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Team:BCCS-Bristol/Project/Modelling
From 2009.igem.org
iGEM 2009
In order to model outer membrane vesicles we have used an agent-based modelling package. BSim 2009 is derived from the iGEM 2008 BCCS Bristol team's model. BSim 2009 has been redesigned from the ground up. All parameters required in the package are as accurate as possible, both physically and biologically and are fully referenced. By completely basing BSim on the literature, we can ensure that all modules remain reliably synchronised, as well as minimising the effort required by the user to create new simulations. Further details into BSim 2009 and its features can be found here.
Agent-based models require a large amount of computing power in order to the run simulations, particularly over long time periods or with many bacteria. In order to perform some of our large simulations we have used the [http://www.acrc.bris.ac.uk/acrc/hpc.htm Blue Crystal] high performance computing cluster at the university.
The results for all of the simulations, including those run on Blue Crystal, can be found on the case studies page. These include experiments into outer membrane vesicles, as well as case studies into magnetotactic bacteria and coupled repressilators. Showing that while we have used BSim 2009 to aid the lab work into the directed delivery of specific proteins with outer membrane vesicles, the package can be easily adapted to answer many other questions in synthetic biology.
