This project is an agent-based model of collective cell migration. It consists of three files: cell.py, paramup_fxn.py, and Main.py. It also contains a single folder. These files and the folder are summarized below.
cell.py defines the Cell class. It holds four key pieces of data: cell id, parent cell id, cell parameters, and the parameter updater function.
paramup_fxn.py defines the function paramup_fxn, which updates cell parameters given the cell's current parameters, local substrate, local medium, and neighboring cells.
Main.py defines environmental variables (i.e. environment dimensions) as well as the initial conditions and perturbations.
vid is a folder that contains png depictions of the environment at intervals specified by the frame_pic_mod variable described below.
filename is the name of the output csv file. In this file each row is a separate timepoint and each column represents a single unit width of the grid. Each element of this matrix contains the number of cells found within that column of the environment at the corresponding timepoint.
num_cells is the number of cells to seed into the environment.
num_timepoints is the number of timepoints to simulate.
frame_pic_mod indicates the frequency at which environment depictions should be created in the vid folder.
proportion is the proportion of seeded cells that are initialized as rJEB (rescued junctional epidermolysis bullosa) cells. Cells not initialized as rJEB are initialized as JEB cells.
scratch_time is the timepoint at which scratching will occur. It is a good idea to let the sheet reach a steady state before scratching. The number of timepoints needed to reach a steady state should be determined experimentally.
rjeb_params and jeb_params are dictionaries that define initial parameters for the two cell types. Descriptions of these parameters are found in Main.py itself.
x_grid_dim and y_grid_dim define the horizontal and vertical dimensions of the environment, respectively.
scratch_left and scratch_right define the left and right boundaries of the scratch.