Computational Biomedicine

Edited by Peter Coveney, Vanessa Diaz, Peter Hunter, and Marco Viceconti

The first text to make this burgeoning area of multidisciplinary research accessible to the student reader
Brings together the fields of mathematics, physics, computer science, biology, engineering and medicine to provide a single, coherent view of the subject
Carefully edited by leaders in the field to present latest knowledge in a way that those new to the field can readily understand
Emphasis throughout on the power of computational biomedicine as a tool demonstrates how theory can translate into clinical benefit
An Online Resource Centre provides additional teaching and learning resources for both academic and students

Computational Biomedicine

Edited by Peter Coveney, Vanessa Diaz, Peter Hunter, and Marco Viceconti

Description

By the end of the twenty-first century, computer-based modelling and simulation will be integral to the way clinical decisions are taken. Drugs will be selected on the basis of an individual patient's "digital profile", while clinical treatments will be tailor-made for the individual in question. For this to come to pass, however, we must prepare for a future where we can simulate our own bodies with precision, drawing upon remarkable advances in information technology, computer, mathematical, physical and engineering science, data management, and high performance computing.

Computational Biomedicine lays the foundations for a new approach to the subject - one that unifies the different strands of a broad-ranging subject, and demonstrates how computational biomedicine is a powerful tool with the potential to revolutionise our understanding of the human body, and the therapeutic strategies available to maintain and protect it.

Written by a team of world-leading experts in the field, it explores the modelling of physiological systems at different scales - cells, tissues, organs - before considering the issues around biomedical computing, and data collection and analysis. It emphasises how a theoretical understanding of computational biomedicine translates into practice, with illustrative examples and case studies used throughout.

Computational Biomedicine is the perfect introduction to the subject for anyone new to the field, from student to researcher.

Online Resource Centre
The Online Resource Centre to accompany Computational Biomedicine features figures from the book in electronic format, for download by registered adopters.

Computational Biomedicine

Edited by Peter Coveney, Vanessa Diaz, Peter Hunter, and Marco Viceconti

1. Introduction
2. Molecular Foundations of Computational Bioscience
2.1 Introduction
2.2 Types of Omics Data
2.3 Databases and Data Sources
2.4 Management of Omics Data Types
2.5 Software Systems and Interoperability
2.6 Clinical Phenotypes, Security and Data Sharing
2.7 Conclusions
3. Understanding the Genotype-Phenotype Relationship
3.1 Introduction
3.2 Quantitative Genetics Theory
3.3 Systems Genetics
3.4 Implementing CGP Models
3.5 CGP Applications
3.6 Linking CGP Models to Data
3.7 Conclusions
4. Image Based Modelling
4.1 Introduction
4.2 Biomedical Imaging Techniques
4.3 Image Based Modelling
4.4 Medical Image Simulation
4.5 Statistical Atlases, Populational Imaging and Modelling
4.6 Open Source Image Modelling Tools
4.7 Conclusions
5. Modelling Cell Function
5.1 Introduction
5.2 General Cell Functions
5.3 Cell Fundamentals
5.4 Levels of Abstraction
5.5 Cell Simulation
5.6 Approaches to Modelling and Simulation
5.7 Simulation Tools
5.8 Example: An Agent Model in Skeletal Mechanobiology
5.9 Reproducible Modelling: Ordinary Differential Equations
5.10 Conclusions
6. Modelling Tissues and Organs
6.1 Introduction
6.2 Modelling Epithelia
6.3 Cardiac Modelling
6.4 Modelling the Gastro-Intestinal Tract
6.5 Modelling Kidney Function and Homeostasis
6.6 General Homeostasis and Blood Pressure Regulation
6.7 Conclusions
7. Multi-Scale Modelling
7.1 Introduction
7.2 Why Multi-Scale Modelling?
7.3 A Framework for Multi-Scale Modelling and Computing
7.4 Scale Bridging
7.5 Multi-Scale Computing
7.6 Example of a Multiscale Model: In-Stent Restenosis in Coronary Arteries
7.7 Conclusions
8. Workflows: Principles, Tools and Clinical Applications
8.1 Introduction: What is a Workflow?
8.2 Computational Workflows
8.3 Workflow Implementations
8.4 Provenance
8.5 Examples of Scientific Workflows
8.6 Key Considerations
8.7 Conclusions
9. Distributed Biomedical Computing
9.1 Introduction
9.2 Parallel Applications
9.3 The Computational Ecosystem
9.4 Computing Beyond the Desktop
9.5 Simulations in a High Performance Computing Environment
9.6 Case Study 1: Calculating Drug Binding Affinities
9.7 Computational Infrastructures
9.8 Distributed Applications
9.9 Orchestrated Workflows from Distributed Applications
9.10 Case Study 2: Computational Investigations of Cranial Haemodynamics
9.11 Conclusions
10. Managing Security and Privacy of Patient Data Sharing Platforms
10.1 Introduction
10.2 Legal Background
10.3 Brief Overview of Information Security Concepts
10.4 Common Data Sharing Requirements
10.5 The Data Sharing Lifecycle
10.6 Data Warehousing Architecture
10.7 Conclusions
11. Toward Clinical Deployment: Verification and Validation of Models
11.1 Introduction: Technology Assessment versus Health Assessment
11.2 Code and Model Verification
11.3 Sensitivity Analysis
11.4 Model Validation
11.5 Validation of Integrative Models
11.6 Clinical Accuracy
11.7 Efficacy, Risk and Cost-Benefit
11.8 Impact
11.9 Sustainability
11.10 Conclusions
Appendix: Modelling Standards and Model Repositories
A.1 Introduction
A.2 Infrastructure for Computational Biomedicine
A.3 Syntax, Semantics and Annotation of Models
A.4 Markup Languages
A.5 Model Repositories
A.6 Conclusions

Computational Biomedicine

Edited by Peter Coveney, Vanessa Diaz, Peter Hunter, and Marco Viceconti

Author Information

Peter Coveney, Centre for Computational Science, University College London,Vanessa Diaz, Department of Mechanical Engineering, University College London,Peter Hunter, Auckland Bioengineering Institute,Marco Viceconti, Department of Mechanical Engineering , The University of Sheffield

Professor Peter Coveney, Centre for Computational Science, University College London

Dr Vanessa Diaz, Department of Mechanical Engineering, University College London

Professor Peter Hunter, Auckland Bioengineering Institute, New Zealand

Professor Marco Viceconti, Department of Mechanical Engineering , The University of Sheffield

Contributors:

- Clare Sansom (Assistant Editor) (Birkbeck College, University of London, UK)
- Denis Noble (University of Oxford, Oxford, UK)
- Imad Abugessaisa (The Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden)
- David Gomez-Cabrero (The Unit of Computational Medicine, Karolinska University Hospital)
- Jesper Tegnér (The Unit of Computational Medicine, Karolinska University Hospital)
- Jon Olav Vik (Centre for Integrative Genetics, Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway)
- Bernard De Bono (University College London, UK)
- Stig W. Omholt (Centre for Integrative Genetics, Norwegian University of Life Sciences)
- Alejandro Frangi (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain) and (Department of Mechanical Engineering, University of Sheffield, Sheffield, UK)
- Denis Friboulet (Université de Lyon, CREATIS ; CNRS UMR5220 ; Inserm U1044 ; INSA-Lyon ; Université Lyon 1, France)
- Nicholas Ayache (INRIA Asclepios Research Project, INRIA, Sophia Antipolis, France)
- Hervé Delingette (INRIA Asclepios Research Project, INRIA, Sophia Antipolis, France)
- Tristan Glatard (Université de Lyon, CREATIS)
- Corné Hoogendoorn (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Ludovic Humbert (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Karim Lekadir (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Ignacio Larrabide (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Yves Martelli (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Françoise Peyrin (Université de Lyon, CREATIS)
- Xavier Planes (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- Maxime Sermesant (INRIA Asclepios Research Project, INRIA, Sophia Antipolis)
- Maria-Cruz Villa-Uriol (Department of Mechanical Engineering, University of Sheffield)
- Tristan Whitmarsh (Center for Computational Imaging & Simulation Technologies in Biomedicine Information & Communication Technologies Department, Universitat Pompeu Fabra)
- James B. Bassingthwaighte (Department of Bioengineeering, University of Washington, Seattle, USA )
- Colin Boyle (Department of Mechanical Engineering, University College London, London, UK)
- Cesar Pichardo-Almarza (InScilico Ltd, London, UK)
- S. Randall Thomas (IR4M UMR8081 CNRS, Orsay & Villejuif, France) and (Université Paris-Sud XI, Orsay, France)
- Rod Smallwood (University of Sheffield)
- Nic Smith (King's College, London, UK)
- Alfons Hoekstra (Computational Science, Faculty of Science, University of Amsterdam, the Netherlands)
- Bastien Chopard (Computer Science, University of Geneva, Switzerland)
- Pat Lawford (Medical Physics Group, Department of Cardiovascular Science, University of Sheffield)
- Steven Wood (Sheffield Teaching Hospitals, UK)
- Daniel Silva (University of Sheffield, UK)
- Susheel Varma (University of Sheffield, UK)
- Rodney Hose (University of Sheffield, UK)
- Stefan Zasada (Centre for Computational Science, University College London, London, UK)
- Ali Nasrat Haidar (Centre for Computational Science, UCL)
- Nikolaus Forgó (Institut für Rechtsinformatik / Institute for Legal Informatics, Leibniz Universität, Hannover, Germany)
- Hartwig Gerhartinger (Institut für Rechtsinformatik / Institute for Legal Informatics, Leibniz Universität)
- Norbert Graf (Saarland University, Saarbrücken, Germany)
- Poul Nielsen (Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand) - Arne B. Gjuvsland (Centre for Integrative Genetics, Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway) - David Atkinson (Centre for Medical Image Computing, University College London, London, UK)