Graphical user interface

The ProCope package contains a graphical user interface (GUI) you provides fast access to most of the functionality of the library.

Starting the GUI

The GUI java program is launched with a start-up script located in the main directory of the ProCope package. Choose the right script, depending on your system:

Basic features of the GUI

First steps

Check out the First steps guide for a 5-minute tutorial to the ProCope GUI.

Memory

By default 256MB of memory will be available for the Java VM when using a command line tool. If you want to change this amount, specificy -Xmx000m as the first argument where 000 is the amount of megabytes which will be available. (Note: the -Xmx parameter is directly passed to the Java virtual machine, syntax errors will cause error messages of the Java interpreter).

Example:
gui.sh -Xmx1024m

Bootstrap

Note that the bootstrap confidence calculation methods (s) are not integrated in the ProCope GUI. The bootstrap approach is very CPU-intensive and should be parallelized over several computers. You can access these method using the Command line tools of ProCope.

Functionality

Main window menus
Pop-up menus

Cytoscape

ProCope can produce Cytoscape-compatible XGMML files or, alternatively, can be integrated directly as a plugin into Cytoscape. For further information, see: Cytoscape integration



ProCope documentation