Team:BCCS-Bristol/BSim-User-Guide

From 2008.igem.org

(Difference between revisions)

Revision as of 13:34, 21 October 2008

Home	The Team	The Project	Submitted Parts	Modelling	Wet Lab	Calendar	Miscellaneous

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:

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.

Download & Install Java
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
- Eg2
- Eg3

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

4.2 Explanation of videos produced from running three examples, tracers, wrapping boundaries, etc.

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

@@ Line 45: / Line 45: @@
 *''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 '''(will be!!)''' been 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:
+*''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
 **Eg2