Model of memory linking through memory allocation (Kastellakis et al. 2016)

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Accession:206249
Here, we present a simplified, biophysically inspired network model that incorporates multiple plasticity processes and explains linking of information at three different levels: (a) learning of a single associative memory (b) rescuing of a weak memory when paired with a strong one and (c) linking of multiple memories across time. By dissecting synaptic from intrinsic plasticity and neuron-wide from dendritically restricted protein capture, the model reveals a simple, unifying principle: Linked memories share synaptic clusters within the dendrites of overlapping populations of neurons
Reference:
1 . Kastellakis G, Silva AJ, Poirazi P (2016) Linking Memories across Time via Neuronal and Dendritic Overlaps in Model Neurons with Active Dendrites. Cell Rep 17:1491-1504 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; C or C++ program (web link to model);
Model Concept(s): Active Dendrites;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
/
stdmodel
exportfig
.ignore
README.md *
.gitignore *
append_pdfs.m *
copyfig.m *
crop_borders.m *
eps2pdf.m *
export_fig.m *
fix_lines.m *
ghostscript.m *
im2gif.m *
isolate_axes.m *
LICENSE *
pdf2eps.m *
pdftops.m *
print2array.m *
print2eps.m *
read_write_entire_textfile.m *
user_string.m *
using_hg2.m *
                            
%EPS2PDF  Convert an eps file to pdf format using ghostscript
%
% Examples:
%   eps2pdf source dest
%   eps2pdf(source, dest, crop)
%   eps2pdf(source, dest, crop, append)
%   eps2pdf(source, dest, crop, append, gray)
%   eps2pdf(source, dest, crop, append, gray, quality)
%
% This function converts an eps file to pdf format. The output can be
% optionally cropped and also converted to grayscale. If the output pdf
% file already exists then the eps file can optionally be appended as a new
% page on the end of the eps file. The level of bitmap compression can also
% optionally be set.
%
% This function requires that you have ghostscript installed on your
% system. Ghostscript can be downloaded from: http://www.ghostscript.com
%
%IN:
%   source - filename of the source eps file to convert. The filename is
%            assumed to already have the extension ".eps".
%   dest - filename of the destination pdf file. The filename is assumed to
%          already have the extension ".pdf".
%   crop - boolean indicating whether to crop the borders off the pdf.
%          Default: true.
%   append - boolean indicating whether the eps should be appended to the
%            end of the pdf as a new page (if the pdf exists already).
%            Default: false.
%   gray - boolean indicating whether the output pdf should be grayscale or
%          not. Default: false.
%   quality - scalar indicating the level of image bitmap quality to
%             output. A larger value gives a higher quality. quality > 100
%             gives lossless output. Default: ghostscript prepress default.

% Copyright (C) Oliver Woodford 2009-2011

% Suggestion of appending pdf files provided by Matt C at:
% http://www.mathworks.com/matlabcentral/fileexchange/23629

% Thank you to Fabio Viola for pointing out compression artifacts, leading
% to the quality setting.
% Thank you to Scott for pointing out the subsampling of very small images,
% which was fixed for lossless compression settings.

% 9/12/2011 Pass font path to ghostscript.

function eps2pdf(source, dest, crop, append, gray, quality)
% Intialise the options string for ghostscript
options = ['-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="' dest '"'];
% Set crop option
if nargin < 3 || crop
    options = [options ' -dEPSCrop'];
end
% Set the font path
fp = font_path();
if ~isempty(fp)
    options = [options ' -sFONTPATH="' fp '"'];
end
% Set the grayscale option
if nargin > 4 && gray
    options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray'];
end
% Set the bitmap quality
if nargin > 5 && ~isempty(quality)
    options = [options ' -dAutoFilterColorImages=false -dAutoFilterGrayImages=false'];
    if quality > 100
        options = [options ' -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode -c ".setpdfwrite << /ColorImageDownsampleThreshold 10 /GrayImageDownsampleThreshold 10 >> setdistillerparams"'];
    else
        options = [options ' -dColorImageFilter=/DCTEncode -dGrayImageFilter=/DCTEncode'];
        v = 1 + (quality < 80);
        quality = 1 - quality / 100;
        s = sprintf('<< /QFactor %.2f /Blend 1 /HSample [%d 1 1 %d] /VSample [%d 1 1 %d] >>', quality, v, v, v, v);
        options = sprintf('%s -c ".setpdfwrite << /ColorImageDict %s /GrayImageDict %s >> setdistillerparams"', options, s, s);
    end
end
% Check if the output file exists
if nargin > 3 && append && exist(dest, 'file') == 2
    % File exists - append current figure to the end
    tmp_nam = tempname;
    % Copy the file
    copyfile(dest, tmp_nam);
    % Add the output file names
    options = [options ' -f "' tmp_nam '" "' source '"'];
    try
        % Convert to pdf using ghostscript
        [status, message] = ghostscript(options);
    catch me
        % Delete the intermediate file
        delete(tmp_nam);
        rethrow(me);
    end
    % Delete the intermediate file
    delete(tmp_nam);
else
    % File doesn't exist or should be over-written
    % Add the output file names
    options = [options ' -f "' source '"'];
    % Convert to pdf using ghostscript
    [status, message] = ghostscript(options);
end
% Check for error
if status
    % Report error
    if isempty(message)
        error('Unable to generate pdf. Check destination directory is writable.');
    else
        error(message);
    end
end
end

% Function to return (and create, where necessary) the font path
function fp = font_path()
fp = user_string('gs_font_path');
if ~isempty(fp)
    return
end
% Create the path
% Start with the default path
fp = getenv('GS_FONTPATH');
% Add on the typical directories for a given OS
if ispc
    if ~isempty(fp)
        fp = [fp ';'];
    end
    fp = [fp getenv('WINDIR') filesep 'Fonts'];
else
    if ~isempty(fp)
        fp = [fp ':'];
    end
    fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype'];
end
user_string('gs_font_path', fp);
end

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