The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
The main home page of the CDK is now at: http://cdk.github.io
Nengo is a suite for building and simulating models of large neural networks. It is based on Eliasmith & Anderson's Neural Engineering Framework, which provides a coherent theory of computation, representation, and dynamics in neural circuits.