Systems Biology Modelling and Analysis - Formal Bioinformatics Methods and Tools

Systems Biology Modelling and Analysis
 
Describes important modelling and computational methods for systems biology research to enable practitioners to select and use the most suitable technique
 
Systems Biology Modelling and Analysis provides an overview of state-of-the-art techniques and introduces related tools and practices to formalize models and automate reasoning for systems biology. The authors present and compare the main formal methods used in systems biology for modelling biological networks, including discussion of their advantages, drawbacks, and main applications.
 
Each chapter includes an intuitive presentation of the specific formalism, a brief history of the formalism and of its applications in systems biology, a formal description of the formalism and its variants, at least one realistic case study, some applications of formal techniques to validate and make deep analysis of models encoded with the formalism, and a discussion on the kind of biological systems for which the formalism is suited, along with concrete ideas on its possible evolution.
 
Edited by a highly qualified expert with significant experience in the field, some of the methods and techniques covered in Systems Biology Modelling and Analysis include:
* Petri nets, an important tool for studying different aspects of biological systems, ranging from simple signaling pathways to metabolic networks and beyond
* Pathway Logic, a formal, rule-based system and interactive viewer for developing executable models of cellular processes
* Boolean networks, a mathematical model which has been widely used for decades in the context of biological regulation networks
* Answer Set Programming (ASP), which has proven to be a strong logic programming paradigm to deal with the inherent complexity of biological models
 
For systems biologists, biochemists, bioinformaticians, molecular biologists, pharmacologists, and computer scientists, Systems Biology Modelling and Analysis is a comprehensive all-in-one resource to understand and harness the field's current models and techniques while also preparing for their potential developments in coming years with the help of the author's expert insight.

List of contents

List of Contributors xv
 
Preface xix
 
Acknowledgments xxv
 
1 Introduction 1
Elisabetta De Maria
 
1.1 Why Writing Models 2
 
1.2 Modelling and Validating Biological Systems: Three Steps 4
 
1.2.1 Modelling Biological Systems 4
 
1.2.2 Specifying Biological Systems 7
 
1.2.3 Validating Biological Systems 8
 
References 9
 
2 Petri Nets for Systems Biology Modelling and Analysis 15
Fei Liu, Hiroshi Matsuno, and Monika Heiner
 
2.1 Introduction 15
 
2.2 A Running Example 16
 
2.3 Petri Nets 16
 
2.3.1 Modelling 17
 
2.3.2 Analysis 18
 
2.3.3 Applications 20
 
2.4 Extended Petri Nets 20
 
2.5 Stochastic Petri Nets 20
 
2.5.1 Modelling 21
 
2.5.2 Stochastic Simulation 21
 
2.5.3 CSL Model Checking 22
 
2.5.4 Applications 23
 
2.6 Continuous Petri Nets 24
 
2.6.1 Modelling 24
 
2.6.2 Deterministic Simulation 24
 
2.6.3 Simulative Model Checking 25
 
2.6.4 Applications 27
 
2.7 Fuzzy Stochastic Petri Nets 27
 
2.7.1 Modelling 27
 
2.7.2 Fuzzy Stochastic Simulation 27
 
2.7.3 Applications 29
 
2.8 Fuzzy Continuous Petri Nets 29
 
2.8.1 Modelling 29
 
2.8.2 Fuzzy Deterministic Simulation 29
 
2.8.3 Applications 30
 
2.9 Conclusions 30
 
Acknowledgment 31
 
References 31
 
3 Process Algebras in Systems Biology 35
Paolo Milazzo
 
3.1 Introduction 35
 
3.2 Process Algebras in Concurrency Theory 36
 
3.2.1 pi-Calculus 38
 
3.3 Analogies between Biology and Concurrent Systems 42
 
3.3.1 Elements of Cell Biology 43
 
3.3.2 Cell Pathways 44
 
3.3.3 "Molecules as Processes" Abstraction 48
 
3.4 Process Algebras for Qualitative Modelling 51
 
3.4.1 Formal Analysis Techniques 51
 
3.5 Process Algebras for Quantitative Modelling 53
 
3.5.1 Chemical Kinetics 54
 
3.5.2 Stochastic Process Algebras 59
 
3.6 Conclusions 61
 
Acknowledgments 61
 
References 62
 
4 The Rule-Based Model Approach: A Kappa Model for Hepatic Stellate Cells Activation by TGFB1 69
Matthieu Bouguéon, Pierre Boutillier, Jérôme Feret, Octave Hazard, and Nathalie Théret
 
4.1 Introduction 69
 
4.1.1 Modelling Systems of Biochemical Interactions 69
 
4.1.2 Modelling Languages 70
 
4.1.3 Kappa 71
 
4.1.3.1 Overview 71
 
4.1.3.2 Semantics of Kappa 72
 
4.1.3.3 Kappa Ecosystem 73
 
4.1.3.4 Main Limitations 75
 
4.1.4 Modelling a Population of Hepatic Stellate Cells 76
 
4.1.5 Outline 78
 
4.2 Kappa 78
 
4.2.1 Site Graphs 78
 
4.2.1.1 Signature 79
 
4.2.1.2 Complexes 81
 
4.2.1.3 Patterns 82
 
4.2.1.4 Embeddings Between Patterns 84
 
4.2.2 Site Graph Rewriting 86
 
4.2.2.1 Interaction Rules 86
 
4.2.2.2 Reactions Induced by an Interaction Rule 87
 
4.2.2.3 Underlying Reaction Network 88
 
4.3 Model of Activation of Stellate Cells 91
 
4.3.1 Overview of Model 91
 
4.3.2 Some Elements of Biochemistry 91
 
4.3.2.1 Reaction Half-Time 92
 
4.3.2.2 Conversion 93
 
4.3.2.3 Production Equilibrium 93
 
4.3.2.4 Erlang Distributions 94
 
4.3.3 Interaction Rules 94
 
4.3.3.1 Behavior of TGFB1 Proteins 95
 
4.3.3.2 Renewal of Quiescent HSCs 96
 
4.3.3.3 Activation and Differentiation 97
 
4.3.3.4 Proliferation of Activated Hepatic Stellate Cel

About the author

Elisabetta De Maria, PhD, is an Associate Professor at the Université Côte d'Azur. From 2011-13, she was Coordinator of the International Research Master Program "Computational Biology and Biomedicine" at the University of Nice-Sophia Antipolis. Dr. De Maria has expertise in bioinformatics and computational systems biology and served as program chair of the conferences BIOINFORMATICS 2019, CSBio 2019 (International Conference on Computational Systems-Biology and Bioinformatics), and BIOINFORMATICS 2020.

Summary

Systems Biology Modelling and Analysis

Describes important modelling and computational methods for systems biology research to enable practitioners to select and use the most suitable technique

Systems Biology Modelling and Analysis provides an overview of state-of-the-art techniques and introduces related tools and practices to formalize models and automate reasoning for systems biology. The authors present and compare the main formal methods used in systems biology for modelling biological networks, including discussion of their advantages, drawbacks, and main applications.

Each chapter includes an intuitive presentation of the specific formalism, a brief history of the formalism and of its applications in systems biology, a formal description of the formalism and its variants, at least one realistic case study, some applications of formal techniques to validate and make deep analysis of models encoded with the formalism, and a discussion on the kind of biological systems for which the formalism is suited, along with concrete ideas on its possible evolution.

Edited by a highly qualified expert with significant experience in the field, some of the methods and techniques covered in Systems Biology Modelling and Analysis include:
* Petri nets, an important tool for studying different aspects of biological systems, ranging from simple signaling pathways to metabolic networks and beyond
* Pathway Logic, a formal, rule-based system and interactive viewer for developing executable models of cellular processes
* Boolean networks, a mathematical model which has been widely used for decades in the context of biological regulation networks
* Answer Set Programming (ASP), which has proven to be a strong logic programming paradigm to deal with the inherent complexity of biological models

For systems biologists, biochemists, bioinformaticians, molecular biologists, pharmacologists, and computer scientists, Systems Biology Modelling and Analysis is a comprehensive all-in-one resource to understand and harness the field's current models and techniques while also preparing for their potential developments in coming years with the help of the author's expert insight.

Product details

• Authors: De Maria, Elisabetta de Maria
• Assisted by: Elisabetta de Maria (Editor)
• Publisher: Wiley, John and Sons Ltd
• Languages: English
• Product format: Hardback
• Released: 31.01.2023
• EAN: 9781119716532
• ISBN: 978-1-119-71653-2
• No. of pages: 464
• Subjects: Natural sciences, medicine, IT, technology > Biology > Biochemistry, biophysics; Chemie, Biochemie, Bioinformatik, Life Sciences, Biowissenschaften, Systembiologie, chemistry, Bioinformatics & Computational Biology, Biochemie u. Chemische Biologie, Biochemistry (Chemical Biology)