Team:BCCS-Bristol/Modelling/BSIM

From 2010.igem.org

Latest revision as of 19:46, 27 October 2010

Introduction to BSim

BSim is BCCS Bristol's award winning modelling package. It is an agent-based modelling framework written in Java. BSim's agents operate on the level of individual bacteria, vesicles and particles. The internal state of bacteria can be modelled with ODE's which are solved numerically by BSim.

We hope that BSim can be used as a 'virtual microscope', a tool that all biologists can use to investigate almost any microbiological system, from the level of GRN's to multicelluar interaction to environmental interaction.

BSim through the ages

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 last year's project, the 2009 team 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 was 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.

BSim 2010 is the next phase of this modeling package. Building on the modular form of last year's we have added the ability to accurately model the interaction between cells and their microenvironment. The user can now fully specify arbitrary 3D boundary conditions and simulate chemical fields and bacterial motility with respect to these boundaries. BSim 2010 also includes a fully featured 'point-and-click' graphical user interface, which allows a user to develop a simulation without knowing any Java.

A screenshot from BSim 2008

A screenshot from BSim 2009

A screenshot from BSim 2010

BSim 2010 Features

Modelling Environmental Interactions

Interactions between cells and their microenvironment are increasingly relevent for a wide variety of applications. In the case of agrEcoli we needed to be able to simulate how E. coli behaved within the confines of a gel matrix, so we developed a suite of tools to integrate environmental interactions into BSim. There are many other areas of research where environmental interactions are important and we belive that the tools we've developed will be extremely useful. Examples include micro-fluidics, host-pathogen interactions and drug design and delivery.

Graphical User Interface

While an improvement on 2008, the 2009 edition of BSim relied heavily on the user having a working knowledge of the Java programming language. By removing the need for JAVA knowledge, we have opened up BSim to a much wider category of users. The GUI only requires users to be able to express their biological system mathematically; it can then translate the user’s description of a system into Java code. This code can then be edited by Java savvy users if they so wish.