Kinetic Modelling in Systems Biology

Kinetic Modelling in Systems Biology

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Features

  • Covers model creation techniques, model verification and validation, and simulations and interpretation of biological results
  • Describes underlying algorithms for selected reference methods
  • Presents several examples of applications, ranging from drug safety mechanisms to multiple target identification analysis to optimization of E. coli amino acid biosynthesis
  • Includes a CD-ROM with diagrams, model examples, and modeling software

Summary

With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging field.

The book introduces the basic biological cellular network concepts in the context of cellular functioning, explains the main aspects of the Edinburgh Pathway Editor (EPE) software package, and discusses the process of constructing and verifying kinetic models. It presents the features, user interface, and examples of DBSolve as well as the principles of modeling individual enzymes and transporters. The authors describe how to construct kinetic models of intracellular systems on the basis of models of individual enzymes. They also illustrate how to apply the principles of kinetic modeling to collect all available information on the energy metabolism of whole organelles, construct a kinetic model, and predict the response of the organelle to changes in external conditions. The final chapter focuses on applications of kinetic modeling in biotechnology and biomedicine.

Encouraging readers to think about future challenges, this book will help them understand the kinetic modeling approach and how to apply it to solve real-life problems.

CD-ROM Features
Extensively used throughout the text for pathway visualization and illustration, the EPE software is available on the accompanying CD-ROM. The CD also includes pathway diagrams in several graphical formats, DBSolve installation with examples, and all models from the book with dynamic visualization of simulation results, allowing readers to perform in silico simulations and use the models as templates for further applications.

Table of Contents

Introduction

Systems Biology, Biological Knowledge, and Kinetic Modelling
Dependence of enzyme reaction rate on the substrate concentration
What are the model limitations? Or, in other words, what can be modeled?

Cellular Networks Reconstruction and Static Modelling
Pathway reconstruction
The high-quality network reconstruction: description of the process
Visual notations: three categories

Edinburgh Pathway Editor (EPE)
Introduction
Feature summary of EPE
A flexible visual representation
Conclusion

Construction and Verification of Kinetic Models
Introduction
Basic principles of kinetic model construction
Basic principles of kinetic model verification
Study of dynamic and regulatory properties of the kinetic model

Introduction to DBSolve
Creation and analysis of the models using DBSolve: functional description

Enzyme Kinetics Modelling
Introduction
Basic principles of modeling individual enzymes and transporters
"Hyperbolic" enzymes
Allosteric enzymes
Transporters

Kinetic Models of Biochemical Pathways
Modelling of the mitochondrial Krebs cycle
Modelling of the Escherichia coli branched-chain amino acid biosynthesis

Modelling of Mitochondrial Energy Metabolism
Oxidative phosphorylation and superoxide production in mitochondria
Development of kinetic models
Description of individual processes of the model
Model predictions

Application of the Kinetic Modelling Approach to Problems in Biotechnology and Biomedicine
Study of the mechanisms of salicylate-hepatotoxic effect
Multiple target identification analysis for antituberculosis drug discovery
Application of the kinetic model of E. coli branched-chain amino acid biosynthesis to optimize production of isoleucine and valine

Conclusion and Discussion

References

Index

Editorial Reviews

…This book will help the reader to understand the kinetic modeling approach, apply it to solve real-life problems, and give the opportunity to think about future challenges. It also illustrates how to apply the principles of kinetic modeling to perform various functions. …
ISCB News #49, June 2010

Downloads / Updates

Resource OS Platform Updated Description Instructions
C6676_CD_Files.zip Cross Platform March 18, 2014

 
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