Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

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Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
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 *
                            
%GHOSTSCRIPT  Calls a local GhostScript executable with the input command
%
% Example:
%   [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript 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 Ghostscript installed on your
% system. You can download this from: http://www.ghostscript.com
%
% IN:
%   cmd - Command string to be passed into ghostscript.
%
% OUT:
%   status - 0 iff command ran without problem.
%   result - Output from ghostscript.

% Copyright: Oliver Woodford, 2009-2013

% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on
% Mac OS.
% Thanks to Nathan Childress for the fix to the default location on 64-bit
% Windows systems.
% 27/4/11 - Find 64-bit Ghostscript on Windows. Thanks to Paul Durack and
% Shaun Kline for pointing out the issue
% 4/5/11 - Thanks to David Chorlian for pointing out an alternative
% location for gs on linux.
% 12/12/12 - Add extra executable name on Windows. Thanks to Ratish
% Punnoose for highlighting the issue.
% 28/6/13 - Fix error using GS 9.07 in Linux. Many thanks to Jannick
% Steinbring for proposing the fix.
% 24/10/13 - Fix error using GS 9.07 in Linux. Many thanks to Johannes
% for the fix.
% 23/01/2014 - Add full path to ghostscript.txt in warning. Thanks to Koen
% Vermeer for raising the issue.

function varargout = ghostscript(cmd)
% Initialize any required system calls before calling ghostscript
shell_cmd = '';
if isunix
    shell_cmd = 'export LD_LIBRARY_PATH=""; '; % Avoids an error on Linux with GS 9.07
end
if ismac
    shell_cmd = 'export DYLD_LIBRARY_PATH=""; ';  % Avoids an error on Mac with GS 9.07
end
% Call ghostscript
[varargout{1:nargout}] = system(sprintf('%s"%s" %s', shell_cmd, gs_path, cmd));
end

function path_ = gs_path
% Return a valid path
% Start with the currently set path
path_ = user_string('ghostscript');
% Check the path works
if check_gs_path(path_)
    return
end
% Check whether the binary is on the path
if ispc
    bin = {'gswin32c.exe', 'gswin64c.exe', 'gs'};
else
    bin = {'gs'};
end
for a = 1:numel(bin)
    path_ = bin{a};
    if check_store_gs_path(path_)
        return
    end
end
% Search the obvious places
if ispc
    default_location = 'C:\Program Files\gs\';
    dir_list = dir(default_location);
    if isempty(dir_list)
        default_location = 'C:\Program Files (x86)\gs\'; % Possible location on 64-bit systems 
        dir_list = dir(default_location);
    end
    executable = {'\bin\gswin32c.exe', '\bin\gswin64c.exe'};
    ver_num = 0;
    % If there are multiple versions, use the newest
    for a = 1:numel(dir_list)
        ver_num2 = sscanf(dir_list(a).name, 'gs%g');
        if ~isempty(ver_num2) && ver_num2 > ver_num
            for b = 1:numel(executable)
                path2 = [default_location dir_list(a).name executable{b}];
                if exist(path2, 'file') == 2
                    path_ = path2;
                    ver_num = ver_num2;
                end
            end
        end
    end
    if check_store_gs_path(path_)
        return
    end
else
    executable = {'/usr/bin/gs', '/usr/local/bin/gs'};
    for a = 1:numel(executable)
        path_ = executable{a};
        if check_store_gs_path(path_)
            return
        end
    end
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('Ghostscript not found. Please locate the program.'))
    end
    base = uigetdir('/', 'Ghostcript 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)
        for b = 1:numel(bin)
            path_ = [base bin_dir{a} bin{b}];
            if exist(path_, 'file') == 2
                if check_store_gs_path(path_)
                    return
                end
            end
        end
    end
end
error('Ghostscript not found. Have you installed it from www.ghostscript.com?');
end

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

function good = check_gs_path(path_)
% Check the path is valid
shell_cmd = '';
if ismac
    shell_cmd = 'export DYLD_LIBRARY_PATH=""; ';  % Avoids an error on Mac with GS 9.07
end
[good, message] = system(sprintf('%s"%s" -h', shell_cmd, path_));
good = good == 0;
end

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