Earlier

Source: Darren JW

Source: Darren JW

Source: Darren JW

Source: Darren JW

Source: 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

Introduction
Rainier is an interesting new probabilistic programming library for Scala recently open-sourced by Stripe. Probabilistic programming languages provide a computational framework for building and fitting Bayesian models to data. There are many interesting probabilistic programming languages, and there is currently a lot of interesting innovation happening with probabilistic programming languages embedded in strongly typed functional programming languages such as Scala and Haskell. However, most such languages tend to be developed by people lacking expertise in statistics and numerics, leading to elegant, composable languages which work well for toy problems, but don’t scale well to the kinds of practical problems that [...]

Fri, Jun 01, 2018Source: Darren JW

EvilPlot
EvilPlot is a new functional data visualisation library for Scala. Although there are several data viz libraries for Scala, this new library has a nice functional API for producing attractive, flexible, compositional plots which can be rendered in JVM applications and in web applications (via Scala.js). For a quick introduction, see this blog post from one of the library’s creators. For further information, see the official documentation and the github repo. For a quick overview of the kinds of plots that the library is capable of generating, see the plot catalog.
The library is designed to produce plots which can be [...]

Fri, May 11, 2018Source: Darren JW