PEPPER - Protein complex membership Expansion using Protein-Protein intERaction networks

Copyright (C) 2013  Charles Winterhalter
Institute of Systems and Synthetic Biology (CNRS, University of Evry Val-d'Essonne, Genopole)

This program is a free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details:
http://www.gnu.org/licenses/gpl.html


DESCRIPTION
-----------

PEPPER is a Cytoscape plugin for meaningful protein complexes
identification in the context of single-experiment proteomics studies.
The program aims at adjusting proteins co-membership in predicted
complexes to remove non-specific proteins and add the ones that were
not detected during biological experiments but remain suitable to form
a complex with the input set.

It uses a multi-objective optimisation algorithm to generate a set of
optimal Pareto solutions then merged into a consensus sub-graph
by modularity (greedy algorithm).

PEPPER includes an automated post-processing pipeline to provide
an annotated and visual-friendly sub-graph as an output.
The latter corresponds to the initial set of seed proteins extracted
from a biological experiment.


THIRD-PARTY SOFTWARE
--------------------

The following free software libraries are distributed with PEPPER:
* Jama platform - in /org/Jama
  available as a Public Domain software
* JMetal - in /org/jmetal
  released under GNU Lesser General Public License v2.1 (http://www.gnu.org/licenses/lgpl-2.1.html)

  
REQUIREMENTS
------------

PEPPER is platform independent and runs on Java virtual machine within
the Cytoscape environment. It requires minimum 512MB RAM but 2GB RAM
is recommended for better speed performances.

To run it requires the following software installed:
* Open JDK >= 6 (GNU General Public Licence + classpath exception)
  or Oracle Java SE => 6 (Oracle Binary Code Licence)
* Cytoscape >= 3.0.0 (GNU Lesser General Public Licence)

To compile PEPPER additional software is needed (mainly the dependencies
of the Cytoscape API). This software is downloaded automatically if PEPPER
is build with Maven:
* JFreeChart - http://www.jfree.org/jfreechart/ (GNU LGPL)
* JUnit - http://junit.org/ (BSD Licence)
* Mockito - https://code.google.com/p/mockito/ (MIT Licence)
* Pax Logging - https://ops4j1.jira.com/wiki/display/paxlogging/ (Apache Licence 2.0)


INSTALLATION
------------

To install PEPPER in Cytoscape you can either:
* use the App Manager and select PEPPER from the list of available apps
* you can download the jar file from http://apps.cytoscape.org/apps/pepper
  and install the app jar file directly (Apps -> App Manager -> Install from file)

You can use Maven plugin for Eclipse (http://eclipse.org/m2e/download/)
to compile PEPPER from source files added to the source_folder.zip file.
Then import the extracted pom.xml file as a new Maven project in Eclipse to
re-build the PEPPER project. 
