• The current stable version of this library is "1.1", 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 "1.2-SNAPSHOT" (cross-built for Scala 2.13 and Scala 3)

Binaries are published to Sonatype.

This library is published to the Sonatype Central Repository (formally known as Maven Central), and hence can be used with any standard Scala build tool. The recommended ways to use it are via either sbt or scala-cli, and the recommended way to install and set up your Scala environment is using coursier. Coursier setup (cs setup) will install both sbt and scala-cli by default.

A minimal example for scala-cli is given below:

//> using scala 3.3.4
//> using dep com.github.darrenjw::scala-smfsb:1.1
//> using dep org.scalanlp::breeze-viz:2.1.0

import smfsb.*
import breeze.linalg.*

@main
def run() =
  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)

• Copy this into a file called (say) lv.scala, and then run from the command line with scala-cli lv.scala.
• 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

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" % "1.1"

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" % "1.2-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).