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:
gui.bat
for Windows users
gui.sh
for Linux and Mac OS users
Basic features of the GUI
- The GUI consists of three lists containing networks, complex sets and purification datasets.
- All functionality is accessed via menus: The main menus at the
top of the window and one popup window for each list which are accessed
by right-clicking on the respective list. You can select multiple items in each list by holding the SHIFT or CTRL key.
- Instead of loading data objects using the popup menus you can
directly drag&drop files from your file browser into the lists.
- You can save and restore your work sessions (i.e. all loaded objects and settings). See also: Session menu
- Most components in the GUI have tooltips, hold your mouse over them to get corresponding information
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