Systems Biology: International Research and Development / Edition 1

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Overview

Systems biology is defined for the purpose of this study as the understanding of biological network behaviors, and in particular their dynamic aspects, which requires the utilization of mathematical modeling tightly linked to experiment. This involves a variety of approaches, such as the identification and validation of networks, the creation of appropriate datasets, the development of tools for data acquisition and software development, and the use of modeling and simulation software in close linkage with experiment. All of these are discussed in this volume. Of course, the definition becomes ambiguous at the margins, but at the core is the focus on networks, which makes it clear that the goal is to understand the operation of the systems, rather than the component parts. It was concluded that the U.S. is currently ahead of the rest of the world in systems biology, largely because of earlier investment by funding organizations and research institutions. This is reflected in a large number of active research groups, and educational programs, and a diverse and growing funding base. However, there is evidence of rapid development outside the U.S., much of it begun in the last two to three years. Overall, however, the picture is of an active field in the early stages of explosive growth.

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Product Details

  • ISBN-13: 9781402054679
  • Publisher: Springer Netherlands
  • Publication date: 3/6/2007
  • Edition description: 2007
  • Edition number: 1
  • Pages: 262
  • Product dimensions: 6.50 (w) x 9.50 (h) x 0.60 (d)

Table of Contents

Foreword vii

Table of Contents ix

List of Figures xiii

List of Tables xv

Preface xvii

1 Executive Summary and Introduction Marvin Cassman

Background 1

Objectives of the WTEC Study 4

Panel Members 4

Study Scope 5

Plan of the Study 5

Principal Findings 7

References 12

2 Data and Databases Fumiaki Katagiri Adam Arkin

Introduction 15

Research Activities in the U.S. 20

Research Activities in Europe 22

Research Activities in Japan 24

Modeling and Data Collection 25

References 29

3 Network Inference Frank Doyle Douglas Lauffenburger

Introduction 31

Network Inference and Model Structure 35

Validation, Iteration, Discrimination, and Identifiability 40

Regression 41

Comparison of Efforts in Europe, Japan, and the U.S. 42

Summary 43

References 44

4 Modeling and Network Organization Cynthia Stokes Adam Arkin

Introduction 47

Overview of Worldwide Efforts 51

Interest and Involvement of Industry 67

Infrastructure Supporting Modeling and Network Organization Analysis 70

Needs and Recommendations 75

Summary of Key Findings 77

References 77

5 Systems Biology in Plant Research Fumiaki Katagiri

Introduction 83

Metabolic Networks 85

Regulatory Networks in Developmental Processes 86

Concluding Remarks 89

References 89

6 Education, National Programs, and Infrastructure in Systems Biology Marvin Cassman Douglas Lauffenburger Frank Doyle

Introduction 91

Education 91

National Programs for Support of Systems Biology 99

Infrastructure 105

References 109

Appendices

A Panelist Biographies 111

B Site Reports-Europe

Cambridge University 115

European Bioinformatics Institute (EBI) 117

European Commission (EC)119

German Cancer Research Center (DKFZ) 123

Humboldt University 132

Max Planck Institute for Molecular Genetics 136

Max Planck Institute for Molecular Plant Physiology 139

Oxford Brookes University 144

Oxford University, Centre for Mathematical Biology/Mathematical Institute 147

Oxford University, Dept. of Physiology 151

Sheffield University 156

SystemsX-A New Systems Biology Institute in Switzerland 161

University College London 163

Universite Libre de Bruxelles 166

University of Warwick 168

Vrije Universiteit (Free University) Amsterdam 172

C Site Reports-Japan

Computational Biology Research Center (CBRC) 177

Japan Biological Information Research Center (JBIRC) 181

Kazusa DNA Research Institute (KDRI) 186

Keio University, Institute for Advanced Biosciences (IAB) 190

Kitano Symbiotic Systems Project 194

Kyoto University, Bioinformatics Center 199

Kyoto University, Cell/Biodynamics Simulation Project 201

RIKEN Yokohama Institute 205

Tokyo Medical and Dental University 216

University of Tokyo, Department of Computational Biology 218

University of Tokyo, Institute of Medical Science 221

University of Tokyo, Laboratory of Systems Biology and Medicine 223

D Summary of U.S. Workshop, June 4, 2004 229

E Glossary 253

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