Foundations of systems biology: using cell illustrator and pathway databases

Foreword

Preface

1. Introduction

1.1. Intracellular Events

1.1.1. Transcription, Translation, and Regulation

1.1.2. Signaling Pathways and Proteins

1.1.3. Metabolism and Genes

1.2. Intracellular Reactions and Pathways

2. Pathway Databases

2.1. Major Pathway Databases

2.1.1. KEGG

2.1.2. BioCyc

2.1.3. Ingenuity Pathways Knowledge Base

2.1.4. TRANSPATH

2.1.5. ResNet

2.1.6. Signal Transduction Knowledge Environment (STKE): Database of Cell Signaling

2.1.7. Reactome

2.1.8. Metabolome.jp

2.1.9. Summary and Conclusion

2.2. Software for Pathway Display

2.2.1. Ingenuity Pathway Analysis (IPA)

2.2.2. Pathway Builder

2.2.3. Pathway Studio

2.2.4. Connections Maps

2.2.5. Cytoscape

2.3. File Formats for Pathways

2.3.1. Gene Ontology

2.3.2. PSI MI

2.3.3. CellML

2.3.4. SBML

2.3.5. BioPAX

2.3.6. CSML/CSO

3. Pathway Simulation Software

3.1. Simulation Software Backend

3.1.1. Architecture: Deterministic, Probabilistic, or Hybrid?

3.1.2. Methods of Pathway Modeling

3.2. Major Simulation Software Tools

3.2.1. Gepasi/COPASI

3.2.2. Virtual Cell

3.2.3. Systems Biology Workbench (SBW), Cell Designer, JDesigner

3.2.4. Dizzy

3.2.5. E-Cell

3.2.6. Cell Illustrator

3.2.7. Summary

4. Starting Cell Illustrator

4.1. Installing Cell Illustrator

4.1.1. Operating Systems and Hardware Requirements

4.1.2. Cell Illustrator Lineup

4.1.3. Installing and Running Cell Illustrator

4.1.4. License Install

4.2. Basic Concepts in Cell Illustrator

4.2.1. Basic Concepts

4.2.2. Entity

4.2.3. Process

4.2.4. Connector

4.2.5. Rules for Connecting Elements

4.2.6. Icons for Elements

4.3. Editing a Model on Cell Illustrator

4.3.1. Adding Elements

4.3.2. Model Editing and Canvas Controls

4.4. Simulating Models

4.4.1. Simulation Settings

4.4.2. Graph Settings

4.4.3. Executing Simulation

4.5. Simulation Parameters and Rules

4.5.1. Creating a Model with Discrete Entity and Process

4.5.2. Creating a Model with Continuous Entity and Process

4.5.3. Concepts of Discrete and Continuous

4.6. Pathway Modeling Using Illustrated Elements

4.7. Creating Pathway Models Using Cell Illustrator

4.7.1. Degradation

4.7.2. Translocation

4.7.3. Transcription

4.7.4. Binding

4.7.5. Dissociation

4.7.6. Inhibition

4.7.7. Phosphorylation by Enzyme Reaction

4.8. Conclusion

5. Pathway Modeling and Simulation

5.1. Modeling Signaling Pathway

5.1.1. Main Players: Ligand and Receptor

5.1.2. Modeling EGFR Signaling with EGF Stimulation

5.2. Modeling Metabolic Pathways

5.2.1. Chemical Equations and Pathway Representations

5.2.2. Michaelis-Menten Kinetics and Cell Illustrator Pathway Representation

5.2.3. Creating Glycolysis Pathway Model

5.2.4. Simulation of Glycolysis Pathway

5.2.5. Improving the Model

5.3. Modeling Gene Regulatory Networks

5.3.1. Biological Clocks and Circadian Rhythms

5.3.2. Gene Regulatory Network for Circadian Rhythms in Mice

5.3.3. Modeling Circadian Rhythms in Mice

5.3.4. Creating Hypothesis by Simulation

5.4. Summary

6. Computational Platform for Systems Biology

6.1. Gene Network of Yeast

6.2. Computational Analysis of Gene Network

6.2.1. Displaying Gene Network

6.2.2. Layout of Gene Networks

6.2.3. Pathway Search Function

6.2.4. Extracting Subnetworks

6.2.5. Comparing Two Subnetworks

6.3. Further Functionalities for Systems Biology

6.3.1. Languages for Pathways: CSML 3.0 and CSO

6.3.2. SaaS Technology

6.3.3. Pathway Parameter Search

6.3.4. Much Faster Simulation

6.3.5. Exporting Pathway Models to Programming Languages

6.3.6. Pathway Layout Algorithms

6.3.7. Pathway Database Management System

6.3.8. More Visually: Automatic Generation of Icons

Bibliographic Notes

Index