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!
Ermentrout GB, Terman DH (2010) Mathematical Foundations of Neuroscience Interdisciplinary Applied Mathematics, Antman SS:Marsden JE:Sirovich L:Wiggins, ed. pp.1