Explore
View the clustered data
Figures
View figures from the paper
Supplement
Additional information
Help
Get help interpreting
the data  
Download Data

Download Software

People

FuzzyExplorer Installation Instructions

FuzzyExplorer is based on the program GeneExplorer developed by Christian Rees.

You can install FuzzyExplorer on any computer that runs Apache, PERL, and has the PERL module GD.pm (created by Lincoln Stein for the GD Graphics library developed by Tom Boutell). Please do not email us with questions about installing these features.

Installing FuzzyExplorer procedes in two steps:
  • Installing the appropriate libraries (into two directories: one in cgi-bin and one in html)
  • Creating the image files for each data set

    A. Installing files

    1. Create a subdirectory in cgi-bin called "FuzzyExplorer" with the correct permissions 
       > mkdir FuzzyExplorer
   > chmod 755 FuzzyExplorer
    2. Download and unpack the cgi-bin Package into the FuzzyExplorer directory 
       > tar -zxvf fuzzyX_cgi-bin.tar.gz
    This will create five files and one subdirectory 
       >ls -l
   Microarray/                  # contains the program class libraries
        explorer.pm		# PERL modules used by the fx program	
	dataset.pm
   fx*                          # the FuzzyExplorer executable program
   makeMicroarrayDataset.pl     # Perl program to generate the initial images
   sc.feature_style             # a markup stylesheet for the gene annotation features
    3. Edit the fx program to set the correct paths for your system (change text highlighted in orange below) 
       >pico fx
    
    # at line 50
    my $repository = "/YOUR_PATH/cgi-bin/FuzzyExplorer/";
    my $dataset    = new Microarray::dataset($name, $repository);

    # create a new explorer object 
    my $stylesheet = "sc.feature_style";
    my $explorer = new Microarray::explorer({ dataset     => $dataset,
                                           server_root => '/YOUR_PATH/html',
                                           ht_tmp      => '/FuzzyExplorer/tmp/',
                                           img_path    => '/FuzzyExplorer/images/',
                                           stylesheet  => $stylesheet
                                           });
    4. Create a subdirectory in html called "FuzzyExplorer". Download and unpack the html Package into the FuzzyExplorer directory 
       > mkdir FuzzyExplorer
   > tar -zxvf fuzzyX_html.tar.gz
    This will create two subdirectories 
       > ls
   images/            # contains icon images used by fx
   tmp/               # a temporary repository where fx images are dumped
    Change the permissions on the tmp directory 
       > chmod 666 tmp

    B. Creating images

    The program requires three files: the complete dataset, in text tab-delimited .cdt format, the table of the centroid gene expression patterns identified by FuzzyK, and the table of gene-centroid memberships identified by FuzzyK.

    1. Create a new dataset using the program makeMicroarrayDataset.pl - to see the required commands, simply call the program 
       > perl makeMicroarrayDataset.pl
    ------------------------------------------------------------------------------------
    -file     = Centroid file from FuzzyK, in .fct format
    -datafile = data file in .cdt format
    -membfile = membership file in .mb format
    -repdir   = cgi-bin repository directory
    -imgdir   = html image repository directory
    -contrast = contrast value for the generated images
    -colschem = color scheme used for generating the images, rg = red/green, yb = yellow/blue
    -verbose  = show feedback messages during run
    2. Now call the program with the required commands (as shown here for the file FuzzyClustering_K100) 
       >perl makeMicroarrayDataset.pl -file FuzzyClustering_K100.fct -datafile YeastStressData.cdt 
   -membfile FuzzyClustering_K100.mb -repdir /YOUR_PATH/cgi-bin/FuzzyExplorer
   -imgdir /YOUR_PATH/html/FuzzyExplorer/images/ -contrast 2 -colschem rg -verbose
    3. If the program was set up correctly, it should create the required .png image files to be used by the program. If it was not set up correctly, you will get errors. Common errors: GD is not installed, the PERL libraries cannot be found by the program, the subdirectory paths in the fx program are incorrect.

    4. If all went well, you should now be able to view your data over the web by typing the correct path: 
       http://YOUR_PATH/cgi-bin/FuzzyExplorer/fx?n=NAME_OF_FUZZYK_FILE
    example: 
       http://rana8.lbl.gov/cgi-bin/FuzzyExplorer/fx?n=FuzzyClustering_K100
    5.Important Note: FuzzyExplorer writes temporary image (.png) files to the html/FuzzyExplorer/tmp directory - the files accumulated in this directory must be periodically purged to free space.

    6. To change the links shown in the gene annotation field, change the sc.feature_style file accordingly.

     

    		•