programming the cell matrix

Programming of the cell matrix begins at the single-cell level. To build up complex functionality within the matrix, individual cells must be configured to operate cooperatively with their neighboring cells. Collectively, small groups of cells can interact with nearby groups to achieve higher functionalities, which are used to perform more complex functions, and so on.
     The lowest level of programming is a single cell's configuration. This is like the machine code of a CPU, or the DNA of a living cell. It dictates the full scope of the cell's behavior. When the cell is responding to input based on its cellular configuration, that is called the D-MODE behavior of the cell. This is the mode in which a cell is processing inputs and generating outputs according to its current configuration.
     The power of the cell matrix is that the configuration of its cells can be changed, again through cooperation with neighboring cells. When a cell is undergoing such modification, it is said to be in C-MODE.
     In a typical complex application, the cell matrix will have some cells that are processing data, others whose configuration is being modified, and still others that are performing those cell modifications. This involves close cooperation, interaction and exchange among the D-MODE and C-MODE cells within the cell matrix.
     The ideas behind the cell matrix are simple, yet elusive. The only way to gain a profound understanding of the cell matrix is to use it to solve problems. The quickest way to learn about the cell matrix is to get your hands dirty doing low-level programming. You can download a cell matrix simulator below, which runs under windows. This simulator allows you to perform direct manipulations on cells, to watch cells as they operate in D-MODE and C-MODE, and to view their interactions with each other. You can interact with cells in the same way as neighboring cells do (that is, only via the cells' inputs and outputs), or you may "step in from above," completely changing a cell's configuration by directly editing its truth table. There is also an instruction manual provided with the simulator, which includes suggestions on how to use the simulator to learn about the cell matrix.