Alternativley you may want to specify where those libraries are in the '''java -Djava.ext.dirs=''' directive. In this case edit the cytoscape.sh or cytoscape.bat file and add this parameter to the java instruction that runs Cytoscape.

'''/Library/Java/Extensions'''

On windows systems, copy all of them in (something like):
'''C:\Program Files\Java\jreX.X.X\lib\ext'''

On a Linux system, copy all of them in (something like):
'''j2sdk1.5/jre/lib/ext'''

Alternativley you may want to specify where those libraries are in the java -Djava.ext.dirs= parameter. In this case edit the cytoscape.sh or cytoscape.bat file and add this parameter to the java instruction that runs Cytoscape.

'''4)''' Unpack the context of your Analysis Contyext in the Cytoscape directory. The result (the listing of your Cytoscape directory) should be look like:

This is the complete list:
(:table :)
(:cell :) antlr-2.7.5.jar
(:cell :) icu4j_3_4.jar
(:cell :) json.jar
(:cell :) wstx-asl-2.8.jar
(:cellnr :) arq.jar
(:cell :) iri.jar
(:cell :) junit.jar
(:cell :) xercesImpl.jar
(:cellnr :) commons-logging.jar
(:cell :) jena.jar
(:cell :) log4j-1.2.12.jar
(:cell :) xml-apis.jar
(:cellnr :) concurrent.jar
(:cell :) jenatest.jar
(:cell :) stax-api-1.0.jar
(:cellnr :)pellet.jar
(:tableend :)

'''0)''' You will need a standard Java environment set up. You will need it also for Cytoscape alone, so nothing to add here.

'''1)''' First, you'll need Cytoscape [[http://www.cytoscape.org/download_list.php | here]]. See [[Dependencies]] for details on compatibility and versions.

'''2)''' Second, you will need Jena and Pellet. Download them [[http://prdownloads.sourceforge.net/jena/Jena-2.4.zip?download | here]] and [[http://www.mindswap.org/2003/pellet/download.shtml | here]]. See [[Dependencies]] for details on compatibility and versions.

'''3)''' You will need an Analysis Context, download one [[DownloadAnalysis | here]].

'''4)''' Unpack the context of your Analysis Contyext in the Cytoscape directory. The result (of your Cytoscape directory) should be look like:

'''5)''' Make the Jena and Pellet libraries visible to the RDFScape plugin. This is the most complex part.

'''6)''' Start Cytoscape, go to edit->preferences then add plugin and then restart it.

(:cell :) annotation
(:cell :) Cytoscape-v2.2.lax
(:cell :) plugins

(:cellnr :) Cytoscape2_2Manual.pdf
(:cell :) INSTALL.txt
(:cell :) '''rdfscapecontexts'''

(:cellnr :)cytoscape.bat
(:cell :) jre
(:cell :) sampleData

(:cellnr :) cytoscape.jar
(:cell :) lax.jar
(:cell :) tax_report.txt

(:cellnr :) cytoscape.props
(:cell :) lib
(:cell :) Uninstall_Cytoscape-v2.2

(:cellnr :) cytoscape.sh
(:cell :) licenses
(:cell :) vizmap.props

(:cellnr :) Cytoscape-v2.2
(:cell :) LICENSE.txt
(:cell :)
(:tableend :)

(:table :)
(: cell :) annotation
(: cell :) Cytoscape-v2.2.lax
(: cell :) plugins

(: cellnr :) Cytoscape2_2Manual.pdf
(: cell :) INSTALL.txt
(: cell :) '''rdfscapecontexts'''

(: cellnr :)cytoscape.bat
(: cell :) jre
(: cell :) sampleData

(: cellnr :) cytoscape.jar
(: cell :) lax.jar
(: cell :) tax_report.txt

(: cellnr :) cytoscape.props
(: cell :) lib
(: cell :) Uninstall_Cytoscape-v2.2

(: cellnr :) cytoscape.sh
(: cell :) licenses
(: cell :) vizmap.props

(: cellnr :) Cytoscape-v2.2
(: cell :) LICENSE.txt
(: cell :)
(: tableend :)

1) First, you'll need Cytoscape [[http://www.cytoscape.org/download_list.php | here]]. See [[Dependencies]] for details on compatibility and versions.

2) Second, you will need Jena and Pellet. Download them [[http://prdownloads.sourceforge.net/jena/Jena-2.4.zip?download | here]] and [[http://www.mindswap.org/2003/pellet/download.shtml | here]]. See [[Dependencies]] for details on compatibility and versions.

3) You will need an Analysis Context, download one [[DownloadAnalysis | here]].

4) Unpack the context of your Analysis Contyext in the Cuytoscape directory. The result should be look like:
annotation Cytoscape-v2.2.lax plugins
Cytoscape2_2Manual.pdf INSTALL.txt '''rdfscapecontexts'''
cytoscape.bat jre sampleData
cytoscape.jar lax.jar tax_report.txt
cytoscape.props lib Uninstall_Cytoscape-v2.2
cytoscape.sh licenses vizmap.props
Cytoscape-v2.2 LICENSE.txt

2) Second, you will need Jena and Pellet. Donwload them [[http://prdownloads.sourceforge.net/jena/Jena-2.4.zip?download | here]] and [[http://www.mindswap.org/2003/pellet/download.shtml | here]]. See [[]] for details on compatibility and versions.

! How to install and run RDFScape

0) You will need a standard Java environment set up. You will need it also for Cytoscape alone, so nothing to add here.

1) First, you'll need Cytoscape [[http://www.cytoscape.org/download_list.php | here]]. See [[]] for details on compatibility and versions.

2) Second, you will need Jena and Pellet. Donwload them [[here]] and [[here]]. See [[]] for details on compatibility and versions.

3) You will need an Analysis Context, download one [[here]].

4) Unpack the context of your Analysis Contyext in the Cuytoscape directory. The result should be the following:


5) Make the Jena and Pellet libraries visible to the RDFScape plugin. This is the most complex part.
First, which libraries ?
All the libraries in the /lib directory in Jena and and pellet-1.3.jar

This is the complete list.

Now, on macosx system, copy all of them in:

On windows systems, copy all of them in:

On a Linux system, copy all of them in:

Alternativley copy all of them in a directory accessible to the system, then edit the cytoscape.sh file provided with the RDFScape distribution and replace the original cytoscape.sh file in the Cytsocape distribution.
You will need to specify where those libraries are in the java -Djava.ext.dirs= parameter.
You can do the same for the .bat file on windows.

6) Start Cytoscape, go to edit->preferences then add plugin and then restart it.

Your plugin is ready. More will be in the [[Instructions]] page.