This is the readme for the models associated with the paper

Peter Jedlicka, Thomas Deller, Boris S. Gutkin, Kurt H. Backus (2011)
Activity-dependent intracellular chloride accumulation and diffusion
controls GABAA receptor-mediated synaptic transmission
Hippocampus 21:885-898.

Send bug reports, comments and questions on how to use this model to
jedlicka@em.uni-frankfurt.de/mohapatra@em.uni-frankfurt.de

The code for 8 granule cell morphologies and passive properties was
taken from Schmidt-Hieber et al. 2007:
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=95960
See their readme file for the description of .hoc files in the ./share
and ./cell_x folders.

Usage:

1. Download and install NEURON (available from
http://www.neuron.yale.edu/neuron/download)
   
2. Compile the NEURON mod files:

	mswin: run mknrndll and select this folder to create the
	       nrnmech.dll
	linux: run nrnivmodl in this folder
	mac os x: drag and drop this folder onto mknrndll

3. Start the simulations:

	Figure 6 simulation - EGABA shift following activation of
	multiple GABAA synapses:

	-------------------------------------------------------------

	mswin: double click the mosinit.hoc file using windows
               explorer
	linux: type "nrngui mosinit.hoc" in the shell prompt in this
	       folder
	mac os x: drag and drop the mosinit.hoc file onto the nrngui
                  icon

	To run the simulation click on Init & Run button.

	The simulation automatically executes stochastic activation of
	multiple dendritic and somatic GABA-A synapses with mean
	frequency of 10 Hz/synapse. The simulation starts running and
	begins to generate a shape plot of the granule cell, with
	colour code indicating EGABA changes. The simulation
	reproduces Figure 6A of the paper, but since the synapses are
	activated randomly, each run's result is unique.  Zooming in
        on one of the simulation generated figures should look like:


	- Note: Default cell morphology is cell_7.  This can be
	changed in the ./share/controlpanelGC.hoc file by changing
	defaultCellIndex variable (ranging from 0 to 7).

	Figure 7 simulation - EGABA shift following activation of a
        single GABAA synapse:

---------------------------------------------------------------------

        mswin: double click the mosinit_single.hoc file using windows
               explorer
        linux: type "nrngui mosinit_single.hoc" in the shell prompt in
               this folder
        mac os x: drag and drop the mosinit_single.hoc file onto the
                  nrngui icon

	To run the simulation click on Init & Run button.

	The simulation automatically executes stochastic activation of
	a single dendritic GABA-A input with mean frequency of 40
	Hz. The simulation starts running and begins to generate a
	shape plot of the granule cell, with colour code indicating
	EGABA changes.

	- Note: Default location of the synapse is in the middle of a
	dendrite.  This can be changed in the
	./init_ClmIPSCs_GC_single.hoc file by setting
	DISTAL_SIMULATION = 1 (to move the synapse to the distal end
	of the dendrite).

	For further simulation parameters please refer to the paper.

Description of mod files:

./cldifus.mod           Chloride radial/longitudinal diffusion and
			accumulation mechanism with chloride extrusion
			mechanism mediating exponential recovery of
			intracellular chloride concentration to
			resting chloride level.
					
./cldifus2.mod          Chloride radial/longitudinal diffusion and
			accumulation mechanism with chloride pump
			(Lineweaver-Burke equation) and chloride leak.
			Not used in Fig6/7 simulations.
					
./gabaA_Cl.mod          Ohmic synaptic GABAergic mechanism with
                        dynamic GABA reversal.

./gaghk.mod             GHK synaptic GABAergic mechanism with dynamic
			GABA reversal.  Not used in Fig6/7
			simulations.