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xCellerator installation instructions
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revised 7 Feb 2008

(0) Mathematica must be installed on your machine. If you do not have mathematica
	you will not be able to use xCellerator. Mathematica is commercial software
	that is avaiable from Wolfram Research.
	
	These instructions assume you are using Mathematica Version 6.
	
	xCellerator may downloaded from Sourceforge.
	
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Installation Method 1: Use Installer Script (Linux /Mac OSX /Unix)
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In a terminal window:

(1) cd to the folder that was created when you unpacked the tarball.

(2a) linux users enter:  ./linux_install 

     [ linux install file assumes that gcc, make, and math (mathematica
       command line tool)  are already installed, and that a bash shell
       is installed. Bash does not have to be your default shell. ]

     [ If gcc & make are not installed xCellerator will still install normally
       but qhull will need to be installed manually if you use mPower.]
        
(2b) mac users enter:   ./mac_install
     [ mac install file assumes that the developer tools have already
       been installed and that Mathematica is installed in the usual
       Applications folder.]

     [ If developer tools are not installed xCellerator will still install normally
       but qhull will need to be installed manually if you use mPower.]
 
(3) If you see any error messages proceed to the manual installation instructions.

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Installation Method 2: Manual installation (required for Windows, optional for Linux/Unix/Mac OSX)
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(1) Open Mathematica

(2) Type 

      ToFileName[$UserBaseDirectory, "Applications"]
      
    and note the name of the directory identified. Typical locations are: 

	On Mac OSX:
	   ~/Library/Mathematica/Applications/

	On Linux: 
	   ~/.Mathematica/Applications/

	On Windows:
	   \Documents_and_Settings\username\Application_Data\Mathematica\Applications
 
    This folder should have been created by Mathematica during when it was installed. 
    In some cases the folder is not there and you will need to create it. 
    This folder will be hidden on some installations so make sure you have checked for 
    hidden files before you attempt to create it. 
	
    For more details on system-specific folders see the Mathematica Documentation

(3) Copy the entire "install/xlr8r" folder from the distribution into the 
    folder identified in step (2): 

	On Mac OSX the folder will be called:
	   ~/Library/Mathematica/Applications/xlr8r/

	On Linux the folder will be called: 
	   ~/.Mathematica/Applications/xlr8r/

	On Windows the folder will be called:
	   \Documents_and_Settings\username\Application_Data\Mathematica\Applications\xlr8r\

	Make sure you copy the entire contents of the folder, don't just create an empty folder.
	If you don't then the palettes won't work. Th contents of the xlr8r folder will look something
	like this:

		
(4) Copy the file "xlr8r.m" into the same Applications directory. 

	On Mac OSX the folder will be called:
	   ~/Library/Mathematica/Applications/xlr8r.m

	On Linux the folder will be called: 
	   ~/.Mathematica/Applications/xlr8r.m

	On Windows the folder will be called:
	   \Documents_and_Settings\username\Application_Data\Mathematica\Applications\xlr8r.m

(5) From within Mathematica type

	ToFileName[{$UserBaseDirectory, "SystemFiles", "FrontEnd", "Palettes"}]

	On Mac OSX this should be: 
	    ~/Library/Mathematica/SystemFiles/FrontEnd/Palettes/ 
	
	On Linux this should be:
	   ~/.Mathematica/SystemFiles/FrontEnd/Palettes/ 

	On Windows this should be: 	
	   \Documents_and_Settings\username\Application_Data\Mathematica\SystemFiles\FrontEnd\Palettes
		
(6) Copy the file xCelleratorPalette.nb into the directory identified in step (5).

(7) Install any desired plugins by copying the .m files from the plugins folder 
    in the distribution to the Applications folder identified in step (2) above.
    Please note that the copies of the plugins included in this distribution
    may not be the latest versions and only represent a minimal installation
    of these files. 

    In particular
	(a) If you use MathSBML, the layout, eigenvalue, and SBML validator
	    plugins are not included and should be installed directly from
	    the MathSBML download site if you wish to use them. They are
	    not required by xlr8r.
	(b) If you use mPower you will need to install qhull
	    as per the mPower installation instructions
	    [ A copy of the source code (along with standard configure & make files) is included 
	    in the plugins folder. Some binary installations are available directly from qhull.org.]

(8) You may have to quit and restart mathematica for the palettes to become
	visible.  To use xCellerator, you should  evaluate the line

	<<xCellerator.m
	
	in your notebook before you evaluate any xCellerator commands. 

(9) See the users guide at 

	http://www.xcellerator.info/usersguide/
	
    for further information. 
	
    [ A local copy of the html  user's guide is also included in the doc directory of the distribution. ]
	
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This package is free software; you can redistribute it and/or modify it under the 
terms of the GNU Lesser General Public License as published by the Free Software 
Foundation; either version 2.1 of the License, or any later version.

This package 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.  The software and  documentation provided hereunder is on an 
"as is" basis, and the  California Institute of Technology has no obligations 
to provide maintenance, support, updates, enhancements or modifications.  In no 
event shall the California Institute of Technology  be liable to any party for 
direct, indirect, special, incidental or consequential damages, including lost 
profits, arising  out of the use of this software and its documentation, even if 
the California Institute of Technology have been advised of the possibility of 
such damage.  See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along 
with this package; if not, write to the Free Software Foundation, Inc., 59 
Temple Place, Suite 330, Boston, MA 02111-1307 USA.

xCellerator, xlr8r, cellzilla and arrowzilla are trademarks of the California 
Institute of Technology.

Click here to view the complete license