The 140828 from modeldbrepository

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This model was developed for the paper:

Tiago Branco, Beverley Clark and Michael Hausser Dendritic
discrimination of temporal input sequences in cortical neurons.
Science. 2010 Sep 24;329(5999):1671-5. Epub 2010 Aug 12.

It has also been used for all simulations presented in:

Tiago Branco and Michael Hausser 
Synaptic integration gradients in single cortical pyramidal cell
dendrites.  Neuron. 2011 Mar 10;69(5):885-92.


The directory contains the NEURON mod and hoc files necessary to
reproduce the basic sequence sensitivity result shown in Fig. S5 panel
B in Branco et al. 2010:

<img src="./screenshot.jpg" alt="Fig S5 simulation" height="300" width="500">

The above was generated from octave by plotting the matrix tempV.dat
which is written from the simulation.  The traces correspond to the
AMPA+NMDA (there are actually four more traces per sequence in the
simulation; in the paper the time intervals shown are from 0-5 ms).
The code was developed and tested using NEURON 7.1 under Linux.  To
run: auto-launch from ModelDB or install by unzipping Branco_2010.zip
into a folder, compile the mod files and start "init_sim.hoc".  For
further information please contact Tiago Branco at [email protected].

Description of files:

./rc19.hoc Cell morphology. Cm has been doubled in apical and basal
           dendrites to account for dendritic spines.

./init_biophys.hoc Set biophysical parameters. Includes procedures to
           add active conductances to soma, axon and basal dendrites.

./init_synapses.hoc Procedures to add AMPA and NMDA synapses. If using
                    active dendrites edit NMDAgmax as indicated.

./synapse_loc.dat Location of synapses in the basal dendritic
		tree. Left-hand side column is the number of the basal
		dendrite and right-hand side the relative position of
		the synapse in the dendrite (1 is distal, 0 is
		proximal). First line has the number of lines and
		number of columns. To add/change the position and
		number of synapses edit this file and update the first
		line accordingly.
			
./synapse_order.dat Temporal sequences to be tested. Each number
		corresponds to a synapse (in the current format there
		are 9 synapses, 0 is the most distal and 8 the most
		proximal), and the sequence defines the order of
		activation of each synapse.  The two sequences in the
		file correspond to the IN and OUT sequences
		respectively. First line has the number of lines and
		number of columns. To test more sequences just add
		them to the file and update the first line.
			
./init_sim Starts the simulation. Currently set to passive mode,
		uncomment lines where indicated to switch to active
		model. The simulation runs through each of the
		sequences defined in synapse_order, and for each
		sequence tests different stimulation intervals set by
		the variable "nTs". This is currently set to 10, which
		results in iterating from 0 (ie: simultaneous
		activation) to 9 ms in steps of 1 ms.

20120409 mod.files/cad.mod updated from euler to derivimplicit as per
http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592

20200818 by NTC:  mod.files/NMDA_Mg_T.mod INITIAL block fixed 
so that initialization brings transition 
U <-> UMg
to steady state. Prior to this fix, NMDA_Mg_T needed at least 50 ms of
model time to settle before it became ready for "synaptic activation."

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