SINS

Overview

SINS, a Java program to Simulate INdividuals in Space.

Prerequisites

Download the latest package from our release page (https://github.com/PopConGen/SINS/releases) and unzip it.

Make sure you have Java version 8 (or later) installed in your machine.

You can check this in the command line with:

java --version

User guide

You can check the detailed user guide here: https://github.com/PopConGen/SINS/blob/main/SINS_Userguide.pdf

Getting started

We include a toy example that you can use to try SINS.

In the command line, move to the folder where SINS is located. If you downloaded our release (sins.zip) to your "Downloads" folder, then after you unzip it, the folder where SINS is located is called "sins" and it will be under "~/Downloads/sins".

In the command line type or paste the following command:

java -jar SINS2.jar -projectName Premade_SINS_Project -outDir output -numberOfSimulations 4 -compress noComp -parallel true -parallelCores 4 -verbose true -outputFormat sins -makeDemographicImages false

You should see something like the following output:

Simulation Premade_SINS_Project is starting...
Simulation 2 Generation 0
Simulation 4 Generation 0
Simulation 3 Generation 0
Simulation 1 Generation 0
...
...
...
Simulation 4 Generation 999
Simulation 2 Generation 998
Simulation 2 Generation 999
Simulation Premade_SINS_Project has finished, time elapsed: 00hh : 00mm : 04ss 228ms

You can now check the output of your simulation in the output folder inside the SINS folder (eg. at "~/Downloads/SINS/output/")

If you want to know which other command line options are available when running SINS type or paste the following command in the command line:

java -jar SINS2.jar -help

Plot demographic stats

If you want to create the demography statistics plots set '-makeDemographicImages true' in the command line, eg:

java -jar SINS2.jar -projectName Premade_SINS_Project -outDir output -numberOfSimulations 4 -compress noComp -parallel true -parallelCores 4 -verbose true -outputFormat sins -makeDemographicImages true

Make sure you have the python library 'matplotlib' installed.