If you are starting with Neural Networks you should check out my online book on the subject. It contains over 300 pages of information on Neural Network Programming in Java. You can access it here.
Hava Siegelmann is an associate professor at the computer science department. She is the director of the bio-computation laboratory. Within this lab, a few fascinating projects run, which relate computational modeling to biological and cognitive processes
SIMBRAIN is a free tool for building, running, and analyzing neural-networks (computer simulations of brain circuitry). Simbrain aims to be as visual and easy-to-use as possible.
Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks. Cross-platform execution