Team:BCCS-Bristol/Modeling-Agent Based

Stochastic Agent Based Simulation

Welcome to BSim

The stochastic agent based simulation framework we have developed is called BSim. This allows for differing configurations of particles and bacteria to easily be modelled in an interactive way. The framework has been developed from scratch in Java allowing it to be run on the majority of computer systems. In addition to an easy to use GUI, a command line based interface is also provided to permit the running of large scale simulations on remote computing clusters.

Simulation Process

Parameter File Definition

User Interface

Two different user interface exist in BSim to serve the varying requirements when designing and running simulations. The first is an interactive graphical user interface (GUI) which provides easy to use controls for loading, running and exporting single simulations. The second is a command line based batch interface. This is provides functionality to allow for batches of simulations to be run in the background or on large cluster based computing systems, such as Blue Crystal.

BSimApp - Interactive Graphical User Interface (GUI)

The interactive graphical user interface to BSim is also know as BSimApp. It is a single user program that enables visual loading, running and exporting of simulations. It's main purpose is to allow for a single user to experiment with different parameters and simulation setups (e.g. number of bacteria, locations of objects, boundaries, etc) and to see any obvious problems that may arise before running the simulation hundreds of times to gain statistically significant results. It also provides a nice environment in which to debug any new simulation features that have been written, such as new bacteria types or simulation objects.

BSimBatch - Command Line Batch Interface

The command line based batch interface is also known as BSimBatch. This provides a more advanced way to run large numbers of simulations and to handle the output files of statistics from these. Because the output from BSim is stochastic due to the way bacteria move, it is necessary to perform large numbers of simulation runs to gain statistically significant results. BSimBatch allows for this using the same simulation definition file as BSimApp but adding a few additional parameters such and number of runs and export directories. BSimBatch has also been designed to make it easy to run simulations on large computing clusters as jobs can be scheduled to run with no user intervention required.

Batch Simulations

Batch simulations allow us to perform statistical analysis on our simulations and in particular look at the affect of altering one or many of the parameters. This will enable us to inform the wet lab team of the optimum conditions for their experiments.

Statistical Analysis

For every simulation statistical analysis will be performed on six aspects:

1. The direction (angle) the particle has moved towards the chemoattractant.
2. The distance (x axis) travelled by the particle.
3. The mean direction (angle) of movement by all particles towards the chemoattractant.
4. The mean distance (x axis) travelled by all particles.
5. The mean direction (angle) of bacterial movement towards the chemoattractant
6. The mean distance (x axis) bacteria travelled.

For each altered parameter 100 simulations (if feasible) will be run with each simulation running for 10 000 time steps containing 1-10 particles.

Methods of Statistical Analysis

Methods of Statistical analysis will include:

• T tests to show that results observed due to parameter changes are statistically significant.
• Histograms.
• Scatter plots.
• Means.

Framework Design

BSim Class Diagram