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Team:BCCS-Bristol/BSim-User-Guide
From 2008.igem.org
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==== Menu bar ==== | ==== Menu bar ==== | ||
| - | ''Load Parameters…'' | + | *''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: | 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: | ||
| - | Eg1 | + | **Eg1 |
| - | Eg2 | + | **Eg2 |
| - | Eg3 | + | **Eg3 |
The process of defining a parameter file is explained in this section of the wiki. | The process of defining a parameter file is explained in this section of the wiki. | ||
| - | ''Play / Pause'' <br> | + | *''Play / Pause'' <br> |
| - | ''Reset'' <br> | + | *''Reset'' <br> |
| - | ''Video Length'' <br> | + | *''Video Length'' <br> |
| - | ''Frame Skip'' <br> | + | *''Frame Skip'' <br> |
| - | ''Record Video'' <br> | + | *''Record Video'' <br> |
4.2 Explanation of videos produced from running three examples, tracers, wrapping boundaries, etc. | 4.2 Explanation of videos produced from running three examples, tracers, wrapping boundaries, etc. | ||
Revision as of 13:14, 21 October 2008
Contents |
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
- 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:
- Eg1
- Eg2
- Eg3
The process of defining a parameter file is explained in this section of the wiki.
- Play / Pause
- Reset
- Video Length
- Frame Skip
- Record Video
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 full address of the parameter file defining simulation to be run, eg:
Java BSimBatch C:/BSim/Parameter_Files/Parameter_File_1.txt
