Team:BCCS-Bristol/BSim

The original BSim package from the BCCS Bristol team competing in iGEM 2008 was designed primarily for analysis of the specific problem at the time i.e. chemotactic behaviour of bacteria and basic quorum signalling. Although it was robust and powerful, it was felt that adding new features required a very in-depth knowledge of Java as the biological and physical aspects of the program were very closely intertwined with performance and system related code. Motivated by the wet lab work and this year's project, we decided to take the best features of BSim 2008 and create a new, more modular platform, where only a basic programming background is required to create advanced simulations.

BSim 2009 has been designed from the ground up to allow for advanced agent-based modelling. All parameters used throughout the package demonstrate physical and biological plausibility and are fully referenced. By completely basing BSim on the literature, it is easy to ensure that all modules remain reliably synchronised and work correctly together, as well as minimising the effort required to create new simulations.

The main features of BSim 2009 are summarised below. For more detailed information on features, please see the extensive user manual .

BSim is available as a standalone pre-compiled library which can be compiled against like any other Java library, or as archived source code (for more details please see here). A brief tutorial for one method of obtaining BSim using SVN is also provided here.