Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)

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Accession:142104
This model produces the hippocampal CA3 neural network model used in the paper below. It has two modes of operation, a default mode and a circadian mode. In the circadian mode, parameters are swept through a range of values. This model can be quite easily adapted to produce theta and gamma oscillations, as certain parameter sweeps will reveal (see Figures). BASH scripts interact with GENESIS 2.3 to implement parameter sweeps. The model contains four cell types derived from prior papers. CA3 pyramidal are derived from Traub et al (1991); Basket, stratum oriens (O-LM), and Medial Septal GABAergic (MSG) interneurons are taken from Hajos et al (2004).
Reference:
1 . Stanley DA, Talathi SS, Parekh MB, Cordiner DJ, Zhou J, Mareci TH, Ditto WL, Carney PR (2013) Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. J Neurophysiol 110:1070-86 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Hippocampus; Medial Septum;
Cell Type(s): Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron; Hippocampus septum medial GABAergic neuron;
Channel(s): I Na,t; I A; I K; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Epilepsy; Brain Rhythms; Circadian Rhythms;
Implementer(s): Stanley, David A ;
Search NeuronDB for information about:  Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; GabaA; AMPA; I Na,t; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
function [Hscale,Htext]=plot_scale(Pos,Scale,Length,Color,UnitsName,Orient);
%-------------------------------------------------------------------
% plot_scale function     Add a scale bar on a plot or image.
% Input  : - Scale bar position [X, Y].
%          - Scale [Units per pixel].
%          - Scale bar length in units (e.g., arcsec).
%          - Color, default is 'k';
%          - Units name, default is 'arcsec'.
%          - Scale bar orientation:
%            'h' - Horizontal (default).
%            'v' - Vertical. 
% Output : - Handle for the scale line.
%          - Handle for the text.
% Tested : Matlab 7.0
%     By : Eran O. Ofek          July 2005
%    URL : http://wise-obs.tau.ac.il/~eran/matlab.html
%-------------------------------------------------------------------
DistFactor = 0.05;
if (nargin==3),
   Color     = 'k';
   UnitsName = 'arcsec';
   Orient    = 'h';
elseif (nargin==4),
   UnitsName = 'arcsec';
   Orient    = 'h';
elseif (nargin==5),
   Orient    = 'h';
elseif (nargin==6),
   % do nothing
else
   error('Illegal Number of input arguments');
end

NextPlot = get(gca,'NextPlot');
hold on;

XLim   = get(gca,'XLim');
YLim   = get(gca,'YLim');
Xdiff  = abs(diff(XLim));
Ydiff  = abs(diff(YLim));

switch Orient
 case 'h'
    LineX = Pos(1) + 0.5.*Length./Scale.*[-1;+1];
    LineY = Pos(2).*[+1;+1];
    DistXdir = 0;
    DistYdir = -1;
 case 'v'
    LineX = Pos(1).*[+1;+1];
    LineY = Pos(2) + 0.5.*Length./Scale.*[-1;+1];
    DistXdir = +1;
    DistYdir = 0;
 otherwise
    error('Unknown Orient Option');
end

%--- plot line ---
Hscale = plot(LineX,LineY,'LineWidth',2);
set(Hscale,'Color',Color);

%--- plot text ---
DistX    = DistXdir.*DistFactor.*Xdiff;
DistY    = DistYdir.*DistFactor.*Ydiff;

% Htext    = text(Pos(1)+DistX,Pos(2)+DistY,sprintf('%5.1f %s',Length,UnitsName));

switch Orient,
 case 'h'
    % do nothing
 case 'v'
%     set(Htext,'Rotation',90);
 otherwise
    error('Unknown Orient Option');
end
% set(Htext,'HorizontalAlignment','center','Color',Color);

set(gca,'XLim',XLim);
set(gca,'YLim',YLim);

set(gca,'NextPlot',NextPlot);

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