3DScape Intro

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  Cytoscape Plugins

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3DScape Installation Guide

To use 3DScape , you need to install Cytoscape first. Besides, 3DScape requires VTK libraries to run. The VTK shared libraries can be obtained here. You can also compile VTK from source code by following this instruction. The vtkCys libraries are updated along with 3DScape, and can be downloaded here.
After download, extract vtk and vtkCys packages to a directory. Keep in mind you need to point $DYLD_LIBRARY_PATH to that directory. This can be done by add these lines to your ~/.profile file:

export DYLD_LIBRARY_PATH=/Users/yourusername/Downloads/VTK:$DYLD_LIBRARY_PATH

If you do not have a .profile file in your home directory, you may have a .bash_profile or .bash_login, add the lines to that. If you do not have any of these files, just make a .profile file. Moreover, Bash looks for profile information in this order: .bash_login, .bash_profile, and .profile. If .bash_login exists, it won’t look in .bash_profile or .profile and so on. Open up a new terminal window restart your shell and make your changes take effect.

Put vtkCysPlugin.jar into cytoscape/plugins/ folder, start Cytoscape via a bash script like this:

For Windows users:
set JAVA_HOME=C:\Program Files\Java\jdk1.6.0
"%JAVA_HOME%\bin\java.exe" -Djava.library.path="plugins\3DScape;%PATH%;%JAVA_HOME%\bin" -classpath .\;plugins/3DScape/vtk.jar -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar cytoscape.CyMain -p plugins %*
For Linux users:
java -Djava.library.path="/Users/yourusername/Downloads/VTK:$DYLD_LIBRARY_PATH" \
-Xss10M -Xmx1550M -jar cytoscape.jar -p plugins "$@"

Save and execute the script, the 3DScape will be automatically loaded upon the startup of Cytoscape.

See also 3DScape Online User Manual