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Table 1 Explanation of Controls (Blue-Green Windows)

From: A simple and accurate rule-based modeling framework for simulation of autocrine/paracrine stimulation of glioblastoma cell motility and proliferation by L1CAM in 2-D culture

Control Parameter Explanation Functions Affected in code
Cellular-adhesion Switch that turns on adhesion feature that tethers cells together with adjustable spring-like connections. Cells can wiggle or shift around in the monolayer to varying degrees. update-params
time-scale Slider that chooses the simulated runtime, currently ranging from 1 to 72 h. However, if a cell reaches the end of the simulation (towards the right) it will end prematurely. go
randomness Slider that determines the randomness of cell movements. The closer this is to 1, the cell path will be more random. When closer to 0, the cells move towards open space if possible, which usually results in straighter forward (east) movement. cell-diffuse
L-randomness Slider that determines the randomness of the yellow L1 ligand molecule movement. Closer to 1, L1 molecules have a better chance at random movement, vs. diffusing towards cells when set near 0. L-diffuse
show-L? Switch that allows the yellow L1 molecules to be hidden. go
trailers? Switch that will create colored trail markers behind the green cells that were initially at the scratch edge. update-params
%_in_S-phase_Base Input by the user to reflect the % of cells in the S-phase under normal, uninhibited conditions. initialize
%_in_S-phase_Max_Inhibition Input by the user to reflect the % of cells in the S-phase if all pathways were fully inhibited. initialize
scratch-line Slider that determines the initial cell density of the simulation and the location of the simulated scratch. The range is from −32 to 32, reflecting the x-coordinates of the NetLogo grid. initialize; populate; make-scratch; L-production
LigandSpeed Input from the user that has been determined to produce visual behavior that represents the speed of the ligand. initialize
doubling-time User input, in hours, to specify the average doubling time of the simulated cells. populate; update-params; update-phase
Base_Motility_A User input, in microns/ min, of the motility rate when the B pathway has been inhibited fully. populate; update-params
Base_Motility_B User input, in microns/ min, of the motility rate when the A pathway has been inhibited fully. populate; update-params
Base_Motility_C User input, in microns/ min, of the motility rate when the C pathway has been inhibited fully Populate; update-params
UninhibitedMotility User input, in microns/ min, of the motility rate for an uninhibited cell. initialize
%DecreaseA These sliders are set based on experimental data. They reflect the % inhibition in motility if the particular pathway is totally inhibited. populate; update-params
%DecreaseB
%DecreaseC
A-inhibition These sliders are set to reflect the degree to which that particular pathway is inhibited by a specific inhibitor. initialize; populate; update-params
B-inhibition
C-inhibition
deviation-from-avg This is an arbitrary input that is used to tune the variance in motility to that observed in experiments. initialize
clear-cells This button allows for the cells to be removed from the model. Typically, this option would be used to see the trailers more clearly.  
show-cells This button will show the cells in the model after they have been cleared with the “clear-cells” button.  
show-scratch? This switch gives the option to show the scratch line. The line itself is shown by the patches located to the left of the scratch line, which are colored white when the switch is on. make-scratch
motility-check? This switch is used to prevent the motility from being a negative number. populate; update-params
S-phase_to_G1? This switch is used to direct the change in S-Phase cells to G1 (on) or G2 (off). update-params
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