COBrA 1.17 is available for academic use under the GNU General Public License.

Quick start: type %./cobra at the command line
Note: this is an alpha version intended only for use to view the ontology files provided.


Copyright (c) 2004, University of Edinburgh, Edinburgh, Scotland. All rights reserved.
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; 
see the file gnu-gpl, if not, write to the Free Software Foundation, Inc., 59 Temple Place, 
Suite 330, Boston, MA 02111-1307 USA or see http://www.opensource.org/licenses/gpl-license.php



       COBrA 1.17  Mon Dec 06 15:53:30 GMT 2004
       A Concept Ontology Browser for Anatomy 
       XSPAN Project www.xspan.org
       Stuart Aitken stuart@aiai.ed.ac.uk 
       Roman Korf Roman.Korf@ed.ac.uk


This distribution includes:
cobra.html	: help file for COBrA, this is viewable via the COBrA Help menu, or in any browser
cobra		: the COBrA executable shell script LINUX/OS X
cobra.bat	: the COBrA executable for Windows
Ontologies/	: anatomies and the cell ontology from OBO
lib/		: the cobra 1.17 jar file, including Jena 2.0
img/		: images used in the help file
README		: license and instructions
gnu-gpl		: GNU General Public License


Installation	
No further installation is required after untarring the cobra-1.17.tar.gz file.

Running COBrA
LINUX, Solaris and Mac OS X	$./cobra
Windows XP/2000			Double-click of the cobra.bat executable, or
                                 in a shell, type $java -Xmx1500m -jar ./lib/cobra.1.17.inc_jena.jar
A Mac OS X                      A Mac OS X application is also available

System Requirements
Java 1.4 Compiled under Java version "1.4.1_01"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.1_01-69.1)
Java HotSpot(TM) Client VM (build 1.4.1_01-24, mixed mode)

Notes: java is invoked using the flag -Xmx1500m to reserve memory for reading the entire
gene ontology - this is not generally required and may cause problems if you have many 
applications open. In this case, run COBrA by: $java -jar ./lib/cobra.1.17.inc_jena.jar




The COBrA jar file includes HP's Jena 2.0 Semantic Web Toolkit in binary form. The Jena license found here:
http://www.hpl.hp.com/semweb/jena-license.htm is reproduced below.

Jena License:
Copyright 2000, 2001, 2002, 2003 Hewlett-Packard Development Company, LP
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided 
that the following conditions are met: 

   1. Redistributions of source code must retain the above copyright notice, this list of conditions and 
      the following disclaimer.
   2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and 
      the following disclaimer in the documentation and/or other materials provided with the distribution.
   3. The name of the author may not be used to endorse or promote products derived from this software without 
      specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT 
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This package includes software developed by the Apache Software Foundation (http://www.apache.org/). 

 

