4.2 BiologicalNetworks Panes

4.2.1 Project Pane

 The Project Pane contains:
  • Project properties pane.
  • Choose organism drop-down menu.
  • Project Folders .
Project properties pane allows you to define your personal project settings in order to be recognized by database sequrity system allowing to add, edit, remove data from database.

Choose organism drop-down menu allows you to choose the database to be studied.

Figure 4-2-1: Choose organism drop-down menu
Figure 4-2-1: Choose organism drop-down menu



4.2.2 Project Folders

 The Project folders in the Folder Pane help you to organize your personal data and can include both subfolders and single objects. With the Project Folders you can create your personal working area. You can add your own subfolder in the Projects Folders.

The Project Pane has next folder types:

  • The Index folder shows the database content organized by object and process types.
  • The BiologicalNetworks Project folders are designed to help you to organize your personal data and can include both subfolders and single objects.
  • The Microarray folder contains Microarray heatmap of the opened microarray analysis project.
  • The Groups/Clusters folder contains functional groups, microarray clusters, protein lists, and other groups of objects.
  • The Analysis folder contains different types of microarray analysis (clustering, sorting, filtering, GeneOntology analysis) subfolders.

4.2.3 Pathways Pane

 The Pathway Navigation Pane or Graph Display is capable of displaying several pathway views, one window per pathway. The pathway map is completely configurable. The map shows individual pathways or any selection of nodes. For a selected group of proteins, more detailed information can be viewed in the List Pane. For example, Figures 4-2-1, 4-2-2 show how you can find a description of selected proteins.

Figure 4-2-2: Metabolic Pathways Pane
Figure 4-2-2: Metabolic Pathways Pane

4.2.4 List Pane

 The List Pane functionality allows you to:
  • Show query results and group contents.
  • Copy and paste contents of the table into the pathway.
  • Copy and paste contents of the table into MS Excel.
  • Select nodes from the table on the pathway diagram.
  • Retrieve the selection from the pathway diagram.
  • Find pathways and groups that contain nodes of interest.
  • Link Protein names stored in the List Pane tables to HUGO, LocusLink, and GenBank. Hyperlinks are shown in the blue color.


When the List Pane shows contents of groups or search results, the List Pane functionality allows you to examine useful characteristics for nodes and controls. Some characteristics to be displayed include: symbol, gene name, functional group, links to external databases (GenBank, LocusLink, Golden Path, HUGO2, experimental conditions, etc. These characteristics can serve as the basis for filtering or sorting objects in the table. Table selections can be highlighted on a pathway map and vice versa.

To show nodes of interest in the List Pane:

  • Create a query. For example, find nodes are containing string LAT in their names, using menu Edit > Find Nodes by String or Edit>Find Nodes by Attributes;
  • Run the query;
  • The results appear in the List Pane.


To copy a node of interest from the List Pane to the pathway diagram:

  • Select the node of interest from the List Pane;
  • Add the selected node to the pathway diagram using copy and paste from the List Pane, or simply draganddrop the selection into the Pathway Pane.


To select a node of interest on the graph:

  • In the List Pane, put mouse over the record with node of interest;
  • Open the rightclick menu and choose Select on Graph;
  • If the node of interest is included in the current pathway diagram, it will be selected on the graph.


To retrieve selection from the graph:

  • Open the List Pane;
  • Open the pathway of interest. Select the node of interest on the graph;
  • Open the context menu on the List Pane and choose Get Selection from Graph;
  • If the node of interest is included in the current list of nodes, it will be selected on the List Pane;


The List Pane functionality allows you to find groups and pathways that the node of interest is a member of. Find groups and pathways containing the selected object(s) by using the following steps:

  • Select the node of interest from the list of nodes;
  • Open the List Pane context menu and choose Find Pathways;
  • The List of Groups and Pathways dialog box appears;
  • Select a pathway or a group and press the Open button;
  • The pathway of interest appears in the Graph Window; or the group of interest opens. See Figure 4-2-4.


Figure 4-2-5: List Pane
Figure 4-2-4: List Pane

4.2.5 Palette Pane

 The Palette Pane contains a full list of nodes and controls types and their graphical representation. Property values can be displayed by shape and color of the node in the Pathway Pane. Every kind of node or control in the software has a unique name and graphic representation. By default, BiologicalNetowrks has a builtin styles for all kinds of nodes and controls stored in the List Pane. See Figure 4-2-5.

Figure 4-2-5: Palette Pane
Figure 4-2-5: Palette Pane