KarlJack47 / HybridCAFieldCancerization

Hybrid Cellular Automata that represents field cancerization.

HybridCAFieldCancerization

The parameters are set such that two carcinogens are possible, alcohol and nicotine, and there are 10 genes that are allowed to mutate. The parameters are tuned towards the formation of tongue carcinomas.

Notes

1. This program only currently supports Ubuntu and requires one NVIDIA gpu to run.
2. The default gpu block size is 16.
3. The stability of the program has only been checked up to a time step of 10966 and grid size of 1024.
4. If you want to consider more carcinogens you need to update the main.cu file and change the appropriate variables.
5. If you want to consider different genes you will have to edit the appropriate variables.
6. The program might not run in a cloud environment like GoogleCloud since it depends on being able to display a GUI.

Compile

To compile the program run the bin/compile.sh bash script in the directory you want the program. The program depends on the following non-system libraries:

1. omp
2. cuda
3. curand
4. turbojpeg
5. lz4frame

Running Simulations

Results for the thesis were generated using bin/simulations.sh. For more information on how to generate custom results run bin/create_results.sh help.

GUI Instructions

1. If the GUI is active the simulations are initially paused.
2. When any window is the currently active one pressing the space key pauses the simulation.
3. When any window is the currently active one pressing the escape key ends the simulation.
4. Initially there is only one window, and it initially shows the CA window. You can cycle through the different types of windows using the 'A' and 'D' keys.
5. To detach a window from the main windows press 'X'. To reattach the window press 'X' again when that window is active.
6. While the CA window is the currently active one:
   1. Press the right arrow key to step through the simulation, hold to keep it going. Note this functionality only really makes sense from a paused state.
   2. Press the 'K' key to set excision mode on. While this is active all tumor cells and their neighbours are killed. Note that the key 'K' acts as a toggle switch so to stop tumour excision one must hit the key again. Also if the simulation is currently paused tumour excision won't occur till it is unpaused and will occur at the end of the timestep.
   3. If excision mode is active and a user clicks on a cell in the grid then they will be specifying the center for an excision to be formed and asked to enter a radius (in number of cells). If they specify a radius of -1 no excision occurs.
7. When the Gene Families is the current active one:
   1. Press the right arrow key to step through the simulation.
8. While the Cell window is the currently active one:
   1. The directional arrows are used to control what cell is currently being viewed.
   2. If the simulation is paused pressing the 'S' key saves the current screen as a picture.
   3. Clicking on a cell in the CA window will cause that to be the selected cell.
9. While the carcinogen window is the currently active one:
   1. The right and left arrow keys are used to go through the different carcinogens.