Team:BCCS-Bristol/BSim-User-Guide

BSim User Guide

Preliminary

BSim uses the [http://en.wikipedia.org/wiki/Java_programming_language Java programming language] so any computer using BSim must have a [http://en.wikipedia.org/wiki/Java_Runtime_Environment Java virtual machine] (JVM) before any simulations can be run. The following steps explain how to set up a Java environment:

1. First of all it is a good idea to check if a JVM is already set up on the computer you are using. Typing java -version into the command prompt will give information about any version of java that is available.
2. Download & Install Java
3. Define environmental variables

Compile package – compileAll

Parameter files

BSimApp

BSimApp is a graphical interface that enables a user to view simulations. It can be used to help users familiarise themselves with the process of defining simulations, watch small-scale simulations or verify the initial conditions of large-scale simulations.

Typing the command

java BSimApp

Will run BSimApp and open up the graphical interface:

[PICTURE]

Menu bar

• Play / Pause - Plays or pauses the simulation
• Reset - Stops the current simulation and reverts to the initial conditions defined by the current parameter file
  
• Video Length - Length of video to be recorded (frames)
• Frame Skip - Number of time steps to be skipped per frame
• Record Video - Records a video with properties defined in Video Length and Frame Skip
• Load Parameters… - The large black area is where the initial conditions of a simulation will appear once a parameter file has been loaded. Several example parameter files have been (will be!!) packaged with BSim and can be loaded by pressing the ‘Load Parameters…’ button then selecting one of the files from the ‘Parameter Files’ folder. The simulations defined by these files are summarised below:
  • Eg1 (Explanations of videos produced from running three examples, tracers, wrapping boundaries, etc.)
  • Eg2
  • Eg3

The process of defining a parameter file is explained in this section of the wiki.

BSimBatch

Due to the high levels of randomness in the run and tumble motion of bacteria it is likely that the user will want to run the same simulation many times and use statistical analysis to investigate emergent behaviour. BSimBatch enables the user to run batches of simulations, saving time series of the mean bacteria position and particle positions for each simulation.

BSimBatch is run using the command:

java BSimBatch ParameterFileLocation

Where ParameterFileLocation is the location of the parameter file defining simulation to be run, eg:

java BSimBatch ./Parameter_Files/Parameter_File_1.txt