1. Introduction
=======================================

This directory contains a copy of the Cytoscape PeSca PlugIn.

The PeSca PlugIn enables Cytoscape users to calculate the shortest path between
two proteins in a given pathway.

2. About PeSca
=======================================

PeSca is currently available at:

http://www.petterlini.it/pesca

3. PlugIn Installation Instructions
=======================================

To use the PeSca Plugin, you must first obtain a copy of Cytoscape,
Version 2.1. You can download a copy from: http://cytoscape.org/.

Once you have downloaded Cytoscape and verified that it works, install the
PeSca PlugIn:

1. Copy all the .jar files in the /plugin directory to your
[Cytoscape_Home]/plugins directory.

2. Restart Cytoscape from the command line. For example, run:
cytoscape.sh or cytoscape.bat.

4. Using the PeSca PlugIn
=======================================

To use the PeSca PlugIn:

1. Start Cytoscape. For example, on Unix/Linux or MacOS X, run:

cytoscape.sh

On Windows, run:

cytoscape.bat

2. Load the network which you want to apply the plugin. Using your mouse,
select exactly two proteins using the shift key on the keyboard.

3. From the Main Menu, Select "PlugIns" --> "PeSca Shortest..."

. A new PeSca query window will appear. The window show you the protein names
you've selected and a "shortest path" button.If everything is ok, just click the button.

Your search results will
PeSca's result is a selection of the proteins involved in the shortest path. You can click
"select","to new network","select nodes,all edges" to extract the shortest path of proteins.

5. 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.

Updates regarding this plugin will be posted to the Cytoscape-announce
mailing list. You can subscribe to the mailing list or browse the archives
at: http://groups-beta.google.com/group/cytoscape-announce.

6. Contacts
=======================================

For any questions concerning this plugin, please contact:

Michele Petterlini: michele AT petterlini.it
Giovanni Scardoni : scardoni AT sci.univr.it

This software is made available under the GPL (General Public License).

Enjoy!