AnimatLab is a software tool that combines biomechanical simulation and biologically realistic neural networks.
You can build the body of an animal, robot, or other machine and place it in a virtual world where the physics of its interaction with the environment are accurate and realistic. You can then design a nervous system that controls the behavior of the body in the environment. The software currently has support for simple firing rate and leaky integrate and fire spiking neural models. In addition, there a number of different synapse model types that can be used to connect the various neural models to produce your nervous system. On the biomechanics side there is support for a variety of different rigid body types, including custom meshes that can be made to match skeletal structures exactly. The biomechanics system also has hill-based muscle and muscle spindle models. These muscle models allow the nervous system to produce movements around joints. In addition, there are also motorized joints for those interested in controlling robots or other biomimetic machines. This allows the user to generate incredibly complicated artificial lifeforms, otherwise known as animats, that are based on real biological systems. Best of all AnimatLab is completely free and it includes free source code!