Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases (Book with CD- ROM)

by Nagasaki, Masao

• ISBN13: 9781848820227
• ISBN10: 1848820224
• Edition: 1st
• Format: Hardcover
• Copyright: 2009-04-01
• Publisher: SPRINGER

Summary

The Computational Biology series publishes the very latest, high-quality research devoted to specific issues in computer-assisted analysis of biological data. The main emphasis is on current scientific developments and innovative techniques in computational biology (bioinformatics), bringing to light methods from mathematics, statistics and computer science that directly address biological problems currently under investigation.

Table of Contents

Foreword	p. v
Preface	p. vii
Introduction	p. 1
Intracellular Events	p. 1
Transcription, Translation, and Regulation	p. 1
Signaling Pathways and Proteins	p. 3
Metabolism and Genes	p. 3
Intracellular Reactions and Pathways	p. 3
Pathway Databases	p. 5
Major Pathway Databases	p. 5
KEGG	p. 6
BioCyc	p. 8
Ingenuity Pathways Knowledge Base	p. 8
TRANSPATH	p. 8
ResNet	p. 9
Signal Transduction Knowledge Environment (STKE): Database of Cell Signaling	p. 9
Reactome	p. 11
Metabolome.jp	p. 12
Summary and Conclusion	p. 12
Software for Pathway Display	p. 13
Ingenuity Pathway Analysis (IPA)	p. 13
Pathway Builder	p. 14
Pathway Studio	p. 14
Connections Maps	p. 14
Cytoscape	p. 14
File Formats for Pathways	p. 15
Gene Ontology	p. 15
PSI MI	p. 16
CellML	p. 16
SBML	p. 16
BioPAX	p. 16
CSML/CSO	p. 17
Pathway Simulation Software	p. 19
Simulation Software Backend	p. 19
Architecture: Deterministic, Probabilistic, or Hybrid?	p. 20
Methods of Pathway Modeling	p. 20
Major Simulation Software Tools	p. 21
Gepasi/COPASI	p. 21
Virtual Cell	p. 21
Systems Biology Workbench (SBW), Cell Designer, JDesigner	p. 21
Dizzy	p. 22
E-Cell	p. 22
Cell Illustrator	p. 22
Summary	p. 24
Starting Cell Illustrator	p. 25
Installing Cell Illustrator	p. 25
Operating Systems and Hardware Requirements	p. 25
Cell Illustrator Lineup	p. 26
Installing and Running Cell Illustrator	p. 26
License Install	p. 28
Basic Concepts in Cell Illustrator	p. 28
Basic Concepts	p. 28
Entity	p. 28
Process	p. 30
Connector	p. 33
Rules for Connecting Elements	p. 34
Icons for Elements	p. 35
Editing a Model on Cell Illustrator	p. 36
Adding Elements	p. 36
Model Editing and Canvas Controls	p. 39
Simulating Models	p. 41
Simulation Settings	p. 41
Graph Settings	p. 41
Executing Simulation	p. 43
Simulation Parameters and Rules	p. 44
Creating a Model with Discrete Entity and Process	p. 44
Creating a Model with Continuous Entity and Process	p. 49
Concepts of Discrete and Continuous	p. 51
Pathway Modeling Using Illustrated Elements	p. 52
Creating Pathway Models Using Cell Illustrator	p. 55
Degradation	p. 55
Translocation	p. 57
Transcription	p. 60
Binding	p. 62
Dissociation	p. 64
Inhibition	p. 66
Phosphorylation by Enzyme Reaction	p. 68
Conclusion	p. 73
Pathway Modeling and Simulation	p. 75
Modeling Signaling Pathway	p. 75
Main Players: Ligand and Receptor	p. 75
Modeling EGFR Signaling with EGF Stimulation	p. 76
Modeling Metabolic Pathways	p. 87
Chemical Equations and Pathway Representations	p. 87
Michaelis-Menten Kinetics and Cell Illustrator Pathway Representation	p. 88
Creating Glycolysis Pathway Model	p. 89
Simulation of Glycolysis Pathway	p. 101
Improving the Model	p. 101
Modeling Gene Regulatory Networks	p. 106
Biological Clocks and Circadian Rhythms	p. 106
Gene Regulatory Network for Circadian Rhythms in Mice	p. 107
Modeling Circadian Rhythms in Mice	p. 108
Creating Hypothesis by Simulation	p. 119
Summary	p. 124
Computational Platform for Systems Biology	p. 127
Gene Network of Yeast	p. 127
Computational Analysis of Gene Network	p. 128
Displaying Gene Network	p. 128
Layout of Gene Networks	p. 130
Pathway Search Function	p. 131
Extracting Subnetworks	p. 132
Comparing Two Subnetworks	p. 133
Further Functionalities for Systems Biology	p. 136
Languages for Pathways: CSML 3.0 and CSO	p. 136
SaaS Technology	p. 137
Pathway Parameter Search	p. 138
Much Faster Simulation	p. 138
Exporting Pathway Models to Programming Languages	p. 138
Pathway Layout Algorithms	p. 139
Pathway Database Management System	p. 141
More Visually: Automatic Generation of Icons	p. 142
Bibliographic Notes	p. 145
Index	p. 151
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