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

Simulation Process

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

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 that allows for batches of simulations to be run in the background or on large cluster based systems, such as Blue Crystal.

Interactive Graphical User Interface (GUI) - BSimApp

Command Line Batch Interface - BSimBatch