This is the readme for the model associated with the paper:

Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles
underlying optical stimulation of a channelrhodopsin-2 positive
pyramidal neuron J Neurophysiol. 107(12):3235-45

For best results, open directory in ipython notebook and load
"Optical Stimulation". Otherwise, refer to "Optical Stimulation.py".

On an ubuntu 13.10 we can cd to the expanded zip folder and then type
ipython notebook.  Once the notebook starts in a browser you can
select the "Optical Stimulation" notebook.  If you execute all the
cells you shoud see an image at the end like:



-- Tom Foutz
March 15, 2014

20150518 Updates from Ted Carnevale:
1.  The gbar parameters of the mechanisms specified by these files
ca.mod kca.mod km.mod kv.mod na12.mod na16.mod na.mod are now the
actual channel densities.  This eliminates a spurious temperature
dependency of the effective channel density.
2.  These same files are now threadsafe, and use efun rather than
vtrap0 to deal with singularities.  See the mod files for more
information.

20150524 Update from Ted Carnevale: Changed integration method from
euler to derivimplicit which is appropriate for simple ion
accumulation mechanisms.  See Integration methods for SOLVE statements
http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592