Team:BCCS-Bristol/BSim-User-Guide

BSim User Guide

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

cd fileLocation        (where fileLocation is the location the program was downloaded to, eg. c:\IGEM_2008)
java bsim.BSimApp

into the command prompt (Start -> Accessories -> Command Prompt) will run BSimApp and open up the graphical interface:

Menu

• Play / Pause - Plays or pauses the simulation
• Reset - Stops the current simulation and reverts to the initial conditions defined in the 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
• Screenshot - captures the current state of the simulation in a .png picture file
• Load Simulation - 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 using parameter files to define your own simulation is explained here.

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:

cd c:\IGEM_2008
java bsim.BSimBatch ParameterFileLocation

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

java bsim.BSimBatch ./Parameter_Files/Parameter_File_1.txt

Time series relating to the positions of the particles and mean position of bacteria will be outputted to the location defined in the parameter file.

Problem Solving

BSim is written in 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 environment] before any simulations can be run; [http://www.jibble.org/settingupjava.php This page] has a nice guide on setting up a Java environment.