Table 1 Explanation of Controls (Blue-Green Windows)

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