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 *
                            
function varargout = pdftops(cmd)
%PDFTOPS  Calls a local pdftops executable with the input command
%
% Example:
%   [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future reference.
% 
% Once found, the executable is called with the input command string.
%
% This function requires that you have pdftops (from the Xpdf package)
% installed on your system. You can download this from:
% http://www.foolabs.com/xpdf
%
% IN:
%   cmd - Command string to be passed into pdftops.
%
% OUT:
%   status - 0 iff command ran without problem.
%   result - Output from pdftops.

% Copyright: Oliver Woodford, 2009-2010

% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on
% Mac OS.
% Thanks to Christoph Hertel for pointing out a bug in check_xpdf_path
% under linux.
% 23/01/2014 - Add full path to pdftops.txt in warning.

% Call pdftops
[varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd));
end

function path_ = xpdf_path
% Return a valid path
% Start with the currently set path
path_ = user_string('pdftops');
% Check the path works
if check_xpdf_path(path_)
    return
end
% Check whether the binary is on the path
if ispc
    bin = 'pdftops.exe';
else
    bin = 'pdftops';
end
if check_store_xpdf_path(bin)
    path_ = bin;
    return
end
% Search the obvious places
if ispc
    path_ = 'C:\Program Files\xpdf\pdftops.exe';
else
    path_ = '/usr/local/bin/pdftops';
end
if check_store_xpdf_path(path_)
    return
end
% Ask the user to enter the path
while 1
    if strncmp(computer,'MAC',3) % Is a Mac
        % Give separate warning as the uigetdir dialogue box doesn't have a
        % title
        uiwait(warndlg('Pdftops not found. Please locate the program, or install xpdf-tools from http://users.phg-online.de/tk/MOSXS/.'))
    end
    base = uigetdir('/', 'Pdftops not found. Please locate the program.');
    if isequal(base, 0)
        % User hit cancel or closed window
        break;
    end
    base = [base filesep];
    bin_dir = {'', ['bin' filesep], ['lib' filesep]};
    for a = 1:numel(bin_dir)
        path_ = [base bin_dir{a} bin];
        if exist(path_, 'file') == 2
            break;
        end
    end
    if check_store_xpdf_path(path_)
        return
    end
end
error('pdftops executable not found.');
end

function good = check_store_xpdf_path(path_)
% Check the path is valid
good = check_xpdf_path(path_);
if ~good
    return
end
% Update the current default path to the path found
if ~user_string('pdftops', path_)
    warning('Path to pdftops executable could not be saved. Enter it manually in %s.', fullfile(fileparts(which('user_string.m')), '.ignore', 'pdftops.txt'));
    return
end
end

function good = check_xpdf_path(path_)
% Check the path is valid
[good, message] = system(sprintf('"%s" -h', path_));
% system returns good = 1 even when the command runs
% Look for something distinct in the help text
good = ~isempty(strfind(message, 'PostScript'));
end

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