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