Earlier

Source: Xian Blog

Source: Darren JW

Source: Darren JW

Source: Darren JW

Source: Darren JW

Source: Darren JW

Just read in Nature today that Adrian Smith (of MCMC fame!) was to head the search for a replacement to ERC and Marie Curie research funding in the UK. Adrian, whom I first met in Sherbrooke, Québec, in June 1989, when he delivered one of his first talks on MCMC, is currently the director of the Alan Turing Institute in London, of which Warwick is a constituent. (Just for the record, Chris Skimore is the current Science minister in Theresa May’s government and here is what he states and maybe even think about her Brexit deal: “It’s fantastic for science, [...]

Sat, Apr 13, 2019Source: Xian Blog

Introduction
There is a fairly large literature on reaction-diffusion modelling using partial differential equations (PDEs). There is also a fairly large literature on stochastic modelling of coupled chemical reactions, which account for the discreteness of reacting species at low concentrations. There is some literature on combining the two, to form stochastic reaction-diffusion systems, but much less.
In this post we will look at one approach to the stochastic reaction-diffusion problem, based on an underlying stochastic process often described by the reaction diffusion master equation (RDME). We will start by generating exact realisations from this process using the spatial Gillespie algorithm, before switching [...]

Tue, Jan 22, 2019Source: Darren JW

In the previous post I gave a very quick introduction to the smfsb R package. As mentioned in that post, although good for teaching and learning, R isn’t a great language for serious scientific computing or computational statistics. So for the publication of the third edition of my textbook, Stochastic modelling for systems biology, I have created a library in the Scala programming language replicating the functionality provided by the R package. Here I will give a very quick introduction to the scala-smfsb library. Some familiarity with both Scala and the smfsb R package will be helpful, but is not [...]

Thu, Jan 03, 2019Source: Darren JW

Introduction
In the previous post I gave a brief introduction to the third edition of my textbook, Stochastic modelling for systems biology. The algorithms described in the book are illustrated by implementations in R. These implementations are collected together in an R package on CRAN called smfsb. This post will provide a brief introduction to the package and its capabilities.
Installation
The package is on CRAN – see the CRAN package page for details. So the simplest way to install it is to enter
install.packages("smfsb")
at the R command prompt. This will install the latest version that is on CRAN. Once installed, the package can [...]

Tue, Jan 01, 2019Source: Darren JW

The third edition of my textbook, Stochastic Modelling for Systems Biology has recently been published by Chapman & Hall/CRC Press. The book has ISBN-10 113854928-2 and ISBN-13 978-113854928-9. It can be ordered from CRC Press, Amazon.com, Amazon.co.uk and similar book sellers.
I was fairly happy with the way that the second edition, published in 2011, turned out, and so I haven’t substantially re-written any of the text for the third edition. Instead, I’ve concentrated on adding in new material and improving the associated on-line resources. Those on-line resources are all free and open source, and hence available to everyone, irrespective of [...]

Tue, Dec 18, 2018Source: Darren JW

Introduction
In the previous post I gave a brief introduction to Rainier, a new HMC-based probabilistic programming library/DSL for Scala. In that post I assumed that people were using the latest source version of the library. Since then, version 0.1.1 of the library has been released, so in this post I will demonstrate use of the released version of the software (using the binaries published to Sonatype), and will walk through a slightly more interesting example – a dynamic linear state space model with unknown static parameters. This is similar to, but slightly different from, the DLM example in the Rainier [...]

Sat, Jun 09, 2018Source: Darren JW