CoNet README
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Installation of the Cytoscape plugin
====================================

This installation guide assumes that you have downloaded the CoNet release for your Cytoscape version.

Cytoscape 3.X
-------------
In Cytoscape, click on "Apps" menu to open the Apps Manager. 
In the Apps Manager, select "Install Apps" and click on "Install from file...". 
Browse to the CoNet.jar file in the lib directory of the unzipped CoNet3 folder 
and click "Open". CoNet will then be added to the "Apps" menu.

Cytoscape 2.X
--------------
Copy CoNet.jar from the lib folder into the plugins folder of your Cytoscape application.
The entry "CoNet" will then appear in the plugins menu of Cytoscape. Clicking it will open
the CoNet control panel on the left side of Cytoscape (next to the 
Network, VizMapper, Editor and Filter panels).


Command line
============

In general, the command line tool can always be called
by typing:
java -cp ${PATH_TO_JAR}CoNet.jar be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser -h

So if you execute the above command from the CoNet root directory, you can type:
java -cp lib/CoNet.jar be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser -h

The -cp argument can be omitted when adding CoNet.jar to your class path. Setting the class path is system-specific.

Installation on UNIX systems
----------------------------
1. In the bash configuration file, add the following lines:

export LIB=/home/you/CoNet/lib
export CLASSPATH=${CLASSPATH}:${LIB}/CoNet.jar

Then you can call the program as follows:
java be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser -h

2. Set an alias to shorten the program name. Add the line below to your bash configuration:

alias conet="java -Xmx800m be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser"

Then you can call the program as:

conet -h

Installation on Windows
-----------------------
Setting the class path is dependent on your Windows system. Class path setting for various systems is covered here:

http://javarevisited.blogspot.be/2011/01/how-classpath-work-in-java.html

Increasing runtime
------------------
You can increase java runtime memory with option -Xmx, e.g. 

java -Xmx2000M be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser -h

Rserve
------
By default, the command line tool assumes Rserve to be up and running on the default host (127.0.0.1) and port (6311).
To change the host and port or to switch off the Rserve dependency, you need to run the CoNet command
line tool with a configuration file. See the command line help for details (option -h).


Demo
=====
The Demo button in CoNet runs a demo network inference on a subset of the Costello data. 
The demo settings are stored in the demo folder (demo_settings.txt).
To modify the parameters of the demo, configure CoNet with the demo settings (via
button "Settings loading/saving" in the main menu).
The input data (Costello_2009_oral.txt), which are also located in the demo folder, can be set in the Data menu, 
by clicking on the top-most "Select file" button. 
Running CoNet with the demo settings and the demo input data yields the same result as pushing the "Demo" button,
but in addition allows modifying the demo settings.   


License
========
CoNet is distributed under the GNU General Public License version 2. This license as well as licenses of 
dependencies can be found in the licenses folder.
The two core jars of CoNet are be_ac_vub_bsb_cooccurrence.jar and be_ac_vub_bsb_cytoscape.jar. 
Source code for these two core jars is available at: http://sourceforge.net/projects/conet/

Dependencies
============

Adobe Acrobat Viewer (pdf display)
----------------------------------
acrobat.jar
MRJToolkitStubs.zip

Adobe Acrobat Viewer displays its license to the user.
MRJToolkitStubs.zip is a dependency of acrobat.


Bridge to R (Rserve)
--------------------
REngine.jar
Rserve.jar

Rserve is under the GNU General Public License (see licenses folder).


Graph handling
-------------
be_ac_ulb_scmbb_snow_graph_core.jar
be_ac_ulb_bigre_pathwayinference.jar
graphtools.jar

The snow graph library was developed by the aMAZE team and belongs to the Universite Libre de Bruxelles. 
graphtools and be_ac_ulb_bigre_pathwayinference were developed by Karoline Faust at the Universite Libre de Bruxelles.


Light-weight browser lobo (help display)
----------------------------------------
cobra-no-commons.jar
js.jar
lobo-pub.jar 
lobo.jar 

Lobo is under the GNU General Public license (see licenses folder).
Its dependency Cobra is under the GNU Lesser General Public License (see licenses folder).
Its dependency Mozilla Rhino Javascript Engine (js.jar) is under a Dual License (GNU General Public License and Mozilla Public License), both in the licenses folder.


Matrices, vectors and statistics
--------------------------------
colt.jar
commons-math3-3.0.jar
jsc.jar 
MeasurerLibrary-class-source.jar

MeasurerLibrary-class-source was written by Jean-Sebastien Lerat and contains the re-implementation of a number of similarity measures
including their renormalization. The license can be found in the license folder (LICENSE.jsl.txt).
Colt and JSC licenses are also in the licenses folder (LICENSE.colt.txt and LICENSE.jsc.txt).
Commons-math3 is under the Apache license (see licenses folder).


Misc
----
be_ac_vub_bsb_parsers.jar
commons-cli.jar
concurrent-1.3.0
htmlparser.jar
jargs.jar
log4j.jar
xercesImpl-2.6.2-jaxb-1.0.6.jar
xmlrpc.jar

HTML Parser is under the GNU Lesser General Public License (see licenses folder).
Commons CLI, LOG4J, xercesImpl and XML-RPC are under the Apache License (see licenses folder).
The jargs license is in the licenses folder (LICENSE.jargs.txt).
concurrent is license-free.
be_ac_vub_bsb_parsers jar was written by Karoline Faust at VIB/VUB and contains some file handling utilities.
