This directory contains the Neuron code for the CA1 pyramidal cell model and 
the experiments described 
in Poirazi, P. Brannon, T. and Mel, B.W. 'Pyramidal Neuron as 2-Layer Neural
 Network.' In Press, Neuron, February 2003.
and 
Poirazi, P. Brannon, T. and Mel, B.W. 'Arithmetic of Subthreshold Synaptic 
Summation in a Model CA1 Pyramidal Cell.' in Press, Neuron, February 2003. 
and
Poirazi, P. Brannon, T. and Mel, B.W. 'Online Supplement: About the Model.'
in Press, Neuron, February 2003. 

Note for ModelDB users:  Many of these simulations take a considerable length
of time and at present they only run under unix/linux.  The auto-launch 
demonstration runs one of the shorter ones, the hyperpolarization-current 
simulation. Also please note that this model is large in size, the zip
file being about a megabyte.


FOR DETAILED INFORMATION ABOUT THE MODEL DISCRIPTION SEE Detailed Model 
Description

Following is a brief overview of the contents of this directory:

(1) lib: 		This directory contains all the library functions 
			called in the setup of the CA1 model cell as well as 
			functions used in the experiments. Each of the 
			functions is described in detail within the respective
			*.hoc file. 

(2) morphology: 	This directory contains the morphology of the cell
			as well as various lists of dendritic compartments 
			used in the model setup and the experiments (files are
			in subdirectory n123).
			
(3) template:		This directory contains a few files that define
			templates used in the model setup and experiments. 
			Templates are described in the .hoc files. 

(4) experiment: 	This directory contains a selected set of experiments 
			as described in the aforementioned publications. Within
			each subdirectory, the *.hoc files contain the NEURON 
			code for the experiment while the run_* files are the 
			executables used by the user to run the experiment. 
			Each experiment is described in detail in the 
			respective .hoc files. Briefly:
			

tune-synapses		%%%% Code for tuning the AMPA/NMDA conductances of a 
			%%%% synapse placed on any possible location of the 
			%%%% cell such that a local single pulse stimulation 
			%%%% will result in 5mV local depolarization.  For 
			%%%% tuning, the NMDA conductance for each position is
			%%%% calculated using the NMDA/AMPA ratio parameter 
			%%%% provided by the user in 
			%%%% /morphology/n123/nmda-ampa-ratio.hoc

spike-train-attennuation
			%%%% Code for (1) Backpropagating Action Potential 
			%%%% generation (bpap.hoc) with somatic or dendritic 
			%%%% stimulation and (2) somatic/dendritic single trace
			%%%% generation under control, A-current blockade and
			%%%% Ca++ current blockade (Hofman_traces.hoc). The 
			%%%% aim of this experiment is (1) to ensure that BPAPs
			%%%% behave similarly to biophysical data that 
			%%%% differentiate between somatic and dendritic 
			%%%% stimulation as seen in Spruston et al, 1995 and 
			%%%% Golding eta al 1999. (2) to ensure that cell 
			%%%% response to short stimuli under control, 
			%%%% A-current and A,Ca++-current blockade resemble 
			%%%% biophysical data provided by Hofman et al 1997. 
			%%%% The experiment is used to generate figure 2 in 
			%%%% Poirazi,P. Brannon, T. and Mel, B.W. 'Online 
			%%%% Supplement: About the Model.'

hyperpolarization-current	
			%%%% This experiment is used to study the effect of 
			%%%% h-current on (1) input resistances and 
			%%%% (2) propagation of hyperpolarizing voltage 
			%%%% traces at the somatic and dendritic regions 
			%%%% and to ensure that model responses comply with 
			%%%% physiological findings provided by Magee 1998.
			%%%% The experiment is used to generate figure 1 in 
			%%%% Poirazi,P. Brannon, T. and Mel, B.W. 
			%%%% 'Online Supplement: About the Model.'
			
single-shock		%%%% This directory contains code for the Cash and 
			%%%% Yuste 1999 validation experiments shown in 
			%%%% Poirazi,P Brannon, T. and Mel, B.W. 'Arithmetic of
			%%%% Subthreshold Synaptic Summation in a Model CA1 
			%%%% Pyramidal Cell., figures 1 and 2.
			%%%% It includes code for single pulse stimulation of 
			%%%% two synaptic stimuli (a) individually and (b) in 
			%%%% combination. The stimuli are placed on either one
			%%%% or two trunk sections (Trunk_A.hoc, 
			%%%% Trunk_AplusB.hoc) or within a single oblique 
			%%%% dendrite
			%%%% (Apical_Tips.hoc). The aim of this experiment is 
			%%%% to show that the model cell performs the same kind
			%%%% of synaptic integration for single pulse stimuli
			%%%% as the Cash and Yuste 1999 paper shows.


single-branch-potency   %%%% This directory contains code for the generation of
			%%%% figures 3 and 4 in Poirazi,P. Brannon, T. and 
			%%%% Mel, B.W. 'Arithmetic of Subthreshold Synaptic 
			%%%% Summation in a Model CA1 Pyramidal Cell. as well 
			%%%% as figure 3 in Poirazi,P. Brannon, T.and Mel, B.W.
			%%%% 'Pyramidal Neuron as 2-Layer Neural Network.' This
			%%%% includes code for 50Hz or single shock stimulation
			%%%% of two groups of synapses in apical obliques where
			%%%% synapses are stimulated (a) individually and 
			%%%% (b) in combination. Stimulated synapses can be 
			%%%% within the same oblique (A_feq.hoc, A+Bfreq.hoc, 
			%%%% A_shock.hoc, A+Bfreq.hoc) or in two different 
			%%%% obliques (A+Cfreq.hoc, A+Cshock.hoc). The aim of 
			%%%% this experiment is to show that synaptic 
			%%%% integration is different for single pulse vs 
			%%%% high frequency stimulation and for within versus 
			%%%% between side branch stimulation.


cluster-dispersion      %%%% This directory contains code for the generation of
			%%%% figures 2, 5 and 6 in Poirazi,P. Brannon, T. and 
			%%%% Mel, B.W. 'Arithmetic of Subthreshold Synaptic 
			%%%% Summation in a Model CA1 Pyramidal Cell.' This 
			%%%% includes code for 50 Hz stimulation of a fixed 
			%%%% number of excitatory synapses (32, 35, 36, 40, 45,
			%%%% 48, 49 or 63) which are distributed on apical 
			%%%% obliques in increasingly clustered form. In some 
			%%%% cases, inhibition is added to prevent 
			%%%% uncontrolled spiking.Spike rate for different 
			%%%% degrees of synaptic clustering, synchronicity and
			%%%% background activation. (Disperse_equal_sized.hoc,
			%%%% Disperse_equal_sized_tuft.hoc, Disperse_6_2.hoc)
			%%%% is used to validate a mathematical model that 
			%%%% predicts cell firing rate for various synaptic 
			%%%% stimuli (figures 5 & 6).


Within each experiment directory, the *.hoc files contain the code to be 
executed and the respective run* files are the executables.
The user need to turn these files into executables by using the command:

chmod +x run_Afreq

on a unix/linux prompt, in the specific experiment directory. Then to run the 
experiments the user needs to type the run* file name on the unix promt and 
assuming the NEURON path is set correctly in his/her .bashrc file
the experiments should start running.


If you have any problems using the model, please feel free to
contact me at poirazi@imbb.forth.gr.

Hope this is helpful! Good luck,

Yiota Poirazi

2/3/2003

