Prof Darren Wilkinson Professor of Stochastic Modelling
School of Mathematics, Statistics and Physics
Newcastle University

SMfSB / 1st edition

Stochastic Modelling for Systems Biology


This page contains links, code snippets, software and other information relating to my book, Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC on 18th April 2006.

Note that this is the page for the first edition of the book (published 2006). There is now also a separate page for the second edition, published November 2011. The page for the second edition contains details of the R package smfsb, which is likely to be of interest to owners of the first edition.

Quick jump to Chapter 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, Errata.

Information about the book

The book has ISBN-10 1-58488-540-8 and ISBN-13 978-158488-540-5. You can find out more details about it from the CRC book listing. It is Volume 11 in the Mathematical and Computational Biology series. You can buy the book direct from the publisher's site, but it is also listed on, and if you would prefer to buy your copy from there. It is also listed on google books if you want a preview.

A brief description from the CRC book listing:

"Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. Stochastic Modeling for Systems Biology provides an accessible introduction to this theory using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modeling biological systems. Along with the latest simulation techniques and research material, such as parameter inference, the text includes many examples and figures as well as software code in R for various applications."

Independent reviews of the book

The Royal Statistical Society, by John Haigh
BioMedical Engineering Online, by Eric Bullinger
Briefings in Bioinformatics, by Russell Schwartz

Code, software and other web links

Chapter 1: Introduction to biological modelling

Chapter 2: Representation of biochemical networks

Chapter 3: Probability models

Chapter 4: Stochastic simulation

Chapter 5: Markov processes

Chapter 6: Chemical and biochemical kinetics

Chapter 7: Case studies

Chapter 8: Beyond the Gillespie algorithm

Chapter 9: Bayesian inference and MCMC

Chapter 10: Inference for stochastic kinetic models

Chapter 11: Conclusions


Please inform me immediately if you find any broken link on this page.

Darren J Wilkinson Book: Stochastic Modelling for
	      Systems Biology

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