www.neuron.yale.edu

I am an undergraduate student at the University of Texas at Brownsville and currently working with Neuron 6.1. I am trying to construct a simple model of a granule cell to observe the BK channel and calcium fluctuations. I’ve constructed the cell morphological characteristics with cell builder using values from the Neuron Yale Database. I am currently puzzled on how to integrate a calcium accumulation & calcium activated potassium channel mechanisms into my cell. These I have found as examples in the Neuron software. I have gone through several tutorials and searched the forum several times and have not found any information on how I can integrate these mechanisms into my cell. Could someone point me in the right direction or so provide me with a clue on how to go about this?

There are two steps:
specifying the biophysical properties of a mechanism
making the mechanism be an attribute of a section

The first step is discussed here
Adding new mechanisms to NEURON
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=260
A tutorial on the Channel Builder is available at
http://www.neuron.yale.edu/neuron/docs
For more detail about NMODL usage see our article
"Expanding NEURON's Repertoire of Mechanisms with NMODL"
(see http://www.neuron.yale.edu/neuron/docs)
or chapter 9 of The NEURON Book.

The second step, since you're using the CellBuilder, would be accomplished on the
Biophysics page of that tool, as illustrated in the CellBuilder tutorial which you will find at
http://www.neuron.yale.edu/neuron/docs
Of course it can also be done by writing hoc code, as described in
"The NEURON Simulation Environment"
i.e. our first article in Neural Computation, which you will find at the same URL, and also
in chapters 5 and 6 of The NEURON Book.