• The current stable version of this library is "1.0", for Scala 2.13 and Scala 3
• Use version "0.7" for Scala 2.11 and 2.12
• The current unstable snapshot release of this library is "1.1-SNAPSHOT" (cross-built for Scala 2.13 and Scala 3)

Binaries are published to Sonatype.

• To use this software library, you should first install a recent JDK and sbt.
• Run sbt from an empty/temp directory:

sbt "-Dsbt.version=1.8.0"
set libraryDependencies += "com.github.darrenjw" %% "scala-smfsb" % "1.0"
set libraryDependencies += "org.scalanlp" %% "breeze-viz" % "2.1.0"
set scalaVersion := "3.2.1"
console

• You should now have a Scala REPL with a dependency on this library. At the Scala REPL, enter the following:

import smfsb.*
import breeze.linalg.*
val model = SpnModels.lv[IntState]()
val step = Step.gillespie(model)
val ts = Sim.ts(DenseVector(50, 40), 0.0, 20.0, 0.1, step)
Sim.plotTs(ts)

• This should simulate a trajectory from a Lotka-Volterra model and plot the result in a window on the console which looks a little bit like the following:

To get the most out of this library, it will be helpful if you are already familiar with the R package smfsb associated with the (2nd or) 3rd edition of the textbook Stochastic modelling for systems biology, and have a basic familiarity with Scala and Breeze. For those new to Scala, my course on Scala for statistical computing is a good place to start.

• Tutorial - walk through of basic functionality
• There are more interesting examples in the examples directory. To run them, download or clone the repo, and do sbt run from inside the examples directory.
• Latest API docs
• I also have a couple of (oldish) blog posts: An introduction to scala-smfsb - a "taster", and a post looking at stochastic reaction-diffusion modelling using the library. But please note that these use an older version of the library and an older version of Scala, so a few details may need updating.

To create a new Scala sbt project template, just use:

sbt new darrenjw/scala-smfsb.g8

This will create a new project including a dependence on the stable version of the library.

Just add:

"com.github.darrenjw" %% "scala-smfsb" % "1.0"

to your sbt library dependencies. You might also need to add an explicit dependence on breeze-viz:

"org.scalanlp" %% "breeze-viz" % "2.1.0"

Just add something like:

libraryDependencies += "com.github.darrenjw" %% "scala-smfsb" % "1.1-SNAPSHOT"
resolvers += "Sonatype Snapshots" at
    "https://oss.sonatype.org/content/repositories/snapshots/"

to your sbt build file.

Download or clone the repo and do something like:

sbt clean compile doc mdoc test +package

from the top-level directory (the directory containing build.sbt).