The nodes and links are displayed in different colours depending on their function.

Node Colours
Orange nodes are output neurons.
Grey nodes are hidden neurons.
Green nodes have no inputs links and are acting as bias neurons.
Pink nodes are input neurons.

Link Colours
Red links are normal feed forward connections.
Yellow links are recurrent links to a different node.
Blue links are self recurrent links.
Click on the examples below. The first is an an output from the XOR experiment, and the second is from a Forex Trading experiment that I am currently doing. Note on the second example, if you look at the inputs (pink) you should notice that the numbers are non-contiguous showing the input selection evolution.