3.1 Graphical User Interface
The layout of BiologicalNetworks is shown in Figure 3.1. The interface has three major areas: the Project Pane on the left, the Search Result/Microarray Pane on the bottom, and the central Pathway Navigation Pane.

3.1 General Layout of Interface

Figure 3-1 illustrates the BiologicalNetworks Graphical User Interface (GUI).
  • The Pathway Navigation Pane can contain several pathway views, one window per pathway. The Pathway map is completely configurable: it can show the whole pathway or any set of nodes. For the selected group of proteins, more detailed information can be viewed in the List Pane.


  • The Project Pane organizes data in a Workspace. Proteins, small molecules, and cell processes can be stored in folders. Folders are hierarchical and can include both subfolders and single objects. A separate set of folders is reserved to represent a functional protein ontology and/or classification hierarchies.


  • The Search Result Pane is organized as several tables with a set of columns, where each column represents one characteristic of a node or control found for your search. Some useful characteristics include protein symbol, gene name, links to external databases (GenBank, LocusLink, Golden Path, HUGO), experimental conditions, etc. These characteristics can be used for filtering or sorting objects in the table. Selection in the table can be highlighted on the map and vice versa; behind the Project Pane there are three other panels: the Palette Panel, Curated Pathways and Database Tables Pane.


  • The Palette Pane displays whole list of node and control types and their graphical presentation.


Figure 3-1: BiologicalNetworks Graphic User Interface

Figure 3-1: BiologicalNetworks Graphic User Interface