop

Importing Data from a Text File into the SimBiology Desktop

Importing Data from an Excel File into the SimBiology Desktop

Importing Data from a MAT-File into the SimBiology Desktop

Resources for Working with Imported Data

• Working with Imported Data in the SimBiology Desktop

Accessing Imported Data

Identifying Group and Independent Variables in the Data

Visualizing Data Using Plots in the SimBiology Desktop

Excluding Rows of Data

Creating Additional Data Columns Using Derived Data

Calculating Statistics for Imported Data

Saving Your Work as a SimBiology Project File

• Creating Pharmacokinetic Models

How Pharmacokinetic Models Are Represented by SimBiology Models

Creating PK Models at the Command Line

Creating PK Models in the SimBiology Desktop Using a Wizard

About Dosing Types

About Elimination Types

About Intercompartmental Clearance

Unit Conversion for Imported Data and the Model

• Parameter Fitting Using Custom SimBiology Models

Defining Model Components for Observed Response, Dose, Dosing Type, and Parameters to be Estimated

Simulating a Model Containing Dosing Information

• Parameter Fitting in Pharmacokinetic Models

Parameter Fitting Functionality

Prerequisites for Parameter Fitting

• Fitting Pharmacokinetic Model Parameters at the Command Line

Fitting Parameters

Specifying and Classifying the Data to Fit

Setting Initial Estimates

Specifying the Covariance Pattern of Random Effects and a Covariate Model

Performing Population Fitting Using sbionlmefit

Performing Individual Fitting Using sbionlinfit

About Simulation Settings and Specifying Alternate Values for Initial Estimates

• Fitting Pharmacokinetic Model Parameters in the SimBiology Desktop

Fitting Parameters

Opening a SimBiology Project

Adding a Model Task to Fit Parameters

Performing Population Fitting

Performing Individual Fitting

About Simulation Settings and Specifying Alternate Values for Initial Estimates

Visualizing Parameter Fitting Results and Generating Diagnostic Plots

• Minimal Cascade Model for a Mitotic Oscillator

• Goldbeter Model

About the Goldbeter Model

Reaction Descriptions and Model Assumptions

Mathematical Model

• SimBiology Model with Rate Rules

SimBiology Model with Rules

SimBiology Simulation with Rules

• SimBiology Model with Reactions

Converting Differential Rate Equations to Reactions

Calculating Initial Values for Reactions

SimBiology Simulation with Reactions

• Model of the Yeast Heterotrimeric G Protein Cycle

• Background on G Protein Cycles

G Proteins and Pheromone Response

• Modeling a G Protein Cycle

Reactions Overview

Assumptions, Experimental Data, and Units in the G Protein Model

• Building the G Protein Cycle Model

Opening the SimBiology Desktop

Saving Your Work as a SimBiology Project File

Adding a Reaction to the SimBiology Model

Determining the Reaction Rate Equation

Setting the Compartment Name

Setting Initial Amounts of Species

• Completing the SimBiology Model

Alternative Ways to Build Reactions in the Desktop

Creating a Rule for the G Protein Model

Verifying the Model

• Simulating the G Protein Cycle Model

Setting Conditions Before Simulating the G Protein Model

Simulation Results for the Wild-Type Strain Model

• Creating the Mutant Strain Using a Variant

Modeling the Mutant Strain

Applying Alternate Values Using Variants

Simulation Results for the Model of the Mutant Strain

• Creating a Custom Plot-Type to View Simulation Results

Creating a Custom Plot

Visualizing Results for the Mutant Strain Using a Custom Plot

• Plotting Species from Two Different Data Sets

Procedures Described in This Section

Plotting the Active G Protein Fraction from the Wild-Type Strain Model

Creating a Custom Plot to Compare the Data

Plotting the Active G Protein Fraction from the Model of the Mutant Strain

• Plotting Experimental Data with Simulation Data

About the Experimental Data

Creating a Custom Plot for Experimental Data

Plotting the Data

• M-Phase Control in Xenopus Oocyte Extracts

• M-Phase Control Model

Synthesis Reactions

Regulation Reactions with Active MPF

• M-Phase Control Equations

About the Rate Equations in This Example

Converting Differential Equations to Reactions

Equation 1, Cyclin B

Equation 2, M-Phase Promoting Factor

Equation 3, Inhibited M-Phase Promoting Factor

Equation 4, Inhibited and Activated M-Phase Promoting Factor

Equation 5, Activated M-Phase Promoting Factor

Equation 11, Cell Division Control 25

Equation 12, Wee1 Activation/Deactivation

Equation 13, Intermediate Enzyme Activation/Deactivation

Equation 14, APC Activation/Deactivation

Equation 17, Rate Parameter K2

Equation 18, Rate Parameter Kcdc25

Equation 19, Rate Parameter Kwee1

• SimBiology Model with Rate and Algebraic Rules

Writing Differential Rate Equations as Rate Rules

Rate Rule 1, Cyclin B (CycB)

Rate Rule 2, M-Phase Promoting Factor (MPF)

Rate Rule 3, Inhibited M-Phase Promoting Factor (pMPF)

Rate Rule 4, Activated but Inhibited M-Phase Promoting Factor (pMPFp)

Rate Rule 5, Activated M-Phase Promoting Factor (MPFp)

Rate Rule 11, Activated Cdc25 (Cdc25p)

Rate Rule 12, Inhibited Wee1 (Wee1p)

Rate Rule 13, Activated Intermediate Enzyme (IEp)

Rate Rule 14, Activated APC (APCa)

Algebraic Rule 17, Rate Parameter K2

Algebraic Rule 18, Rate Parameter Kcdc25

Algebraic Rule 19, Rate Parameter Kwee1

Simulation of the M-Phase Control Model with Rules

• SimBiology Model with Reactions and Algebraic Rules

Reaction 1, Synthesis of Cyclin B

Reaction 2, Degradation of Cyclin B

Reaction 3, Dimerization of Cyclin B with Cdc2 Kinase

Reaction 4, Degradation of Cyclin B on MPF

Reaction 5, Deactivation of Active MPF

Reaction 6, Activation of MPF

Reaction 7, Remove Inhibiting Phosphate from Inhibited MPF

Reaction 8, Inhibition of MPF by Phosphorylation

Reaction 11, Degradation of Cyclin B on Inhibited MPF

Reaction 12, Deactivation of MPF to Inhibited MPF

Reaction 13, Activation of Inhibited MPF

Reaction 15, Degradation of Cyclin B on Active but Inhibited MPF

Reaction 16, Inhibit MPF by Phosphorylation

Reaction 17, Remove Inhibiting Phosphate from Activated MPF

Reaction 19, Degradation of Cyclin B on Activated MPF

Reaction 36, Activation of Cdc25 by Activated MPF

Reaction 37, Deactivation of Cdc25

Reaction 38, Deactivation of Wee1 by Active MPF

Reaction 39, Activation of Wee1

Reaction 40, Activation of Intermediate Enzyme by Active MPF

Reaction 41, Deactivation of IE

Reaction 42, APC Activation by IEp

Reaction 43, APC Deactivation

Block Diagram of the M-Phase Control Model with Reactions

Simulation of the M-Phase Control Model with Reactions

• Method Reference

Abstract Kinetic Laws

Configuration Sets

Pharmacokinetic Modeling

Units and Unit Prefixes

• Using Object Methods

Constructing (Creating) Objects

Using Object Methods

Help for Objects, Methods, and Properties

• Property Reference

Abstract Kinetic Law

Configuration Sets

• Using Object Properties

Entering Property Values

Retrieving Property Values

Help for Objects, Methods, and Properties

• Release Notes

	Functions:
	By Category
	Alphabetical List

	Methods:
	By Category
	Alphabetical List

	Properties:
	By Category
	Alphabetical List



	Documentation Set

	Getting Started
	Introduction to the features and functions in SimBiology with tutorial examples

	User's Guide
	Topics in modeling, simulation, and analysis

	Model Reference
	Biological models from the literature converted to SimBiology format

	Examples in Documentation
	Lists major examples in the SimBiology documentation



	Product Demos

	SimBiology Demos
	Presents a collection of demos that you can run from the Help browser to help you learn the product



	What's New

	Release Notes
	Summarizes new features, bug fixes, upgrade issues, etc.



	Printable (PDF) Documentation on the Web

PDF documents reflect the most recent version of SimBiology and might describe features not available in earlier versions of the software.
	SimBiology Getting Started Guide
	SimBiology User's Guide
	SimBiology Reference
	SimBiology Model Reference
	SimBiology Release Notes

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