|Prof Darren Wilkinson||Professor of Stochastic Modelling|
|School of Mathematics & Statistics|
This page contains links, code snippets, software and other information relating to the second edition of my book, Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC, November 2011.
The book has ISBN-10 143983772-4 and ISBN-13 978-143983772-6. It can be ordered from CRC Press, Amazon.com, Amazon.co.uk and similar book sellers. You can also get a preview of the book on google books (or using Amazon Look Inside).
New in the second edition: R code updated, extended and properly documented in a free open source R package. All SBML models updated to SBML Level 3. Brief introduction to stochastic process algebras. Greatly extended chapter on Markov processes, with additional emphasis on stochastic differential equations and analytical approaches. Introduction to Kurtz's random time change representation, and informal derivations of Ito's formula, the Kolmogorov equations, the Fokker-Planck equation and the linear noise approximation. New R code for exact and approximate stochastic simulation, using a modular, functional programming approach. Quantification of noise, and an introduction to the modelling of extrinsic as well as intrinsic noise. Extended material on inference for stochastic models from data, covering "likelihood free" and "particle MCMC" approaches. Example code for particle filtering, marginal likelihood estimation and particle MCMC. Updated references and end of chapter exercises.
R is free software, available for all major operating systems, and can
be obtained from the R project
website (or a mirror). The R code associated with this book is freely available as
an R package, which is maintained on R-Forge and distributed via
It should be
possible to install it by entering the following command at the R
On platforms where binary package installs are the default
(eg. Windows), the binary package may not install on older versions of
R - if installation fails, try updating R to the latest version, or find out about installing
packages from source. The R-Forge project has
title "SMfSB 2e" and name "smfsb" - see the package web home pages on
and CRAN for further details.
The package does work on
all major operating systems (Linux, Windows, Mac, ...).
try consulting the available information on CRAN and R-Forge before
emailing me about installation problems.
Once the smfsb package is installed, it can be loaded with
and an overview vignette can be accessed by
using the command
There should be sufficient information provided in the vignette in
order to get started with using the package.
Also note that I have written
a blog post providing a tutorial introduction to the smfsb
package, based closely on the introductory vignette.
Please inform me immediately if you find any broken link on this page.