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

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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).
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;
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 struct = dwt_dave (data, numcoefs, plot_on)

%len = 2^floor(log2(length(data)));
data = data (1:len)';

% figure
if plot_on >=1
    subplot(211), plot(data);title('Analyzed signal.'); 
%set(gca,'Xlim',[0 len])
% Perform discrete wavelet transform at level 5 by sym2. 
% Levels 1 to 5 correspond to scales 2, 4, 8, 16 and 32. 
[coefs,book_keeping] = wavedec(data,numcoefs,'db8');

% Expand(stretch) discrete wavelet coefficients for plot. 
% Levels 1 to 5 correspond to scales 2, 4, 8, 16 and 32. 
stretch_coefs = zeros(numcoefs,len); 
for k = 1:numcoefs 
    d = detcoef(coefs,book_keeping,k); 
    d = d(ones(1,2^k),:);
    d = d(:)';
    stretch_coefs(k,:) = wkeep(d,len,'c');      %i think this 'c' is correct

%Not sure the point of this code, however
%it appears to change all coefficients with a
%value less than squrt (eps) to zeros
% cfd = cfd(:); 
% I = find(abs(cfd)<sqrt(eps)); 
% cfd(I)=zeros(size(I)); 
% cfd = reshape(cfd,numcoefs,len);

% Plot discrete coefficients. 
if plot_on >=1
    subplot(212), colormap(gray(64)); 
    img = image(flipud(wcodemat(stretch_coefs,64,'row'))); 
    title('Discrete Transform, absolute coefficients.') 
    ylabel('level (beginning at scale 2^1)')

%Plot the unstretched wavelet coefficients
% figure
maxd = 0;

if numcoefs > 10
   numsubplots = floor(numcoefs/2) + 1; 
   numsubplots = numcoefs;

for k = 1:numcoefs
    len_log2 = log2(len);
    d = detcoef(coefs,book_keeping,k);
    % choosing fudge factors to get rid of edge effects
    if (len/2^k) > 15
        d = wkeep (d,round(len/2^k - 0),'c');   %default fudge factor = 8
    elseif (len/2^k) > 7
        d = wkeep (d,round(len/2^k - 0),'c');   %default fudge factor = 4
        d = wkeep (d,round(len/2^k - 0),'c');   %default fudge factor = 0

    struct.dwt(k).coefs = d;
    struct.dwt(k).scale = 2^k;
    if plot_on >=1
        if k <= numsubplots
            subplot(numsubplots,1,numsubplots+1-k), colormap(pink(64));
                % Have this option here so to print the overflow if there
                % are too many graphs appearing
            subplot(numsubplots,1,numsubplots+1-(k-numsubplots)), colormap(pink(64));
        if length(d) >= maxd
            maxd = length(d);
%         axis ([1 maxd min(d) max(d)]);
        ylabel(['Wv Scale ' int2str(2^k)]);
        legend (['mean=' num2str(mean(d)) ' & std=' num2str(std(d))]);

% struct.rawdata = data;
struct.cwt = [];
struct.dwtmotherwavelet = [];


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