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: 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 firstname.lastname@example.org. 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."