scala-smfsb

License	GPL2
Categories	Scala Languages
GroupId	com.github.darrenjw
ArtifactId	scala-smfsb_2.12
Last Version	0.7
Release Date	Mar 28, 2020
Type	jar
Description	scala-smfsb scala-smfsb
Project URL	https://github.com/darrenjw/scala-smfsb/blob/master/README.md
Project Organization	com.github.darrenjw
Source Code Management	https://github.com/darrenjw/scala-smfsb

Download scala-smfsb_2.12

Filename	Size
scala-smfsb_2.12-0.7.pom
scala-smfsb_2.12-0.7.jar	101 KB
scala-smfsb_2.12-0.7-sources.jar	14 KB
scala-smfsb_2.12-0.7-javadoc.jar	1 MB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/com.github.darrenjw/scala-smfsb_2.12/ -->
<dependency>
    <groupId>com.github.darrenjw</groupId>
    <artifactId>scala-smfsb_2.12</artifactId>
    <version>0.7</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/com.github.darrenjw/scala-smfsb_2.12/
implementation 'com.github.darrenjw:scala-smfsb_2.12:0.7'

Gradle Kotlin

// https://jarcasting.com/artifacts/com.github.darrenjw/scala-smfsb_2.12/
implementation ("com.github.darrenjw:scala-smfsb_2.12:0.7")

Apache Buildr

'com.github.darrenjw:scala-smfsb_2.12:jar:0.7'

Apache Ivy

<dependency org="com.github.darrenjw" name="scala-smfsb_2.12" rev="0.7">
  <artifact name="scala-smfsb_2.12" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='com.github.darrenjw', module='scala-smfsb_2.12', version='0.7')
)

Scala SBT

libraryDependencies += "com.github.darrenjw" % "scala-smfsb_2.12" % "0.7"

Leiningen

[com.github.darrenjw/scala-smfsb_2.12 "0.7"]

Dependencies

compile (4)

Group / Artifact	Type	Version
org.scala-lang : scala-library	jar	2.12.10
org.scalanlp : breeze_2.12	jar	1.0
org.scalanlp : breeze-viz_2.12	jar	1.0
org.scalanlp : breeze-natives_2.12	jar	1.0

test (1)

Group / Artifact	Type	Version
org.scalatest : scalatest_2.12	jar	3.0.8

Project Modules

There are no modules declared in this project.

scala-smfsb

Scala library for stochastic kinetic modelling, biochemical network simulation, and parameter inference, associated with the 3rd edition of the textbook Stochastic Modelling for Systems Biology

• The current stable version of this library is "0.7"
• The current unstable snapshot release of this library is "0.8-SNAPSHOT"

Binaries are published to Sonatype, cross-built for Scala 2.11.x and 2.12.x.

N.B. Version 0.7 includes SIR and SEIR epidemic models, for convenience, due to their topical interest.

Quickstart

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

set libraryDependencies += "com.github.darrenjw" %% "scala-smfsb" % "0.7"
set libraryDependencies += "org.scalanlp" %% "breeze-viz" % "1.0"
set scalaVersion := "2.12.10"
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.

Documentation

• An introduction to scala-smfsb - a "taster" blog post
• 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.
• A blog post looking at stochastic reaction-diffusion modelling using the library
• Latest API docs

Using the library in your own Scala projects

giter8 template:

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.

Stable:

Just add:

"com.github.darrenjw" %% "scala-smfsb" % "0.7"

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

"org.scalanlp" %% "breeze-viz" % "1.0"

Snapshot:

Just add something like:

libraryDependencies += "com.github.darrenjw" %% "scala-smfsb" % "0.8-SNAPSHOT"
resolvers += "Sonatype Snapshots" at
    "https://oss.sonatype.org/content/repositories/snapshots/"

to your Sbt build file.

Building from source

Download or clone the repo and do something like:

sbt clean compile doc test package

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

Versions

Version
0.7 Mar 28, 2020
0.6 Jan 4, 2019
0.5 Dec 30, 2018
0.4 Nov 29, 2018
0.3 Nov 26, 2018
0.2 Nov 11, 2018