VAMP is a Java applet and therefore the Java Runtime Environment (JRE) must be installed on your computer before running VAMP. We recommend to use Java 1.5.0 (for better rendering and performances), see http://java.sun.com/j2se/1.5.0/ for download.
To visualize a large number of profiles simultaneously the java parameters regarding memory allocation must be correctly set.
For example, if your computer disposes of 1 Gb of RAM memory the java virtual machine memory can be set with the following parameters:
If you have more (or less) memory, these parameters must be adjusted accordingly. 512 Mb of memory is considered as a minimum, and we strongly recommend to dispose of 1Gb.
-Xms defines the minimal memory size allocated to the java virtual machine and -Xmx defines the maximal memory size (note that the -Xmx can not exceed the size of the RAM memory). In the example below the memory allocation ranges from 400Mo up to 800Mo.
With these parameters the users can load up to 700 microarrays (each with 3500 probes) simultaneously.
For more details please visit : http://bioinfo.curie.fr/tutorial/vamp/Java-configuration.html