Figure 9. Functional blocks of the simulation program.

Program initialization is followed by a loop that performs biochemical and biomechanical calculations. This is followed by a check of the status of individual cells – this is where we decide whether a cell advances in the cell cycle, undergoes mitosis, or dies. Next the program computes the geometry and the topology of the cell cluster, and finally it outputs intermediate statistics and results. The loop continues until a user-defined stop condition is met. Some parts of the program can proceed in parallel (like metabolism and cell motion), and we can use multithreaded code.