Team:BCCS-Bristol/Modeling

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BCCS-Bristol
iGEM 2009

Contents

Modelling

This year, in order to motivate the work in the wetlab, we have improved last year's award winning BSim software package. BSim is a free, open source, software package for stochastic simulation of interacting bacterial populations. The package has been improved this year to include more biological features as well as a clearer more user-friendly implementation. See below for details of the BSim package and see this page for more details of its feature set.

Many new features have been added and the process of creating simulation files has been made much more versatile and adaptable allowing for a wide range of biological situations to be simulated. See here for a brief introduction to the creation of BSim simulations.

Need a video here, or some screenshots.


BSim - A stochastic agent-based simulation framework

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. Therefore 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.

Facilitated by the code restructuring, we have been able to implement a variety of new features into BSim 2009 to assist with the modelling of the wet lab work. We briefly describe the main features below. See the BSim features page for more details of the BSim package and its new features.

BSim 2009 Feature Overview

The main features of BSim 2009 include:

  • Versatile and adaptable simulation definition specification
  • Robust, modular components
  • A variety of fully featured simulation objects, including
    • Particles with brownian motion (can simulate beads, vesicles)
    • Bacteria with flagellar motors exhibiting
      • Correct run and tumble behaviour
      • Chemotactic sensing and motion
      • Growth and vesiculation
    • Physically based chemical fields incorporating diffusion and decay
    • Ordinary Differential Equations and systems of ODEs can be fully specified and interact with any object, e.g. to allow agent based GRN simulation (See the link below for an example).
  • Actions and interactions between all objects in a simulation can be easily specified based on requirements.
  • Everything that can be specified by the user can be logged to a file readable by MATLAB, Excel and other numerical analysis packages.
  • Visual output is available, both directly to the screen and to image/movie files.
  • BSim has already been used in other projects: quorum coupled repressilators, simulation of electrically charged microtubule transport.

Links

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