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Contents

Index

• Getting Started Guide

• Introduction

• SimBiology Overview

Features

Integrated Environment

• 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

What Is 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

Models

Analysis Tasks

Data

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 Diagram

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

Getting Started Using the Command Line

This chapter shows how to model a simple gene-regulation pathway using the command-line interface.

Managing SimBiology Projects and Libraries

About The Gene Regulation Model

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