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

• Pharmacokinetic Modeling

• Minimal Cascade Model for a Mitotic Oscillator

• Model of the Yeast Heterotrimeric G Protein Cycle

• M-Phase Control in Xenopus Oocyte Extracts

• Method Reference

• Property Reference

• Release Notes

Learn more about SimBiology

Modeling

This chapter is a collection of topics relevant to modeling in general, but is presented in the context of using SimBiology software to model biological processes.

User's Guide

Defining Reaction Rates with Mass Action Kinetics

Defining Reaction Rates with Mass Action Kinetics

Recommended Products

Get MATLAB trial software

Includes the most popular MATLAB recorded presentations with Q&A sessions led by MATLAB experts.

Get the Interactive Kit

© 1984-2009- The MathWorks, Inc. - Site Help - Patents - Trademarks - Privacy Policy - Preventing Piracy - RSS