Beginners Interactive NetLogo Dictionary (BIND)
Farsi / Persian
NetLogo Models Library:
Note: If you download the NetLogo application, every model in the Models Library is included.
This is a population model of competition between cells in a population of asexually reproducing bacteria E. coli for resources in an environment. Users can experiment with various parameters to learn more about two different mechanisms of evolution: natural selection and genetic drift.
Using the LevelSpace extension of NetLogo, each cell in this population model is actually controlled by a genetic switch model (just like GenEvo 1). In LevelSpace terminology, this population model is called a parent model and each cell is a child model. However, in this info section, we will call this model the population model and each background genetic switch model a cell model.
Depending on the selected options, each cell model begins with a different set of initial parameters. Then, each cell model simulates the DNA-Protein interactions in the lac-operon of E. coli (check out the GenEvo 1 model for a refresher). In the population model, we see the competition for resources between these cells.
When a cell's energy level doubles from its initial level, the cell produces two daughter cells that inherit the cell's genetic and epigenetic information. The cells with a 'fitter' genetic circuit turn their switch on and off faster, resulting in a faster increase in the energy levels, and a faster growth rate.
Because the molecular interactions in each cell model are stochastic, the population model displays the effects of both natural and statistical selection (genetic drift).
You can use this model in two ways.
The simplest way to use this model is to set CHOOSE-MODELS? to OFF. In this mode, the default Genetic Switch model is created for each cell. This method simulates genetic drift as a mechanism of evolution since each cell starts off identical.
If CHOOSE-MODELS? is ON, a user can manually select the NetLogo models (
.nlogo files) to be used for each cell, allowing each cell to have a different genetic switch. This allows for variability in the population. This method simulates natural selection as well as genetic drift.
In both ways, the SETUP button sets up the population of E. coli cells (each type represented by a unique color) and randomly distributes them across the world.
After you setup the model, set the environmental conditions by setting LACTOSE? and GLUCOSE? to ON or OFF.
Click GO to run the population model (and consequently, the cell models) for around 300 ticks. Click GO again to pause the model. Click INSPECT CELLS and click on any cell to see the cell model behind it. Close the individual cell models (Always select 'run in the background' option when closing individual models). Click GO to run the model again.
Change the environmental conditions using the LACTOSE? and GLUCOSE? switches and observe the different behaviors of population. (Note: You have to run the model for a few hundred ticks in order to observe cellular behavior.)
SETUP - Sets up the population model and cell models
GO - Makes the simulation in the population model (and consequently the cell models) begin to tick
INSPECT-CELLS - This button allows you to inspect the cell model of any cell in the population model. Click the button first and then click on a cell to see its cell model. When you close an individual cell model, always select the 'run in the background' option.
LACTOSE? - If ON, lactose is added to the external environment and equally distributed among the cell models. This means that the more the cells, the less lactose each cell gets. In other words, this is how we model carrying capacity.
GLUCOSE? - If ON, glucose is added to the external environment. Transport and digestion of glucose is not explicitly modeled, however since glucose is a preferred sugar, when glucose is present the lac promoter in the Genetic Switch model is inactive. In addition, when glucose is present, the energy of each cell increases with a constant rate (10 units per tick).
INITIAL-NUMBER-OF-CELLS – This is the initial number of cells in the population model. If CHOOSE-MODELS? is ON, this also corresponds to the number of Genetic Switch models the user has to select.
Notice the reproduction of cells as the time progresses. Notice how each cell model behaves with different sugar conditions.
Run the model for a few thousand ticks to see which cell type wins. Notice the cellular behavior of the Genetic Switch in the different types of cells by using the INSPECT CELLS button. Run the simulation several times with the same set of cell models to distinguish between the roles of natural selection and genetic drift. If natural selection is a stronger mechanism for evolution in a given set of cell models, then the same trait will win more frequently.
See if you can make the background color of the view scale with how much lactose and glucose are in the medium.
See if you can modify the model to model the effect of glucose explicitly by introducing the requisite proteins.
This model uses the LevelSpace extension to allow each cell to have its own genetic switch model controlling the protein interactions within.
If you mention this model or the NetLogo software in a publication, we ask that you include the citations below.
For the model itself:
Please cite the NetLogo software as:
To cite the GenEvo Systems Biology curriculum as a whole, please use:
Copyright 2016 Uri Wilensky.
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.
Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at firstname.lastname@example.org.
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