Computational Immunology - 1st Edition - ISBN: 9780128036976, 9780128037157

Computational Immunology

1st Edition

Models and Tools

Authors: Josep Bassaganya-Riera
eBook ISBN: 9780128037157
Paperback ISBN: 9780128036976
Imprint: Academic Press
Published Date: 27th October 2015
Page Count: 210
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Computational Immunology: Models and Tools encompasses the methodological framework and application of cutting-edge tools and techniques to study immunological processes at a systems level, along with the concept of multi-scale modeling.

The book's emphasis is on selected cases studies and application of the most updated technologies in computational modeling, discussing topics such as computational modeling and its usage in immunological research, bioinformatics infrastructure, ODE based modeling, agent based modeling, and high performance computing, data analytics, and multiscale modeling.

There are also modeling exercises using recent tools and models which lead the readers to a thorough comprehension and applicability.

The book is a valuable resource for immunologists, computational biologists, bioinformaticians, biotechnologists, and computer scientists, as well as all those who wish to broaden their knowledge in systems modeling.

Key Features

  • Offers case studies with different levels of complexity
  • Provides a detailed view on cutting-edge tools for modeling that are useful to experimentalists with limited computational skills
  • Explores the usage of simulation for hypothesis generation, helping the reader to understand the most valuable points on experimental setting


graduate students in computational biology, bioinformatics, biotechnology, computer science and immunology.

Table of Contents

  • List of Contributors
  • Chapter 1. Introduction to Computational Immunology
    • Abstract
    • Overview
    • Modeling Tools and Techniques
    • Use Cases Illustrating the Application of Computational Immunology Technologies
    • Acknowledgments
    • References
  • Chapter 2. Computational Modeling
    • Abstract
    • 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
    • Abstract
    • Introduction
    • Computational and Mathematical Modeling of the Immune Response to Helicobacter pylori
    • Inflammatory Bowel Disease
    • ODE Model of CD4+ T-Cell Differentiation
    • T Follicular Helper Cell Differentiation
    • Concluding Remarks
    • Acknowledgments
    • References
  • Chapter 4. Immunoinformatics Cyberinfrastructure for Modeling and Analytics
    • Abstract
    • Introduction
    • Web Portal
    • LabKey-Based Laboratory Information Management System
    • Public Repositories: ImmPort
    • Global Gene Expression Analysis
    • High-Performance Computing Environment
    • HPC Infrastructure for ENISI MSM Modeling
    • CyberInfrastructure for NETwork Science
    • Pathosystems Resource Integration Center
    • Clinical Data Integration
    • Concluding Remarks
    • Acknowledgments
    • Appendix: MIEP Data Uploaded to ImmPort
    • References
  • Chapter 5. Ordinary Differential Equations (ODEs) Based Modeling
    • Abstract
    • Introduction
    • Concluding Remarks
    • Acknowledgments
    • References
  • Chapter 6. Agent-Based Modeling and High Performance Computing
    • Abstract
    • Introduction and Basic Definitions
    • Related Work
    • Technical Implementation of ENISI
    • Formal Representation of ENISI
    • Agent-Based Modeling Using ENISI
    • Calibration and Validation of the Preliminary Model
    • Sensitivity Analysis for ABM
    • Scaling the Sensitivity Analysis Calculations
    • Scalability and Performance
    • Modeling Study Investigating Immune Responses to H. pylori
    • Concluding Remarks
    • Acknowledgment
    • References
  • Chapter 7. From Big Data Analytics and Network Inference to Systems Modeling
    • Abstract
    • Introduction
    • Big Bata Drives Big Models
    • Tools, Techniques, and Pipelines
    • Case Study: Reconstructing the Th17 Differentiation Network
    • Concluding Remarks
    • Acknowledgments
    • References
  • Chapter 8. Multiscale Modeling: Concepts, Technologies, and Use Cases in Immunology
    • Abstract
    • Introduction
    • MSM Concepts and Techniques
    • Sensitivity Analysis
    • MSM of Mucosal Immune Responses
    • Case Study
    • Concluding Remarks
    • Acknowledgment
    • References
  • Chapter 9. Modeling Exercises
    • Abstract
    • Modeling Tools
    • Models
    • Model Complexity and Model-Driven Hypothesis Generation
    • Concluding Remarks
    • Acknowledgment
    • References


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© Academic Press 2016
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About the Author

Josep Bassaganya-Riera

Josep Bassaganya-Riera received a DVM from the College of Veterinary Medicine, Autonomous University of Barcelona, Spain in 1997 and a PhD in Immunology from Iowa State University, Ames, Iowa in 2000. He completed his Postdoc work in Nutritional Immunology at Iowa State University in 2002.

Affiliations and Expertise

Professor of Immunology & Director, Nutritional Immunology & Molecular Medicine Laboratory (NIMML) and Center for Modeling Immunity to Enteric Pathogens (MIEP), Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA

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