Team:BCCS-Bristol/Modeling/BSim

From 2009.igem.org

Revision as of 20:09, 18 October 2009 by Amaty (Talk | contribs)

BCCS-Bristol
iGEM 2009


Read more about BSim, our Stochastic agent based modelling framework.


Tutorials
Download
Case Studies
Interested in finding out more about the creation of BSim simulations? Click here for a selection of tutorial examples. Want to use the BSim software yourself? Click here to download the core libraries and source code (available freely under the MIT licence). The BSim platform has already been used in a number of other projects! Read more about these projects here.


Contents

BSim Features

There are many new features available in the new version of BSim:

Bacteria

  • Heavy basis on literature
  • Run and tumble by default (flagellar motor)
  • chemotaxis!
  • brownian motion and fluid forces implemented
  • easily adaptable.

Interactions and actions

  • easily specified and adaptable
  • can do whatever you want:
    • Collision
    • Merging (vesicle/bacterium)
    • GRNs
  • other interactions:
    • Everything can interact! chemical fields, GRNs, vesicles...

Vesicles

  • Small, but size based on growth
  • Size and creation rate based on rate of change of surface area [ref - steve?]
  • Vesicle movement - brownian motion in a viscous fluid environment
  • Interaction can be specified

Chemical Fields

  • diffusion
  • decay
  • physical units

GRN modelling

BSim allows the user to specify complex GRNS based on ODEs and apply these to individual bacteria to analyse GRN effects on a population level. It is now possible to analyse the effects of individual GRNs on a population level, all within the same context.

Magnetotaxis

It is now possible to simulate magnetotactic bacteria. These bacteria are sensitive to externally applied magnetic fields and can therefore be influenced to move along the direction of user specified magnetic field lines.

Retrieved from "http://2009.igem.org/Team:BCCS-Bristol/Modeling/BSim"