This is the readme for a model associated with the paper

Polsky A, Mel B, Schiller J (2009) Encoding and decoding bursts by
NMDA spikes in basal dendrites of layer 5 pyramidal neurons.
J Neurosci 29:11891-903

These files were contributed by Dr. A. Polsky

glutamate.mod This is the simulated glutamate impact on the
postsynaptic cell via AMPA/NMDA receptors

Release parameters include 

del: delay for the first pulse
Tspike: interspike (presynaptic release) intervals
Nspike: number of presynaptic pulses
gNMDAmax and gAMPAmax: postsynaptic conductances, in case of NMDA, the
peak possible conductance. In this simulation AMPA conductance was set
to zero.
decayAMPA, decayNMDA: degree of short term plasticity of the
postsynaptic conductances, in the paper it was set to one (meaning
same intensity for all pulses).
taudAMPA,taudNMDA: timecourse of the short term plasticity


layerV.hoc
the morphology and the basec biophysical properties of the cortical
layer 5 pyramidal cell (not the same cell as used in the original
paper)

main.hoc (+ses)
the file that runs the simulation

In the simulation, the glutamatergic synapse is located on a basal
branch (dend[73]). Paired pulse stimulation elicits an NMDA spike with
stimulation >10nS. NMDA spike threshold with a single pulse is
~18nS. Depolarizing the soma to recreate the expected first stimulus
depolarization shifts the single pulse threshold to ~15nS.

Below is a table of NMDA receptor conductance and somatic
depolarization with paired pulse stimulation, single pulse and single
pulse +somatic current injection of 0.15nA

2     0.2  0.1	 0.1
4     0.4  0.2	 0.2
6     0.6  0.3	 0.3
8     0.9  0.2	 0.5
10    1.3  0.5	 0.7
12    2.2  0.7	 1
14    4.1  0.8	 1.3
16    5.1  1	 1.8
18    5.86 1.3	 2.6
20    6.5  1.7	 3.3
22    7	   2.6	 3.8
24    7.5  3.7	 4.2
26    7.8  4.4	 4.6
28    8	   5	 4.9
30    8.2  5.4	 5.2
32    8.4  5.8	 5.5
34    8.5  6	 5.7
36    8.6  6.1	 5.8

Usage:
------
After autolaunching or downloading and compiling the mod files
(nrnivmodl (linux), mknrndll (ms win or mac os x), running the
simulation (with Init & Run button) will produce this default graph:



An illustration analagous to fig 9 in the paper: turn "Keep Lines" on
in the graph through the pop up menu, set the gnmdamax and gampamax to
16; run the simulation. Then set NSpike to 1 and set both conductance
densities to 32 and run the simulation; these graphs should appear: