Arena3D

  Visualizing biological networks in 3D

FAQs

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  Contact

 EMBL, Meyerhofstrasse 1,
 69117 Heidelberg,
 Germany
 Room:: V116
 Tel:: +49 6221 387- 8140

 Author - Developer
 Georgios A. Pavlopoulos
 pavlopou@embl.de

 Scientific supervisor
 Reinhard Schneider
 rschneid@embl.de

 Arena3D

 

HOW DO I INSTALL IT???

 

Just download Java JRE or JDK 1.5 and Java3D 1.5.1 API and that’s it!!! Ready to run!! When you unzip the zip file there is also a folder that contains input files to test it.

WINDOWS USERS:

If still it does not work then it will be 99,9% a Java3D installation problem. Please make sure that you install Java3D AFTER the latest update or your first installation of your JRE.

The installation procedure can also be done manually

The installer will automatically install these in your JRE (user).
\bin:

· j3dcore-d3d.dll
· j3dcore-ogl.dll
· j3dcore-ogl-cg.dll
· j3dcore-ogl-chk.dll



lib\ext:

· vecmath.jar
·
j3dcore.jar
·
j3dutils.jar

Usually java is located in C:\Program Files\Java\jreXXXXX folder for windows


MAC USERS:


Mac users should also install JOGL libraries for the colors to appear properly. Java3D and JOGL (BOTH SEPARATELY DOWNLOADED) need to go to /System/Library/Java/Extensions

 


 To Run The Tool

Initially download and unzip the Arena3D.zip in your desktop. Then go inside the folder that will be created and find the jar file.



Double click on the jar file that is inside the downloadable_Arena3D\Arena3D_classes

folder or



run from command line like

java -Xms32m -Xmx300m -jar downloadable_Arena3D\Arena3D_classes/Arena3D.jar



The -Xmx parameter defines the memory size. In this example it is 300MB (300m)



Or edit the bat file (Windows only) and double click it.





Command line with parameters:

java –jar Arena3D.jar input_file_name





Problem launching the application under Mac OS X (at least 10.5.5 (Leopard))

When launching via the launch link (LAUNCH) the seems to start correctly but then hangs after loading an input file.

Try to start (double click) the Java Web Start application which is located in

"/Applications/Utilities/Java/" first and then launch the application.

Linux users: Depending on Linux version please start Java Web Start application before launching.
 


 Java Web Start from Command Line

One generally starts a Java WebStart application by clicking on a link in a web browser. WebStart is typically registered as the helper application for content with mime type application/x-java-jnlp-file, so the browser downloads the jnlp content and hands it off to WebStart. Depending on configuration, desktop shortcuts may be installed to speed up subsequent launches, and cached applications can also be launched from within the WebStart control panel.

On occasion, though, it is useful to launch WebStart “manually” from the command line, without the overhead of getting a web browser involved. The most straightforward way to do this is to simply use the “javaws” command included in the JDK. This is located in the “bin” directory in Linux and Windows distributions of the JDK or JRE. On OSX, a link is installed as “/usr/bin/javaws“, and a specific version can be accessed from the appropriate framework directory.

The absolute path to the JRE bin directory.

Windows: "C:\Program Files\Java\jre1.5.0_11\bin"
Linux: "/usr/java/jdk1.5.0/jre/"
OSX: "/Applications/Utilities/Java/Java Web Start.app/Contents/MacOS"
 

 

 
European Molecular Biology Laboratory