BSim was created to model the stochastic interactions among bacteria and aims to promote the use of synthetic biology in solving problems in a modern way.
By enabling the description of bacterial behaviours, it attempts to provide an environment in which to investigate how local interactions between individual bacterium leads to the emergence of population level features, such as cooperation and synchronisation.
Detailed instructions on how to install and use the BSim utility on your Mac are available HERE.
BSim is a cross-platform utility capable of running on any operating system that comes with Java support (e.g. Mac OS X, Windows, Linux).
- Realistic 3D Environment - accurate physics, brownian forces and beautiful 3D visualisations provided as standard.
- Built-in Bacterial Traits - includes models from the scientific literature for chemotaxis, replication and vesicle production.
- Gene Regulatory Networks (GRNs) - model bacterium dynamics using GRNs described as sets of ordinary differential equations or user defined rules.
- Complex Micro-Scale Structures - describe the intricate boundaries of the experimental set up, and use these partitions to constrain movement or alter behavioural characteristics.
- Coarse Graining of Simulations - from individual molecules to continuous chemical fields, choose the level of representation appropriate to your question.
- Extendible and Modular Design - every aspect of BSim can be extended or replaced as required allowing for additional knowledge to be incorporated with minimal impact.
- Cross Platform - by using Java, BSim models can be run on all major systems (Windows, Linux and Mac OS X).