Team:BCCS-Bristol/Project/Modelling

From 2009.igem.org

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Latest revision as of 04:00, 22 October 2009

BCCS-Bristol
iGEM 2009

Modelling Overview

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 with the main intention of being used to simulate vesicle based communication to assess the potential applications of wet-lab work. All parameters used 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 of BSim 2009 and its features can be found here.

Results

The results for all of our simulations, 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. While we have used BSim 2009 to aid the lab work into the directed delivery of specific proteins with outer membrane vesicles, the case studies also demonstrate that the package can be easily adapted to answer many other questions in synthetic biology.

High Performance Computing

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 BlueCrystal] high performance computing cluster at the university.

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+<center>
+==Modelling Overview==
+</center>
+{|  align="center" width="90%"
+|width="33%" padding="3px"| <html><center>
+<img src="https://static.igem.org/mediawiki/2009/e/e9/BCCS_BSim_button.jpg" border="0">
+</center></html>
+|width="66%" padding="3px"|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 with the main intention of being used to simulate vesicle based communication to assess the potential applications of wet-lab work. All parameters used 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 of BSim 2009 and its features can be found [[Team:BCCS-Bristol/BSim|here]].
+|}
+<center>
+==[[Team:BCCS-Bristol/BSim/Case_studies/VESECURE|Results]]==
+</center>
+{|  align="center" width="90%"
+|width="33%" padding="3px"| <html><center>
+<img src="https://static.igem.org/mediawiki/2009/5/56/BCCS_Project_button.jpg" border="0">
+</center></html>
+|width="66%" padding="3px"|The results for all of our simulations, can be found on the [[Team:BCCS-Bristol/BSim/Case_studies/VESECURE|case studies]] page. These include experiments into outer membrane vesicles, as well as case studies into magnetotactic bacteria and coupled repressilators. While we have used BSim 2009 to aid the lab work into the directed delivery of specific proteins with outer membrane vesicles, the case studies also demonstrate that the package can be easily adapted to answer many other questions in synthetic biology.
+|}
-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 [[Team:BCCS-Bristol/BSim|here]].
+<center>
+==High Performance Computing==
+</center>
+{|  align="center" width="90%"
-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 Blue Crystal high performance computing cluster at the university.
+|width="33%" padding="3px"| <html><center>
-blue crystal
+<img src="https://static.igem.org/mediawiki/2009/d/d0/Bccs-bristol-cluster.png" border="0">
+</center></html>
+|width="66%" padding="3px"| 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 BlueCrystal] high performance computing cluster at the university.
-case studies
+|}