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Team:Dundee/Project/NetlogoDoc
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Mop Simulation
Software by the Dundee iGEM team is distributed under the terms of the GNU General Public License. GNU General Public License
NetLogo is a multi-agent programmable modelling environment. Dundee iGEM Team used NetLogo as a tool to allow the visualisation of intracellular interactions within our bacterial mops and so to bring the dynamics to life. The aim was to create a simulation in which variables and characteristics can be altered, depending on the cells state, allowing us to observe the effect of such changes on the operation of the mop.
The wet team were utilising two pathways within the cell to transport Protein-Phosphatase 1 to the desired location. The sec system was used in both E. coli and B. Subtilis while the tat system was implemented in E. coli. A full explanation of how these pathways work can be found here.
Within this model, a scenario of our E. coli bacterial mop which utilised the sec protein-translocation pathway was analysed. The investigated section included the cytoplasm, inner & outer membranes, and the periplasm. Fig 1 shows how the world is set up and what the different agents represent.
NetLogo is a multi-agent programmable modelling environment. Dundee iGEM Team used NetLogo as a tool to allow the visualisation of intracellular interactions within our bacterial mops and so to bring the dynamics to life. The aim was to create a simulation in which variables and characteristics can be altered, depending on the cells state, allowing us to observe the effect of such changes on the operation of the mop.
The wet team were utilising two pathways within the cell to transport Protein-Phosphatase 1 to the desired location. The sec system was used in both E. coli and B. Subtilis while the tat system was implemented in E. coli. A full explanation of how these pathways work can be found here.
Model 1 – Sec System in E. Coli
Within this model, a scenario of our E. coli bacterial mop which utilised the sec protein-translocation pathway was analysed. The investigated section included the cytoplasm, inner & outer membranes, and the periplasm. Fig 1 shows how the world is set up and what the different agents represent.
