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E-raamat: Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases

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  • Formaat: PDF+DRM
  • Sari: Computational Biology 13
  • Ilmumisaeg: 21-Apr-2009
  • Kirjastus: Springer London Ltd
  • Keel: eng
  • ISBN-13: 9781848820234
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Foundations of Systems Biology: Using Cell Illustrator and Pathway DatabasesSuurem pilt
  • Formaat: PDF+DRM
  • Sari: Computational Biology 13
  • Ilmumisaeg: 21-Apr-2009
  • Kirjastus: Springer London Ltd
  • Keel: eng
  • ISBN-13: 9781848820234
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Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like Is the database viewable through a web browser? Is there a licensing fee? What is the data type (metabolic, gene regulatory, signaling, etc. )? Is the database developed/maintained by a curator or a computer? Is there any software for editing pathways? Is it possible to simulate the pathway? It then goes on to introduce a speci c such tool, that is, the fabulous Cell - lustrator 3. 0 tool developed by the authors.
Foreword v
Preface vii
1 Introduction 1
1.1 Intracellular Events
1
1.1.1 Transcription, Translation, and Regulation
1
1.1.2 Signaling Pathways and Proteins
3
1.1.3 Metabolism and Genes
3
1.2 Intracellular Reactions and Pathways
3
2 Pathway Databases 5
2.1 Major Pathway Databases
5
2.1.1 KEGG
6
2.1.2 BioCyc
8
2.1.3 Ingenuity Pathways Knowledge Base
8
2.1.4 TRANSPATH
8
2.1.5 ResNet
9
2.1.6 Signal Transduction Knowledge Environment (STKE): Database of Cell Signaling
9
2.1.7 Reactome
11
2.1.8 Metabolome.jp
12
2.1.9 Summary and Conclusion
12
2.2 Software for Pathway Display
13
2.2.1 Ingenuity Pathway Analysis (IPA)
13
2.2.2 Pathway Builder
14
2.2.3 Pathway Studio
14
2.2.4 Connections Maps
14
2.2.5 Cytoscape
14
2.3 File Formats for Pathways
15
2.3.1 Gene Ontology
15
2.3.2 PSI MI
16
2.3.3 Ce11ML
16
2.3.4 SBML
16
2.3.5 BioPAX
16
2.3.6 CSML/CSO
17
3 Pathway Simulation Software 19
3.1 Simulation Software Backend
19
3.1.1 Architecture: Deterministic, Probabilistic, or Hybrid?
20
3.1.2 Methods of Pathway Modeling
20
3.2 Major Simulation Software Tools
21
3.2.1 Gepasi/COPASI
21
3.2.2 Virtual Cell
21
3.2.3 Systems Biology Workbench (SBW), Cell Designer, JDesigner
21
3.2.4 Dizzy
22
3.2.5 E-Cell
22
3.2.6 Cell Illustrator
22
3.2.7 Summary
24
4 Starting Cell Illustrator 25
4.1 Installing Cell Illustrator
25
4.1.1 Operating Systems and Hardware Requirements
25
4.1.2 Cell Illustrator Lineup
26
4.1.3 Installing and Running Cell Illustrator
26
4.1.4 License Install
28
4.2 Basic Concepts in Cell Illustrator
28
4.2.1 Basic Concepts
28
4.2.2 Entity
28
4.2.3 Process
30
4.2.4 Connector
33
4.2.5 Rules for Connecting Elements
34
4.2.6 Icons for Elements
35
4.3 Editing a Model on Cell Illustrator
36
4.3.1 Adding Elements
36
4.3.2 Model Editing and Canvas Controls
39
4.4 Simulating Models
41
4.4.1 Simulation Settings
41
4.4.2 Graph Settings
41
4.4.3 Executing Simulation
43
4.5 Simulation Parameters and Rules
44
4.5.1 Creating a Model with Discrete Entity and Process
44
4.5.2 Creating a Model with Continuous Entity and Process
49
4.5.3 Concepts of Discrete and Continuous
51
4.6 Pathway Modeling Using Illustrated Elements
52
4.7 Creating Pathway Models Using Cell Illustrator
55
4.7.1 Degradation
55
4.7.2 Translocation
57
4.7.3 Transcription
60
4.7.4 Binding
62
4.7.5 Dissociation
64
4.7.6 Inhibition
66
4.7.7 Phosphorylation by Enzyme Reaction
68
4.8 Conclusion
73
5 Pathway Modeling and Simulation 75
5.1 Modeling Signaling Pathway
75
5.1.1 Main Players: Ligand and Receptor
75
5.1.2 Modeling EGFR Signaling with EGF Stimulation
76
5.2 Modeling Metabolic Pathways
87
5.2.1 Chemical Equations and Pathway Representations
87
5.2.2 Michaelis-Menten Kinetics and Cell Illustrator Pathway Representation
88
5.2.3 Creating Glycolysis Pathway Model
89
5.2.4 Simulation of Glycolysis Pathway
101
5.2.5 Improving the Model
101
5.3 Modeling Gene Regulatory Networks
106
5.3.1 Biological Clocks and Circadian Rhythms
106
5.3.2 Gene Regulatory Network for Circadian Rhythms in Mice
107
5.3.3 Modeling Circadian Rhythms in Mice
108
5.3.4 Creating Hypothesis by Simulation
119
5.4 Summary
124
6 Computational Platform for Systems Biology 127
6.1 Gene Network of Yeast
127
6.2 Computational Analysis of Gene Network
128
6.2.1 Displaying Gene Network
128
6.2.2 Layout of Gene Networks
130
6.2.3 Pathway Search Function
131
6.2.4 Extracting Subnetworks
132
6.2.5 Comparing Two Subnetworks
133
6.3 Further Functionalities for Systems Biology
136
6.3.1 Languages for Pathways: CSML 3.0 and CSO
136
6.3.2 SaaS Technology
137
6.3.3 Pathway Parameter Search
138
6.3.4 Much Faster Simulation
138
6.3.5 Exporting Pathway Models to Programming Languages
138
6.3.6 Pathway Layout Algorithms
139
6.3.7 Pathway Database Management System
141
6.3.8 More Visually: Automatic Generation of Icons
142
Bibliographic Notes 145
Index 151
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