Due to the number of connections drawn bitozoon may look very complicated, but it isn't. Every eye is connected to all five neurons of the first layer of the neural network. Every first layer neuron is connected to the second layer neurons, that fire flagella. There is also a glucose level sensor, connected to the second layer neurons. Depending on the type of simulation bitozoa can be blind or have only two eyes, in such a case also number of neurons is smaller, but position of flagella is always the same. Two eyed bitozoa don't have eyes marked with black dot. Blind bitozoa doesn't have first layer of neurons - the only input is from their glucose sensor.
Bitozoa moves on the screen eating fodder. When bitozoon eats its level of glucose jumps to 100%. When bitozoon moves, its level of glucose slowly goes down. When level of glucose falls to zero, bitozoon dies. Eaten fodder reappears somewhere on the screen (thus number of fodders is always the same).
At the beginning there is a preset number of bitozoa present. They are wandering, eating and slowly dying, until their number falls to other - also preset - number. At this moment surviving bitozoa are allowed to have some sex and they are mixing their genes producing the offspring. Neurons of every new bitozoon are a mix of its parents neurons. Some neurons weights are mutated. New generation starts to explore the screen eating fodder and whole cycle repeats again.
This process can be described as a creation of genetic algorithm - every bitozoon is an algorithm, and their genes are neurons.
Please take into account that program starts always the same simulation - blind bitozoa. If you want to see something other you must press Ctrl-P to access parameters windows. If you want to make evolution faster, switch off animation (Ctrl-A). To see history window press Ctrl-H. To restart simulation, press Ctrl-R. Using Ctrl-S and Ctrl-O you may save and later reload simulation. Of course if you don't have keyboard, you can use your mouse and program menu :)
If you change number of bitozoa present at the beginning of simulation, or if you change number of fodders, you must restart simulation. In all other cases you can continue it without problems.