Cytoscape Data Services PlugIn
------------------------------

I.  Introduction
================
This directory contains a copy of the Cytoscape Data Services PlugIn.

This PlugIn enables Cytoscape to import/export to multiple file formats.

The current release includes support for:

1.  Proteomics Standards Initiative Molecular Interaction (PSI-MI) XML Format.  
PSI-MI is a new XML format used to represent and exchange protein-protein 
interaction data.  Information is available online at:  
http://psidev.sourceforge.net/.  You can load PSI-MI files from your local 
file system or from any arbitrary URL.  You can also export Cytoscape graphs to
PSI-MI format.

2.  GEO Simple Omnibus Format in Text (SOFT).  SOFT is a text file format used
to represent and exchange Gene Expression Data.  Information is available
online at:  http://www.ncbi.nlm.nih.gov/geo/info/soft.html.  You can load SOFT
files from your local file system or from any arbitrary URL.  Export functionality
is not currently supported.

II.  Installation Instructions
==============================

To use the Data Services PlugIn, you must first obtain a copy of Cytoscape, 
Version 1.1.  You can download a copy from:  http://www.cytsoscape.org.  
Once you have downloaded Cytoscape and verified that it works, proceed with 
the next steps.  

1.  Copy the ds_plugin.jar file to your [Cytoscape_Home]/plugins directory.

2.  Restart Cytoscape.  For example, on Unix/Linux or MacOS X, run:

cytoscape.sh

On Windows, run:

cytoscape.bat

III.  Using the PSI-MI PlugIn
=============================

Once Cytoscape starts, select "PlugIns" from the Main Menu.  You will see three options
here:  Import PSI-MI Data from File, Import PSI-MI Data from Web, and Export Data to 
PSI-MI Format.

1.  Select PlugIns --> Load PSI Data from File.

2.  Select one of the sample PSI-MI Files in the sampleData/ directory.  Cytoscape will
now load the PSI-MI file, and show a graphical representation of the file.  If you want 
to view information about a specific node or edge, right click on it, and you will see
the node/edge browser.

To export data in PSI-MI format, select Plugins --> Export Data to PSI-MI Format.

IV.  Using the SOFT PlugIn
==========================

The SOFT PlugIn reads in expression data, and adds this data to an existing Cytoscape
graph.  

1.  First, load up a sample Interaction file.  Select File --> Load -->
Interaction.  Then, specify a sample SIF file, such as sampleData/GDS362.sif.

2.  Select PlugIns -->  Import GEO SOFT Data from File.  Then, specify a sample SOFT
file, such as sampleData/GDS362.soft.

3.  Select any node, and right click on it.  Gene Expression data will now appear within
the Cytoscape Node Browser.

V.  Bugs / Feature Requests
============================

If you encounter a bug with this PlugIn, or have a feature suggestion, we  
encourage you to use the Cytoscape Bug Tracker:
http://www.cbio.mskcc.org/cytoscape/bugs/.  

If you log a bug, we will automatically email you when the bug is resolved.

VI.  Contacts
=============

Sander Group, Computational Biology Center
Memorial Sloan-Kettering Cancer Center, New York City
http://www.cbio.mskcc.org/

For any questions concerning this PlugIn, please contact:

Gary Bader:  baderg AT mskcc.org
Ethan Cerami:  cerami AT cbio.mskcc.org

This software is made available under the LGPL (Lesser General Public License).  
Until we develop a better source code distribution system, please email Gary 
or Ethan for a complete copy of the source code.
 
This product includes software developed by the Apache Software Foundation
(http://www.apache.org).