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Stochastic modelling for systems biology

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Author: Wilkinson, Darren James

Year: 2006

Publisher: Boca Raton, Chapmann & Hall CRC

Series: Chapman & Hall CRC mathematical and computational biology series

Media group: Ausleihbestand

available

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Branch	Locations	Status	Reservations	Due date	Barcode	Floor plan	Lending note
Branch: Hauptstelle	Locations: BI-50 50	Status: available	Reservations: 0	Due date:	Barcode: 00178632	Floor plans: Floor plan	Lending note:

Content

Table of Contents

INTRODUCTION TO BIOLOGICAL MODELLING

What is Modelling?

Aims of Modelling

Why is Stochastic Modelling Necessary?

Chemical Reactions

Modelling Genetic and Biochemical Networks

Modelling Higher-Level Systems

Exercises

Further Reading

REPRESENTATION OF BIOCHEMICAL NETWORKS

Coupled Chemical Reactions

Graphical Representations

Petri Nets

Systems Biology Markup Language (SBML)

SBML-Shorthand

Exercises

Further Reading

PROBABILITY MODELS

Probability

Discrete Probability Models

The Discrete Uniform Distribution

The Binomial Distribution

The Geometric Distribution

The Poisson Distribution

Continuous Probability Models

The Uniform Distribution

The Exponential Distribution

The Normal/Gaussian Distribution

The Gamma Distribution

Exercises

Further reading

STOCHASTIC SIMULATION

Introduction

Monte-Carlo Integration

Uniform Random Number Generation

Transformation Methods

Lookup Methods

Rejection Samplers

The Poisson Process

Using the Statistical Programming Language, R

Analysis of Simulation Output

Exercises

Further Reading

MARKOV PROCESSES

Introduction

Finite Discrete Time Markov Chains

Markov Chains with Continuous State Space

Markov Chains in Continuous Time

Diffusion Processes

Exercises

Further reading

CHEMICAL AND BIOCHEMICAL KINETICS

Classical Continuous Deterministic Chemical Kinetics

Molecular Approach to Kinetics

Mass-Action Stochastic Kinetics

The Gillespie Algorithm

Stochastic Petri Nets (SPNs)

Rate Constant Conversion

The Master Equation

Software for Simulating Stochastic Kinetic Networks

Exercises

Further Reading

CASE STUDIES

Introduction

Dimerisation Kinetics

Michaelis-Menten Enzyme Kinetics

An Auto-Regulatory Genetic Network

The Lac operon

Exercises

Further Reading

BEYOND THE GILLESPIE ALGORITHM

Introduction

Exact Simulation Methods

Approximate Simulation Strategies

Hybrid Simulation Strategies

Exercises

Further reading

BAYESIAN INFERENCE AND MCMC

Likelihood and Bayesian Inference

The Gibbs Sampler

The Metropolis-Hastings Algorithm

Hybrid MCMC Schemes

Exercises

Further reading

INFERENCE FOR STOCHASTIC KINETIC MODELS

Introduction

Inference Given Complete Data

Discrete-Time Observations of the System State

Diffusion Approximations for Inference

Network Inference

Exercises

Further reading

CONCLUSIONS

A SBML Models

A.1 Auto-Regulatory Network

A.2 Lotka-Volterra Reaction System

A.3 Dimerisation-Kinetics Model

References

Index

Ratings

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Details

Author: Wilkinson, Darren James

Statement of Responsibility: Darren James Wilkinson

Year: 2006

Publisher: Boca Raton, Chapmann & Hall CRC

Classification: BI-50, MA-10, MA-20

Subject type: Monographien

ISBN: 1584885408

ISBN (2nd): 9781584885405

Description: 254 S. : graph. Darst.

Series: Chapman & Hall CRC mathematical and computational biology series

Tags: Datenverarbeitung; Mathematik; Biologie Methoden; Biologie; Mathematik allgemein

Language: englisch||

Footnote: Literaturangaben

Media group: Ausleihbestand

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