2) Download a complete tarball here (JVM 1.6 JVM 1.5) .

2) Download a complete tarball here(JVM 1.6 JVM 1.5 .

Note: Check to donwload the right binary for your environment, Java1.5 or 1.6.

Available here. Check Dependencies for versions supported.

Note: You currently need Java 1.6 to run rdfscape!

For the time being, use version 2.5.1 or 2.5.2 (You can find it on the website following the link "All releases" on the main bar).

2) Download a complete tarball here.

note: While is binary is compiled for Java 1.5, we suggest the use of Java 1.6, as future versions will be built for this platform.

Just copy the tarball in the Cytoscape main directory (cd Cytoscape_v2.5.2) and unpack it.

Under unix or macosx, run the .sh file. Under windows, run the .bat file. You may need to run them from a terminal. You may have to configure permissions accordingly.

Tested on unix, macosx (limited test on windows)

note on windows the rdfscape.bat file is currently wrong. While the new one is not online, you can easily fix it. Open cytordfscape.bat and replace the "-server" string you'll find in the Java command line with -Djava.ext.dirs=extlibs

an updated version fully windows compatible will be provided soon

note on windows the rdfscape.bat file is currently wrong. While the new one is not online, you can easily fix it. Open cytordfscape.bat and replace the "-server" string you'll find in the Java command line with -Djava.ext.dirs=extlibs

note: this binary will require Java 1.6!!!

4) run cytordfscape.sh or cytordfscape.bat (depending on your system).

You may have to configure permissions accordingly.

Tested on unix! (feedback on other platforms is welcome)

How to install RDFScape

There are two distinct mode to install RDFScape, the simplified install and the step by step install procedure.

Simplified install

1) If you have not done it yet, download and install Cytoscape.

2) Download a complete tarball here.

3) unpack (tar xvzf) the tarball in the Cytoscape directory.

4) run cytordfscape.sh or cytordfscape.bat (depending on your system). You may have to configure permissions accordingly.

Tested on unix! (feedback on other platforms is welcome)

Step-by-Step install procedure

This will make you install each library and file individually.

You can download the above components from http://bioinformatics.org/project/filelist.php?group_id=601. Pick the last RDFSCape.jar plugin and one or more of the last analysis contexts.

You can always access the svn repository for the latest version.

7) You are ready to use or create an analysis context and use RDFScape, refer to Instructions for this.

Note: Whenever you update RDFScape, you will need only to replace RDFScape.jar !!!

For the time being, you have two options to install RDFScape. To follow the step by step intructions given below, or to trye the simplified installation package, avaliable here

For the time being, you have two options to install RDFScape. To follow the step by step intructions given below, or to trye the simplified installation package, avaliable here

(:keywords rdfscape, howto, install, plugin, cytoscape :)

'''For the time being, you have two options to install RDFScape. To follow the step by step intructions given below, or to trye the simplified installation package, avaliable here

For the time being, use version 2.5.1 (You can find it on the website following the link "All releases" on the main bar).

Copy all the libraries (.jar)in Jena-2.5.4/lib and in pellet-1.5.1 (the two files in pellet-1.5.1/lib/xsdlib/) in the Java extension directory: this is typically (for J2SE v1x.y.z):

• extract RDFSCape.jar from the file you downloaded and put it in Cytoscape_vy_x.z/plugins (x_y.z stands for your current version)

You can download the above components from http://bioinformatics.org/project/filelist.php?group_id=601. Pick the last RDFSCape.jar plugin, the vizmap file (last version) and one or more of the last analysis contexts.

Copy all the libraries in Jena-x.y.z/lib and in pellet-1.5.x in the Java extension directory: this is typically (for J2SE v1x.y.z):

• C:\Program Files\Java\j2rex.y.z\lib\ext on Windows
• /usr/java/j2rex.y.z/lib/ext on Linux
• /Library/Java/Extensions on Macosx

As an alternative, you may include required jars in your java execution command with the parameter: java -Djava.ext.dirs=your_dirs ... you will need to edit cytoscape.sh or cytoscape.bat for this. You may also want to optimize this file to improve performances (memory allocated and virtual machine settings)

6) Start RDFScape

Start Cytoscape and select RDFScape from the plugin menu

7) Load the RDFScape Vizmap file

import the vizmap property file you downloaded (from the related voice in the file menu). And select it from the vizmap list.

9) You are ready to use or create an analysis context and use RDFScape, refer to Instructions for this.

Not:e Whenever you update RDFScape, you will need only to replace RDFScape.jar !!!

2) download and install Jena.

Available here. Install it, simply uncompress it.

3) download and install Pellet.

Available here. Install it, simply uncompress it.

4) download and install RDFScape.

RFScape is composed of:

• the plugin itself: RDFScape.jar
• a vizamp.pros file for Cytoscape
• a set of analysis contexts

Only the plugin is strictly required for functioning, but all the components toghether will enable all functionalities and present some ready to use examples.

You can download the above components from http://bioinformatics.org/project/filelist.php?group_id=601. Pick the last RDFSCape.jar plugin, the vizmap file (last version) and one or more of the last analysis contexts. You may also want to pickup the modified version of cytoscape.sh (see below).

From time to time all the files all released toghether with source code in a single tarball.

You can always access the svn repsoitory for the latest version.

To install RDFScape:

• copy RDFSCape.jar in Cytoscape_vy_x.z/plugins (x_y.z stands for your current version)
• unpack (tar xvzf) the analysis contexts in the Cytoscape_vy_x.< directory.

5) Make Cytoscape, RDFScape, Jena and Pellet work toghether.

You need to ensure the Pellet and Jena libraries are accessible by RDFScape while running as a Cytoscape plugin.

On MacOSX systems, copy all the libraries in Jena-x.y.z/lib and in pellet-1.5.x in /Library/Java/Extensions

On Linux

Whenever you update RDFScape, you will need only to replace RDFScape.jar !!!

(instructions in progress... don't be scared if things seems not to work at first!)

1) download and install Cytoscape.

Available here.

For the time being, use version 2.4.1 (You can find it on the website following the link "All releases" on the main bar).

How to install RDFScape

(instructions in progress... don't be scared if the thing seems not to work at first!)

1) download and install http://www.cytoscape.org][Cytoscape (current version tested is 2.4.1).

2) download and install Jena and Pellet.

3) Make sure Jena and Pellet libraries are accessible by your cytoscape plugin

4) Add "analysis contexts"

5) Start RDFScape

6) Load the RDFScape Vizmap file

7) Use one of the analysis contexts provided or create your own, and start using RDFScape.