1. Introduction
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Metabolica plugin find network motifs of arbitrary length in the selected network. For example, you can find every Feed Forward Loop structures in your network. This is very important, since you can easily find relationships between two proteins by an activation / inibition protein chain. Theese relationships cannot be seen easily because networks can be very complex. Using Metabolica, instead, every chain reaction can be find in an automatical way and can be red directly in a text file, called results.mbc , so you can isolate and verify them directy in Cytoscape. PLEASE USE IT CAREFULLY: this computation is very complex so it can take a huge amount of time. For example, using a dual core processor, a network like GalFiltered.sif (provided in Cytoscape) with 331 nodes and 362 edges need 14 minutes to finish a Feed Forward Loop detection with a 5 elements chain activation.

2. About Metabolica
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Metabolica is currently available at:

http://www.petterlini.it/metabolica

3. PlugIn Installation Instructions
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To use the Metabolica 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
Metabolica 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 Metabolica PlugIn
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To use the Metabolica 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.

3. From the Main Menu, Select "PlugIns" --> "Metabolica 1.1"

. A new Metabolica query window will appear. The window allow you to select a
threshold for the length of the network motifs you want to find. You can also select forward loops, like A->B, B->C , A->C or backward loops, like A->B, B->C, C->A.
The main idea is: if you select a threshold 3 and forward loops, Metabolica will find EVERY network motif in the given network
where: A->p1->p2->B , B->p3->p4->C, A->p5->p6->C So the length of every path is 3 atctivation. Obviously Metabolica returns also 2 and 1 path length's motifs. I think it's easier understand it
trying it.

Your search results will
Metabolica's result is a file, called "results.mbc", where you can find every solution generated in this format:
A= B= C= ( )

5. Bugs / Feature Requests
=======================================

If you encounter a bug with this plugin, or have a feature suggestion, write at michele AT petterlini.it.

6. Contacts
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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!