Train a generative model of subcellular location using the LAMP2 dataset from the Murphy Lab on CellOrganizer

gistfile1.matlab

function answer = lamp2( directory )
%LAMP2 Helper script that shows how to train a generative model of
%subcelullar location using the LAMP2 dataset from the Murphy Lab.

% Author: Ivan E. Cao-Berg (icaoberg@scs.cmu.edu)
%
% Copyright (C) 2012 Murphy Lab
% Lane Center for Computational Biology
% School of Computer Science
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to murphy@cmu.edu

if nargin == 0
   directory = '/share/images/Hela/3D';
end

dimensionality = '3D';

answer = false;
pattern = 'LAMP2';
imageDirectory = [ directory filesep 'LAM' ];
if ~exist( imageDirectory )
  warning('Image directory does not exist')

  disp( 'Would you like to download the LAMP2 dataset from the Murphy Lab website?' );
  option = input( 'Yes/No: ' )
  while ~strcmpi( option, 'yes' ) & ~strcmpi( option, 'no' )
     warning('Unrecognized option');
     disp( 'Would you like to download the LAMP2 dataset from the Murphy Lab website?' );
     option = input( 'Yes/No: ' )
  end

  if strcmpi( option, 'yes' )
     if ~exist( 'data.tgz' )
       url = 'http://murphylab.web.cmu.edu/data/Hela/3D/3DHela_LAM.tgz';
       filename = 'data.tgz';
       disp('Downloading data. Please be patient...');
       urlwrite(url,filename);
     else
       disp('File found. Ignoring download.');
     end

     if ~exist( 'LAM', 'dir' )
      disp('Extracting data. Please be patient...');
      untar( 'data.tgz' );
      dna = 'LAM';
      cell = 'LAM';
      protein = 'LAM';
     else
      disp('LAMP2 image folder. Ignoring extraction.');
      dna = 'LAM';
      cell = 'LAM';
      protein = 'LAM';
     end 
  else
     return
  end
else
 dna = imageDirectory;
 cell = imageDirectory;
 protein = imageDirectory;
end

% generic model options
% ---------------------
% model.name                (optional) Holds the name of the model. Default is empty.
param.model.name = 'LAMP2';

% model.id                  (optional) Holds the id of the model. Default is empty.
try
   [status,result] = system( 'uuidgen' ); 
   param.model.id = result(1:end-1);
catch
   param.model.id = num2str(now);
end

% model.filename            Holds the output filename.
param.model.filename = [ lower(pattern) '.xml' ];

% nuclear shape model options
% ---------------------------
% nucleus.type              Holds the nuclear model type. Default is "medial axis".
param.nucleus.type = 'medial axis';

% nucleus.name              (optional) Holds the name of the nuclear model. Default is empty.
param.nucleus.name = 'LAMP2';

% nucleus.id                (optional) Holds the id of the nuclear model. Default is empty.
try
   [status,result] = system( 'uuidgen' ); 
   param.nucleus.id = result(1:end-1);
catch
   param.nucleus.id = num2str(now);
end

% cell shape model options
% ------------------------
% cell.type                 Holds the cell model type. Default is "ratio".
param.cell.type = 'ratio';

% cell.name                 (optional) Holds the name of the cell model. Default is empty.
param.cell.model = 'LAMP2';

% cell.id                   (optional) Holds the id the cell model. Default is empty.
try
   [status,result] = system( 'uuidgen' ); 
   param.cell.id = result(1:end-1);
catch
   param.cell.id = num2str(now);
end

% protein shape model options
% ---------------------------
% protein.type              (optional) Holds the protein model type. The default is "vesicle".
param.protein.type = 'vesicle';

% protein.name              (optional) Holds the name of the protein model. The default is empty.
param.protein.name = 'LAMP2';

% protein.id                (optional) Holds the id of the protein model. The default is empty.
try
   [status,result] = system( 'uuidgen' ); 
   param.protein.id = result(1:end-1);
catch
   param.protein.id = num2str(now);
end

% protein.class             Holds the protein class, e.g. lysosome, endosome.
param.protein.class = 'lysosome';

% protein.cytonuclearflag   (optional) Determines whether the protein pattern will be generated in
%                           the cytosolic space ('cyto'), nuclear space ('nuc') or everywhere ('all').
%                           Default is cyto.
param.protein.cytonuclearflag = 'cyto';

% other options
% -------------
% verbose                   (optional) Displays messages to screen. The default is true.
param.verbose = true;

% debug                     (optional) Reports errors and warnings. Default is false.
param.debug = true;

% train.flag                (optional) Selects what model is going to be trained ('nuclear',
%                           'framework', or 'all'). Default is 'all'
param.train.flag = 'nuclear';

%documentation
param.documentation.author = 'Ivan E. Cao-Berg';
param.documentation.email = 'icaoberg@scs.cmu.edu';
param.documentation.description = ['Lysosomal-associated membrane protein 2 (LAMP2) ' ...
   'also known as CD107b (Cluster of Differentiation 107b)']
param.documentation.website = 'http://www.genenames.org/data/hgnc_data.php?hgnc_id=6501';

answer = img2slml( dimensionality, dna, cell, protein, param );
end%lamp2