Foreword |
Preface |
Introduction / 1: |
Intracellular Events / 1.1: |
Transcription, Translation, and Regulation / 1.1.1: |
Signaling Pathways and Proteins / 1.1.2: |
Metabolism and Genes / 1.1.3: |
Intracellular Reactions and Pathways / 1.2: |
Pathway Databases / 2: |
Major Pathway Databases / 2.1: |
KEGG / 2.1.1: |
BioCyc / 2.1.2: |
Ingenuity Pathways Knowledge Base / 2.1.3: |
TRANSPATH / 2.1.4: |
ResNet / 2.1.5: |
Signal Transduction Knowledge Environment (STKE): Database of Cell Signaling / 2.1.6: |
Reactome / 2.1.7: |
Metabolome.jp / 2.1.8: |
Summary and Conclusion / 2.1.9: |
Software for Pathway Display / 2.2: |
Ingenuity Pathway Analysis (IPA) / 2.2.1: |
Pathway Builder / 2.2.2: |
Pathway Studio / 2.2.3: |
Connections Maps / 2.2.4: |
Cytoscape / 2.2.5: |
File Formats for Pathways / 2.3: |
Gene Ontology / 2.3.1: |
PSI MI / 2.3.2: |
CellML / 2.3.3: |
SBML / 2.3.4: |
BioPAX / 2.3.5: |
CSML/CSO / 2.3.6: |
Pathway Simulation Software / 3: |
Simulation Software Backend / 3.1: |
Architecture: Deterministic, Probabilistic, or Hybrid? / 3.1.1: |
Methods of Pathway Modeling / 3.1.2: |
Major Simulation Software Tools / 3.2: |
Gepasi/COPASI / 3.2.1: |
Virtual Cell / 3.2.2: |
Systems Biology Workbench (SBW), Cell Designer, JDesigner / 3.2.3: |
Dizzy / 3.2.4: |
E-Cell / 3.2.5: |
Cell Illustrator / 3.2.6: |
Summary / 3.2.7: |
Starting Cell Illustrator / 4: |
Installing Cell Illustrator / 4.1: |
Operating Systems and Hardware Requirements / 4.1.1: |
Cell Illustrator Lineup / 4.1.2: |
Installing and Running Cell Illustrator / 4.1.3: |
License Install / 4.1.4: |
Basic Concepts in Cell Illustrator / 4.2: |
Basic Concepts / 4.2.1: |
Entity / 4.2.2: |
Process / 4.2.3: |
Connector / 4.2.4: |
Rules for Connecting Elements / 4.2.5: |
Icons for Elements / 4.2.6: |
Editing a Model on Cell Illustrator / 4.3: |
Adding Elements / 4.3.1: |
Model Editing and Canvas Controls / 4.3.2: |
Simulating Models / 4.4: |
Simulation Settings / 4.4.1: |
Graph Settings / 4.4.2: |
Executing Simulation / 4.4.3: |
Simulation Parameters and Rules / 4.5: |
Creating a Model with Discrete Entity and Process / 4.5.1: |
Creating a Model with Continuous Entity and Process / 4.5.2: |
Concepts of Discrete and Continuous / 4.5.3: |
Pathway Modeling Using Illustrated Elements / 4.6: |
Creating Pathway Models Using Cell Illustrator / 4.7: |
Degradation / 4.7.1: |
Translocation / 4.7.2: |
Transcription / 4.7.3: |
Binding / 4.7.4: |
Dissociation / 4.7.5: |
Inhibition / 4.7.6: |
Phosphorylation by Enzyme Reaction / 4.7.7: |
Conclusion / 4.8: |
Pathway Modeling and Simulation / 5: |
Modeling Signaling Pathway / 5.1: |
Main Players: Ligand and Receptor / 5.1.1: |
Modeling EGFR Signaling with EGF Stimulation / 5.1.2: |
Modeling Metabolic Pathways / 5.2: |
Chemical Equations and Pathway Representations / 5.2.1: |
Michaelis-Menten Kinetics and Cell Illustrator Pathway Representation / 5.2.2: |
Creating Glycolysis Pathway Model / 5.2.3: |
Simulation of Glycolysis Pathway / 5.2.4: |
Improving the Model / 5.2.5: |
Modeling Gene Regulatory Networks / 5.3: |
Biological Clocks and Circadian Rhythms / 5.3.1: |
Gene Regulatory Network for Circadian Rhythms in Mice / 5.3.2: |
Modeling Circadian Rhythms in Mice / 5.3.3: |
Creating Hypothesis by Simulation / 5.3.4: |
Computational Platform for Systems Biology / 5.4: |
Gene Network of Yeast / 6.1: |
Computational Analysis of Gene Network / 6.2: |
Displaying Gene Network / 6.2.1: |
Layout of Gene Networks / 6.2.2: |
Pathway Search Function / 6.2.3: |
Extracting Subnetworks / 6.2.4: |
Comparing Two Subnetworks / 6.2.5: |
Further Functionalities for Systems Biology / 6.3: |
Languages for Pathways: CSML 3.0 and CSO / 6.3.1: |
SaaS Technology / 6.3.2: |
Pathway Parameter Search / 6.3.3: |
Much Faster Simulation / 6.3.4: |
Exporting Pathway Models to Programming Languages / 6.3.5: |
Pathway Layout Algorithms / 6.3.6: |
Pathway Database Management System / 6.3.7: |
More Visually: Automatic Generation of Icons / 6.3.8: |
Bibliographic Notes |
Index |
Foreword |
Preface |
Introduction / 1: |
Intracellular Events / 1.1: |
Transcription, Translation, and Regulation / 1.1.1: |
Signaling Pathways and Proteins / 1.1.2: |