Elements of Computational Systems Biology

CONTENTS

PREFACE

CONTRIBUTORS

PART I OVERVIEW

1 Advances in Computational Systems Biology

Huma M. Lodhi

1.1 Introduction

1.2 Multiscale Computational Modeling

1.3 Proteomics

1.4 Computational Systems Biology and Aging

1.5 Computational Systems Biology in Drug Design

1.6 Software Tools for Systems Biology

1.7 Conclusion

References

PART II BIOLOGICAL NETWORK MODELING

2 Models in Systems Biology: The Parameter Problem and the Meanings of Robustness

Jeremy Gunawardena

2.1 Introduction

2.2 Models as Dynamical Systems

2.2.1 Continuous Models

2.2.2 Discrete Models

2.3 The Parameter Problem

2.3.1 Parameterphobia

2.3.2 Measuring and Calculating

2.3.3 Counter Fitting

2.3.4 Beyond Fitting

2.4 The Landscapes of Dynamics

2.4.1 Qualitative Dynamics

2.4.2 Steady State Attractors of ODE Models

2.5 The Meanings of Robustness

2.5.1 Parameter Biology

2.5.2 Robustness to Initial Conditions

2.5.3 Robustness in Reality

2.5.4 Structural Stability

2.5.5 Classifying Robustness

2.6 Conclusion

References

3 In Silico Analysis of Combined Therapeutics Strategy for Heart Failure

Sung-Young Shin, Tae-Hwan Kim, Kwang-Hyun Cho, and Sang-Mok Choo

3.1 Introduction

3.2 Materials and Methods

3.2.1 Model Construction and Validation

3.2.2 Classification of Different Heart Failure Cases

3.2.3 Simulation Protocol

3.3 Results

3.3.1 β-Adrenergic Receptor Antagonists

3.3.2 β-Adrenergic Receptor Kinase Inhibitor

3.3.3 Phosphodiesterase Inhibitor

3.3.4 Combined Therapies

3.4 Discussion

Acknowledgment

3A.1 Appendix

3A.1.1 ...