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Computational immunology : models and tools / edited by Josep Bassaganya-Riera. -- London : Academic Press, c2016. – (58.6911 /C738) |
Contents
List of
Contributors ix
Chapter
1 Introduction to Computational Immunology
1
Overview 1
Modeling
Tools and Techniques 3
Use
Cases Illustrating the Application of Computational Immunology
Technologies 4
Acknowledgments 6
References 6
Chapter
2 Computational Modeling 9
Overview
on Computational Modeling
Translational
Research Iterative Modeling Cycle
Information
and Knowledge Extraction from the Literature
Collect
New Data and Data from Public Repositories
Model
Development
In
Silico Experimentation
Validation
of Computational Hypotheses and New Knowledge
Considerations
on Computational Modeling Technologies
Computational
Modeling Tools for Immunology and Infectious Disease Research
Concluding
Remarks
Acknowledgments
References
Chapter
3 Use of Computational Modeling in Immunological Research 31
Introduction 31
Computational
and Mathematical Modeling of the Immune Response to Helicobacter pylori 32
Inflammatory
Bowel Disease 35
ODE
Model of CD4 + T-Cell Differentiation 37
T
Follicular Helper Cell Differentiation
39
Concluding
Remarks 41
Acknowledgments 42
References 42
Chapter
4 Immunoinformatics Cyberinfrastrueture for Modeling and Analytics 45
Introduction 45
Web
Portal 46
LabKey-Based
Laboratory Information Management System
48
Public
Repositories: ImmPort 51
Global
Gene Expression Analysis 51
High-Performance
Computing Environment 51
HPC
Infrastructure for ENISI MSM Modeling 52
CyberInfrastructure
for NETwork Science 53
Pathosystems
Resource Integration Center 54
Clinical
Data Integration 56
Concluding
Remarks 59
Acknowledgments 59
Appendix:
MIEP Data Uploaded to ImmPort 59
References 60
Chapter
5 Ordinary Differential Equations (ODEs) Based Modeling 63
Introduction 63
Concluding
Remarks 77
Acknowledgments 77
References 77
Chapter
6 Agent-Based Modeling and High Performance Computing 79
Introduction
and Basic Definitions 79
Related
Work 81
Technical
Implementation of ENISI 85
Formal
Representation of ENISI 86
Agent-Based
Modeling Using ENISI 89
Calibration
and Validation of the Preliminary Model
95
Sensitivity
Analysis for ABM 96
Scaling
the Sensitivity Analysis Calculations 98
Scalability
and Performance 99
Modeling
Study Investigating Immune Responses to H. pylori 102
Concluding
Remarks 106
Acknowledgment 106
References 107
Chapter
7 From Big Data Analytics and Network Inference to Systems Modeling 113
Introduction 113
Big Bata
Drives Big Models 114
Tools,
Techniques, and Pipelines 126
Case
Study: Reconstructing the Thl7 Differentiation Network 135
Concluding
Remarks 139
Acknowledgments 140
References 140
Chapter
8 Multiscale Modeling: Concepts, Technologies, and Use Cases in Immunology 145
Introduction 145
MSM
Concepts and Techniques 146
Sensitivity
Analysis 153
MSM of
Mucosal Immune Responses 157
Case
Study 164
Concluding
Remarks 170
Acknowledgment 170
References 170
Chapter
9 Modeling Exercises 175
Modeling
Tools 175
Models 176
Model
Complexity and Model-Driven Hypothesis Generation 194
Concluding
Remarks 199
Acknowledgment 199
References 199
