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Team:UPO-Sevilla/Project/Basic Flip Flop/Multiagent System/Overview
From 2011.igem.org
Multiagent System based modeling
Spatial simulation of a bacteria
We have also developed a spatial simulation of the basic flip-flop by considering the interaction between the different components in the interior of a bacterium using NetLogo. This kind of model allows to analyze some parameters not considered in the simulations based on the differential equations governing the concentrations of diverse elements, like the spatial (volumetric) variation of these concentrations. Moreover, we wanted to provide a friendly program that allows the researcher to study the influence of several parameters in the global behavior of the system.
About NETLOGO
NetLogo is a programmable modeling environment for simulating natural and social phenomena. It was authored by Uri Wilensky in 1999 and has been in continuous development ever since at the Center for Connected Learning and Computer-Based Modeling.
NetLogo is particularly well suited for modeling complex systems developing over time. Modelers can give instructions to hundreds or thousands of "agents" all operating independently. This makes it possible to explore the connection between the micro-level behavior of individuals and the macro-level patterns that emerge from the interaction of many individuals.
Simulating the bistable
To run the simulation you have to download the NetLogo environment from his web page and open after the file biestable-simulation.nlogo (download here)
Simulation General View
Extending the model
This model could become more complicated adding more and more details of the real biological system, but it would increase the complexity of it and so the ability of making simulations in a reasonable time. Some of the improvements that could be implemented without making the program much more complex is the strength of the SD or adding a cycle life to the ribosomes and the RNA polymerases. A more interesting improvement and still plausible could be representing the growth of the bacterium while the time goes by and the sharply decrease of the size to the half after the binary fission.
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