PeSca Project
Path Extraction by Shortest Cost Algorithms (by
Petterlini & Scardoni)
Home
PeSca 2.0 plug-in for Cytoscape
In complex, highly connected, biological networks, such as intracellular signaling networks, it is possible that two proteins are connected by
multiple paths. Likely, not all these paths are the shortest but it also possible that multiple shortest
paths are present between two proteins. Identification of all these shortest paths may help to detect and score highly communicating nodes. Pesca 2.0 is able to
detect all the Shortest Paths in a Cytoscape network.
Download here the latest versions of Pesca Cytoscape plug-in (Pesca 2.0 available)
If you publish your results obtained with PeSca 2.0 plug-in please cite us!!!
Table of Contents
=================
1. Introduction
2. About PeSca 2.0
3. PlugIn Installation Instructions
4. Using the PlugIn
5. Bugs / Feature Requests
6. Contacts
7. Release Notes
1. Introduction
=======================================
This directory contains a copy of the Cytoscape PeSca 2.0
PlugIn.
The PeSca 2.0 PlugIn enables Cytoscape users to calculate
the shortest path between
two proteins in a given pathway. If the shortest path is not unique, Pesca 2.0 will find all the
shortest paths.
2. About PeSca 2.0
=======================================
PeSca 2.0 is currently available at:
http://profs.sci.univr.it/~scardoni
3. PlugIn Installation Instructions
=======================================
To use the PeSca 2.0 Plugin, you must first obtain a copy
of Cytoscape,
Version 2.4. You can download a copy from: http://cytoscape.org.
Once you have downloaded Cytoscape and verified that it works, install
the
PeSca 2.0 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 2.0 PlugIn
=======================================
To use the PeSca 2.0 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 2.0 "
. A new PeSca 2.0 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 appear
PeSca 2.0's result is a selection of the proteins involved in the shortest
path.
If there is more than one shortest path all the shortest paths will appear.
You may click on one shortest path to select it and visualize it on the Cytoscape window.
You may 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:
Giovanni Scardoni : giovanni.scardoni AT gmail.com
Michele Petterlini: michele AT petterlini.it
7. Release Note
=======================================
This software is made available under the GPL (General
Public License).
You have only to
cite it if you publish some results obtained with Pesca 2.0 plug-in.
Enjoy!
by
Giovanni Scardoni 2007
Path Extraction by Shortest Cost Algorithms (by Petterlini & Scardoni)
Home
PeSca 2.0 plug-in for Cytoscape
In complex, highly connected, biological networks, such as intracellular signaling networks, it is possible that two proteins are connected by multiple paths. Likely, not all these paths are the shortest but it also possible that multiple shortest paths are present between two proteins. Identification of all these shortest paths may help to detect and score highly communicating nodes. Pesca 2.0 is able to detect all the Shortest Paths in a Cytoscape network.
Download here the latest versions of Pesca Cytoscape plug-in (Pesca 2.0 available)
If you publish your results obtained with PeSca 2.0 plug-in please cite us!!!
Table of Contents
=================
1. Introduction
2. About PeSca 2.0
3. PlugIn Installation Instructions
4. Using the PlugIn
5. Bugs / Feature Requests
6. Contacts
7. Release Notes
1. Introduction
=======================================
This directory contains a copy of the Cytoscape PeSca 2.0 PlugIn.
The PeSca 2.0 PlugIn enables Cytoscape users to calculate
the shortest path between
two proteins in a given pathway. If the shortest path is not unique, Pesca 2.0 will find all the
shortest paths.
2. About PeSca 2.0
=======================================
PeSca 2.0 is currently available at:
http://profs.sci.univr.it/~scardoni
3. PlugIn Installation Instructions
=======================================
To use the PeSca 2.0 Plugin, you must first obtain a copy
of Cytoscape,
Version 2.4. You can download a copy from: http://cytoscape.org.
Once you have downloaded Cytoscape and verified that it works, install
the
PeSca 2.0 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 2.0 PlugIn
=======================================
To use the PeSca 2.0 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 2.0 "
. A new PeSca 2.0 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 appear
PeSca 2.0's result is a selection of the proteins involved in the shortest
path.
If there is more than one shortest path all the shortest paths will appear.
You may click on one shortest path to select it and visualize it on the Cytoscape window.
You may 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:
Giovanni Scardoni : giovanni.scardoni AT gmail.com
Michele Petterlini: michele AT petterlini.it
7. Release Note
=======================================
This software is made available under the GPL (General
Public License).
You have only to
cite it if you publish some results obtained with Pesca 2.0 plug-in.
Enjoy!