This section will introduce the Ondex Visualisation ToolKit user interface. A network consists of genes/proteins/metabolites as concepts and interactions represented as links i.e. relations between concepts. Firstly, we will explain how to install and run the OVTK. Secondly, we will look at the basic user interface of OVTK. Then we will load up a network to show all menu features of OVTK and some of the core functionality such as layout algorithms, annotators and filters.

How to set the PATH variable
WINDOWS: Right-click on “My computer” and choose “Properties” from the appearing context menu. Switch to the tab “Advanced” in the appearing window. Click the button “Environment Variables” on the bottom left of the window. You will see a list of variables with their assigned values. If the PATH variable already occurs in it, select it and click “Edit”. Append a semicolon to the end of the value field and then enter the path to your Java binary directory. This is usually something like “C:\Program Files\Java\jdk1.6.0 04\bin”. If the Path contains any white spaces, make sure you put it in double quotes. If the variable PATH didn’t exist yet on your system, create a new one and call it “PATH”. Assign the binary path as it’s value. However you don’t need the semicolon in this case.

LINUX: Go to your home directory and open the file “.bashrc” in your favourite editor. Append the line PATH=$PATH: where is your path to the java binary directory, something like /home/apps/java/bin/ to find out what it actually is you can execute the command “type java” in a console window.

Download pdf Ondex Visualisation ToolKit (OVTK) User Tutorial