Contents

Index

• Getting Started Guide

• Introduction

• 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

• Getting Started in the SimBiology Desktop

Creating or Opening a Model Using the New Project Wizard

Opening a SimBiology Project

• Features and Functions

Using the Command Line versus the SimBiology Desktop

Graphical User Interface

Command-Line Interface

Data Formats and Projects

• SimBiology Support and SBML

Importing SBML Files

Converting a SimBiology Model to SBML Format

• SimBiology Model Components

Organization of SimBiology Objects

Configuration Sets

Simulation Data

• Building SimBiology Models

• Gene Regulation Model

Model Reactions

Opening the Gene Regulation Model in the SimBiology Desktop

• Modeling Using the SimBiology Graphical User Interface

About the Model Used in This Tutorial

Creating a Model

Saving Your Work as a SimBiology Project File

Adding Reactions to a Model

Simulating a Model

• Modeling Using the SimBiology Diagram

About This Example

Creating a Model

Saving Your Work as a SimBiology Project File

Adding Reactions to a Model Diagram

Simulating a Model

Setting Block Appearance and Diagram Layout

Printing and Exporting the Diagram

• Modeling Using the Command-Line Interface

About This Example

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 with an ODE Solver

Simulating the Model with a Stochastic Solver

• Release Notes

Learn more about SimBiology

Getting Started Guide

This document introduces the SimBiology^® software and how to accomplish basic tasks in systems biology with this software.

Introduction	Overview of the features in SimBiology and a conceptual model for using the software
Building SimBiology Models	Tutorial model that demonstrates SimBiology features

Introduction

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