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R2012a Documentation → SimBiology
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Contents

Index

• Getting Started Guide

• Product Description

• SimBiology Product Overview

Integrated Environment

Required Software

Optional Software

Related Software

• Integrating SimBiology Models into Your Existing Workflow

Existing Workflow in Experimental Research

Workflow Incorporating Mathematical Modeling

Workflow Using SimBiology Models for Mathematical Modeling

Using the SimBiology Desktop vs. the Command Line

• SimBiology and SBML

Importing from SBML Files

Exporting a SimBiology Model to SBML Format

• SimBiology Desktop Overview

What is the SimBiology Desktop?

Opening the Desktop

Using the Desktop Tools

Using the Desktop to Learn About the Command Line

• Understanding SimBiology Projects and Libraries

What Are SimBiology Projects?

What Are SimBiology Libraries?

• Managing SimBiology Projects and Libraries from the Desktop

Desktop Management and Navigation Aids

Working with Models in the Desktop

Working with Analysis Tasks in the Desktop

Working with Data in the Desktop

Importing and Exporting Models, Tasks, and Data from the Desktop

Searching a Project from the Desktop

Generating a Report for a Project from the Desktop

Using Libraries from the Desktop

• About The Gene Regulation Model

Model Reactions

Creating a SimBiology Model

Adding the Reaction for Transcription

Adding the Reaction for Translation

Adding the Reactions for Gene Regulation

Adding the Reactions for mRNA and Protein Degradation

• Simulating the Model

• Simulating the Model with a Stochastic Solver

More Examples of Using the Command Line

• User's Guide

• Structural Analysis

Overview of Structural Analysis

• Verifying a Model

What is Model Verification?

When to Verify a Model

Verifying That a Model Has No Warnings or Errors

Example - Verifying a Model

• Determining Conserved Moieties

Introduction to Moiety Conservation

Algorithms for Conserved Cycle Calculations

Example - Determining Conserved Moieties

• Determining the Adjacency Matrix for a Model

What Is an Adjacency Matrix?

Example - Retrieving an Adjacency Matrix for a Model

• Determining the Stoichiometry Matrix for a Model

What Is a Stoichiometry Matrix?

Example - Retrieving a Stoichiometry Matrix for a Model

• Simulation and Analysis

• Pharmacokinetic Modeling

• Creating Reaction Rates

• Creating Rate Rules

• Models Used in Examples

• Method Reference

• Property Reference

• Release Notes

Structural Analysis

Example — Creating and Simulating a Model That Uses
a User-Defined Function in an Expression

Example — Creating and Simulating a Model That Uses a User-Defined Function in an Expression

Overview of Structural Analysis

Overview of Structural Analysis

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