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# CYTOSCAPE INSTALLATION INSTRUCTIONS          #
# Cytoscape version @version@, June., 2006         #
# http://www.cytoscape.org                     #
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# (c) The Cytoscape Collaboration              #
#                                              # 
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LICENSE AGREEMENT AND DISCLAIMER #####################################
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Cytoscape is a collaborative effort between the Institute for Systems
Biology, the University of California at San Diego, Memorial Sloan-
Kettering Cancer Center, the Institut Pasteur, and Agilent Technologies.  
It is available at http://www.cytoscape.org and provided to all users 
free of charge.

Users of Cytoscape must first agree to the license agreement provided
in the file "LICENSE.txt".

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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INSTALLATION AND STARTUP #############################################
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Currently, Cytoscape runs under Java on Linux, Windows, and MacOSX
platforms.  Although Cytoscape handles arbitrary types and sizes
of interaction network, it is most powerful when used in conjunction
with large interaction data sets such as are currently available for
species such as the yeast S. cerevisiae.

(1) Download and unpack the distribution.  Cytoscape is distributed as
a compressed archive containing the following files and directories:

INSTALL.txt ............ Quick-start installation instructions (this file)
manual.pdf.............. Overview and details of Cytoscape functionality
LICENSE.txt ............ The license agreement
LICENSE.html............ The license agreement in a different format

cytoscape.jar .......... Main Cytoscape application (Java archive)

cytoscape.sh ........... Shell script used to run Cytoscape (Linux)*
cytoscape.bat .......... Shell script used to run Cytoscape (Windows)

*Note: the cytoscape.sh shell script can be used to start Cytoscape on
Mac OS X, although the default use for Mac OS X is to double-click on
the Cytoscape application.

sampleData/
   galFiltered.gml ..... Sample molecular interaction network file *
   galFiltered.sif ..... Identical network in Simple Interaction Format *
   galFiltered.cys ..... Cytoscape session file containing galFiltered
                         data.       
   galExpData.pvals .... Sample gene expression matrix file *
   galFiltered.*attr*... Various sample attribute files for the 
                         galFiltered data.
   BINDyeast.sif ....... Network of all yeast protein-protein
                         interactions in the BIND database as of 
                         July, 2004 **
   BINDhuman.sif ....... Network of all human protein-protein
                         interactions in the BIND database as of 
                         July, 2004 **
   yeastHighQuality.sif  Set of high-quality yeast interactions as
                         determined by:
                         von Mering et al., Nature p.399,2002
                         Lee et al., Science p.799,2002

annotation/ ............ Directory containing Gene Ontology database
                         and KEGG ontology entries (currently for
                         yeast only). Info in this directory is used
                         to associate gene names with synonyms as well
                         as process, function, and and cellular location data.

*  Sample data sets taken from Ideker et al, Science 292:929 (2001)
** Obtained from data hosted at http://www.bind.ca/

(2) If not already installed on your computer, download and install
the Java 2 Runtime Environment, version 1.4.2 or higher.  It can be
found at:

http://java.sun.com/j2se/1.4.2/download.html.

(3) Launch the application by running "cytoscape.sh" from the command
line (Linux) or double-clicking "cytoscape.bat" (Windows) or double-
clicking on the Cytoscape icon under Mac OS X.
Alternatively, you can pass the .jar file to Java directly using the
command "java -jar cytoscape".  In Windows, it is also possible to
directly double-click the .jar file to launch it.  However, this does
not allow specification of command-line arguments (such as the
location of the annotation data directory, see MANUAL.txt for details).

!!!!IMPORTANT NOTE!!!!  For the application to work properly, ALL
FILES MUST BE LEFT IN THE DIRECTORY IN WHICH THEY ARE UNPACKED.  [The
core Cytoscape application assumes this directory structure when
looking for plugins.