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R2011b Documentation → SimBiology
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Contents

Index

• Getting Started Guide

• Introduction

• SimBiology 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

• Getting Started Using the SimBiology Desktop

• 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

Desktop Management and Navigation Aids

Importing and Exporting Models, Tasks, and Data

Searching a Project

Generating a Report for a Project

Using Libraries

• Getting Started Using the Command Line

• 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

• Release Notes

Introduction

This chapter introduces SimBiology functions and features to help you develop a conceptual model for working with the software and your biochemical data.

Getting Started Guide

Getting Started Guide

SimBiology Overview

SimBiology Overview

Free Computational Biology Interactive Kit

See how to analyze, visualize, and model biological data and systems using MathWorks products.

Trials Available

Try the latest computational biology products.

Get trial software

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