Symbolic systems biology: theory and methods
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Boston
Jones and Bartlett
2011
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XV, 214 S. graph. Darst. |
| ISBN: | 9780763753702 076375370X |
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MARC
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| 245 | 1 | 0 | |a Symbolic systems biology |b theory and methods |c edited by M. Sriram Iyengar |
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| 300 | |a XV, 214 S. |b graph. Darst. | ||
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| 500 | |a Includes bibliographical references and index | ||
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| 700 | 1 | |a Iyengar, M. Sriram |e Sonstige |4 oth | |
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Record in the Search Index
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|---|---|
| adam_text | Symbolic
Systems Biology
Theory and Methods
Edited by
M. Sriram lyengar, PhD
Assistant Professor
School of Health Information Sciences
University of Texas Health Science Center at Houston
Houston, Texas
JONES AND BARTLETT LEARNING
Sudbury, Massachusetts
BOSTON TORONTO LONDON SINGAPORE
Contents
Preface jx
1 Symbolic Systems Biology and Pathway Logic 1
1.1 Symbolic Modeling of Cellular Processes l
1.2 Pathway Logic Overview 5
1.3 Introduction to Formal Executable Specification
and Maude 7
1.4 Building a Pathway Logic Knowledge Base 14
1.4.1 The Equational Part 14
1.4.2 The Rules Part 7
1.5 Computing with a PL KB Ig
1.5.1 PL Petri Nets 19
1.5.2 Converting a PL KB to a Petri Net T-KB 21
1.5.3 PL Petri Net Models 22
1.6 Conclusion 26
2 Probabilistic Model Checking for Systems Biology 31
2.1 Introduction 31
2.2 Probabilistic Model Checking and PRISM 32
2.2.1 Continuous-Time Markov Chains 3
2.2.2 Continuous Stochastic Logic 34
2.2.3 PRISM 36
2.3 Modeling a Simple Biological System in PRISM 38
2.3.1 A Simple Set of Reactions 35
vi Contents
2.3.2 PRISM Models 40
2.3.3 Model Analysis with PRISM 43
2.4 Modeling Larger Numbers of Molecules 5
2.4.1 Individual-Based Representations 45
2.4.2 Population-Based Representations 7
2.4.3 Model Analysis with PRISM 49
2.5 A More Complex Model: Compartments 51
2.5.1 The PRISM Model 52
2.6 Related Work 56
Petri Nets for Systems Biology 61
3.1 Motivation 61
3.2 Biochemical Context 63
3.3 Qualitative Approach 4
3.3.1 Qualitative Modeling 64
3.3.2 Qualitative Analysis 7
3.3.3 Summary 79
3.4 Quantitative Approaches 80
3.4.1 Quantitative Modeling 0
3.4.2 Stochastic Analysis 1
3.4.3 Continuous Analysis 86
3.4.4 Summary 90
3.5 Tools 91
3.6 Further Reading 1
On Statecharts for Biology 99
4.1 Biology as Reactivity 9
4.2 Visual Languages for Reactivity 101
4.3 On Statecharts . 102
4.4 Statecharts for Biology , 104
4.5 Actual Modeling Efforts 105
4.6 Pancreatic Organogenesis in the Embryonic Mouse 105
4.7 T-Cell Activation and Differentiation
in the Thymus 107
4.8 Development and Function of B Cells
in the Lymph Node 107
4.9 Generic Cell Model 8
A Visual Process Calculus for Biology 113
5.1 Introduction 113
5.1.1 SPiM Processes and Chemical Reactions 115
Contents vii
5.2 Basic Examples 118
5.2.1 Protein Production 118
5.2.2 Protein Interaction 121
5.2.3 Protein Binding 3
5.2.4 Summary 125
5.3 Gene Networks 6
5.3.1 Repressilator Model 127
5.3.2 Model Execution 9
5.3.3 3D Visualization 131
5.3.4 Model Refinement 5
5.3.5 Genetic Logic Gates 138
5.4 C. elegans Development 140
5.4.1 Individual Cell Models 141
5.4.2 System Model 143
5.4.3 Simulation Results 144
5.4.4 Refined Model 6
5.5 SPiM with Compartments 149
5.5.1 Basic Primitives 9
5.5.2 Simple Model of Viral Infection
and T-Cell Response 154
5.6 Conclusion 158
5.7 The SPiM Calculus 158
5.7.1 Syntax 8
5.7.2 Reaction 161
5.7.3 Reaction Probability 162
5.7.4 Graphical Representation 165
5.7.5 SPiM with Compartments 7
Software Tools for Biological Pathway Modeling 175
6.1 Introduction 175
6.1.1 Criteria 6
6.1.2 Methods to Find Tools 177
6.2 Tools 178
6.2.1 BIOCHAM 178
6.2.2 BioCyc 8
6.2.3 BioLayout Express30 179
6.2.4 BiologicalNetworks 180
6.2.5 BioSPI 180
6.2.6 Bio-SPICE (Biological Simulation Program
for Intra- and Inter-Cellular Evaluation) 180
viii Contents
6.2.7 BioWarehouse 181
6.2.8 Cellerator 1
6.2.9 COPASI 182
6.2.10 DEGAS Choreographer 182
6.2.11 DMC 183
6.2.12 Dynetica 3
6.2.13 Ingenuity Pathways Analysis 184
6.2.14 Mathematica 184
« 6.2.15 MATLAB 4
6.2.16 Maude 185
6.2.17 NuSMV 5
6.2.18 OmniGrafne 186
6.2.19 PathCase: Pathways Database System (Web) 186
6.2.20 PathCase: Pathways Database System 2.0
(Desktop) 186
6.2.21 PathwayLab 7
6.2.22 Pathway Tools 187
6.2.23 PEPA 187
6.2.24 PRISM 8
6.2.25 Rhapsody/Play-Engine 189
6.2.26 Sigmoid 189
6.2.27 SimBiology 190
6.2.28 Simpathica 0
6.2.29 Snoopy 191
6.2.30 SPiM 1
6.2.31 STODE 191
6.2.32 Tom Sawyer 2
6.2.33 TRANSPATH 192
6.2.34 Tulip 193
6.2.35 Verus ; 193
6.2.36 Visio 2007 193
6.2.37 xCellerator 4
6.2.38 Ymer 194
6.3 Additional Resources 195
Index 197
|
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| id | DE-604.BV039591615 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:06:57Z |
| institution | BVB |
| isbn | 9780763753702 076375370X |
| language | English |
| lccn | 2009051932 |
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| publishDate | 2011 |
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| spelling | Symbolic systems biology theory and methods edited by M. Sriram Iyengar Boston Jones and Bartlett 2011 XV, 214 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Systems biology Iyengar, M. Sriram Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024442698&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Symbolic systems biology theory and methods Systems biology |
| title | Symbolic systems biology theory and methods |
| title_auth | Symbolic systems biology theory and methods |
| title_exact_search | Symbolic systems biology theory and methods |
| title_full | Symbolic systems biology theory and methods edited by M. Sriram Iyengar |
| title_fullStr | Symbolic systems biology theory and methods edited by M. Sriram Iyengar |
| title_full_unstemmed | Symbolic systems biology theory and methods edited by M. Sriram Iyengar |
| title_short | Symbolic systems biology |
| title_sort | symbolic systems biology theory and methods |
| title_sub | theory and methods |
| topic | Systems biology |
| topic_facet | Systems biology |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024442698&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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