http://www.topographica.org
Topographica is intended to complement the many good low-level neuron simulators that are available, such as Genesis and Neuron. Those simulators focus on modeling the detailed internal behavior of neurons and small networks of them. Topographica instead focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. Many important phenomena cannot be studied without such large networks, including the two-dimensional organization of visual orientation and motion direction maps, and object segmentation and grouping processes.