Ermentrout and Terman's book on dynamical systems and computational methods in neuroscience has associated computer code available at http://www.math.pitt.edu/~bard/bardware/neurobook/allodes.html. The main emphasis in the book is on single-neuron biophysics and there is also systems neuroscience theory and applications to networks. The electronic text of the book is freely available!
Model Concept(s): Tutorial/Teaching
Simulation Environment: XPP (web link to model)
References:
Ermentrout GB, Terman DH. (2010). Mathematical Foundations of Neuroscience Interdisciplinary Applied Mathematics. 35