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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.
We have several mechanisms in place in order to accurately simulate the operation of our bacterial mop. These come in the form of:
i. PP1 production
PP1 can be produced at a user-chosen rate from the right-side of the world (PP1-production slider). This is in simulation of PP1 from the rest of the cell entering our specific segment. Continuing this simulation, PP1 which encounters the right wall of the world is lost to the rest of the cell and so is removed in the simulation.
Although a similar system could be implemented for PP1 which encounters the upper and lower walls, we can simply assume that an equal number of molecules are lost to an equivalent segment above/below as enter the current segment. Thus, if a molecule of any kind encounters the top/bottom wall it will re-appear at the opposite wall (bottom/top respectively).
- Sliders
- Switches
- Input Controls
- Counters
- Graphs
1.Sliders
i. PP1 production
PP1 can be produced at a user-chosen rate from the right-side of the world (PP1-production slider). This is in simulation of PP1 from the rest of the cell entering our specific segment. Continuing this simulation, PP1 which encounters the right wall of the world is lost to the rest of the cell and so is removed in the simulation.
Although a similar system could be implemented for PP1 which encounters the upper and lower walls, we can simply assume that an equal number of molecules are lost to an equivalent segment above/below as enter the current segment. Thus, if a molecule of any kind encounters the top/bottom wall it will re-appear at the opposite wall (bottom/top respectively).
