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Home modified by habermannlab

habermannlab — Wed, 10 Jun 2015 10:06:43 -0000

--- v16
+++ v17
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 PEANuTv3 can be accessed under: <https: sourceforge.net="" projects="" peanutv3=""/>.

-The original PEANuT 2.x plugin was implemented by Falco Hofmann in JavaTM, using both Eclipse Indigo for Java EE Developers (<http: www.eclipse.org=""/>) and Netbeans 7.1.2. (<http: netbeans.org=""/>). 
+The original PEANuT 2.x plugin was implemented by Falko Hofmann in JavaTM, using both Eclipse Indigo for Java EE Developers (<http: www.eclipse.org=""/>) and Netbeans 7.1.2. (<http: netbeans.org=""/>). 

 PEANuTv3 was ported to the Cytoscape 3.x platform as an OSGi Bundle App using Eclipse and Maven by Viktor Senderov.

Home modified by habermannlab

habermannlab — Wed, 10 Jun 2015 10:06:10 -0000

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+++ v16
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 # Installation Instructions

-This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file [here](http://sourceforge.net/projects/peanutv3/files/peanutv3.jar/download) and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.
+This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file [here](http://sourceforge.net/projects/peanutv3/files/peanutv3-1.0.jar/download) and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.

 If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanutv3/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

Home modified by habermannlab

habermannlab — Wed, 10 Jun 2015 09:44:28 -0000

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 # Installation Instructions

-This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file[here](http://sourceforge.net/projects/peanutv3/files/peanutv3.jar/download) and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.
+This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file [here](http://sourceforge.net/projects/peanutv3/files/peanutv3.jar/download) and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.

 If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanutv3/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

Home modified by habermannlab

habermannlab — Wed, 10 Jun 2015 09:44:04 -0000

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+++ v14
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 # Installation Instructions

-This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file
+This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file[here](http://sourceforge.net/projects/peanutv3/files/peanutv3.jar/download) and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.

-[peanutv3-0.0.1-SNAPSHOT.jar](https://sourceforge.net/p/peanutv3/code/ci/master/tree/target/peanutv3-0.0.1-SNAPSHOT.jar)
-
-from the 'target' sub-directory and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/' or creating a symbolic link from that directory to the jar file.
-
-If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanut-cyto/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.
+If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanutv3/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

 Also please notify us when the downloader is not working! It happens from time to time that the databases we are using change their urls or formats. We can only fix it when we are aware of this problem! :)You can use this [google group](https://groups.google.com/forum/#!forum/peanut-cytoscape) to get in direct contact with us.

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 17:23:45 -0000

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 If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanut-cyto/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

-Also please notify us when the downloader is not working! It happens from time to time that the databases we are using change their urls or formats. We can only fix it when we are aware of this problem! :)
-
-You can also use this [google group](https://groups.google.com/forum/#!forum/peanut-cytoscape) to get in direct contact with us to ask questions or report problems.
+Also please notify us when the downloader is not working! It happens from time to time that the databases we are using change their urls or formats. We can only fix it when we are aware of this problem! :)You can use this [google group](https://groups.google.com/forum/#!forum/peanut-cytoscape) to get in direct contact with us.

 For further documentation consult the documentation of the 2.x version found here:

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 17:13:02 -0000

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@@ -10,6 +10,10 @@
 from the 'target' sub-directory and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/' or creating a symbolic link from that directory to the jar file.

 If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanut-cyto/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.
+
+Also please notify us when the downloader is not working! It happens from time to time that the databases we are using change their urls or formats. We can only fix it when we are aware of this problem! :)
+
+You can also use this [google group](https://groups.google.com/forum/#!forum/peanut-cytoscape) to get in direct contact with us to ask questions or report problems.

 For further documentation consult the documentation of the 2.x version found here:

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 17:02:10 -0000

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@@ -8,6 +8,8 @@
 [peanutv3-0.0.1-SNAPSHOT.jar](https://sourceforge.net/p/peanutv3/code/ci/master/tree/target/peanutv3-0.0.1-SNAPSHOT.jar)

 from the 'target' sub-directory and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/' or creating a symbolic link from that directory to the jar file.
+
+If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file [here](http://sourceforge.net/projects/peanut-cyto/files/filesPEANuT.zip/download). After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

 For further documentation consult the documentation of the 2.x version found here:

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 16:55:37 -0000

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 This tool has been compiled for Cytoscape verion 3.2 and up.  If you want to install it, download the compiled jar file

-peanutv3-0.0.1-SNAPSHOT.jar 
+[peanutv3-0.0.1-SNAPSHOT.jar](https://sourceforge.net/p/peanutv3/code/ci/master/tree/target/peanutv3-0.0.1-SNAPSHOT.jar)

 from the 'target' sub-directory and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/' or creating a symbolic link from that directory to the jar file.

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 16:47:21 -0000

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 This App is an OSGi Bundle.  Consult this page on how to set-up Eclipse and then import the code via git:

 http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Create_a_Bundle_App_Using_IDE
-
-Also download and add the giny.jar file from Giny graph library add it to the referenced libraries.
-The file is available e.g. via this link: http://en.osdn.jp/projects/sfnet_csbi/downloads/GINY%20Graph%20INterface%20librarY/1.1/giny-1.1.zip/

 # Background

Home modified by habermannlab

habermannlab — Tue, 09 Jun 2015 16:32:00 -0000