4.3 Menu, Toolbar and Model Kit

Menu, Toolbar and model kit may be used for quick access to various components of BiologicalNetworks. The menu options are listed in the Table 4-1.

Main Menu	Option	Description
File	New	Create a new model workspace
	Load	Open an existing model saved in the .bnm format Import a SBML model file. The imported model may automatically be laid out on the model workspace using two layout algorithms – Force directed and hierarchical.
	Save	Save the model in .bnm format. This will save the current model along with the diagrammatic layout Save as another .bnm or other format file
	Print	Print the model diagram
	Export as	Export a model to a SBML or other file formats.
	Exit	Exit BiologicalNetworks
Edit	Squigle	Mark up your network.
	Create View	Create view for network data.
	Destroy View	Destroy graphical representation of the network.
	Destroy Network	Destroy network data (not yet visualized).
Data	Display attribute browser	Display the attribute browser, which lets you view attributes assigned to both nodes and edges.
Select	Select	Operations for selecting nodes and edges, and using the current selection to create a new network and an associated view Create a new model workspace
Layout	Alyout Manager	Arranges the network drawn using layout algorithms (Force-Directed, Hierarchical-Embedding , etc.)
Visualization	Visualization Menu	The Visualization menu provides options for changing the mapping from biological data to a visual representation: colors of nodes, thickness of edges, etc. These features are explored in-depth in the 9. Visual Styles section. This menu also provides an Overview (Bird's Eye view) of your entire network, which is helpful for navigating very large networks.
Analysis	Find cycles	Find independent cycles in the whole network.
	Statistics	Show network statistic information.
	Network BLAST	Show conversed pathways among networks.
Tools	Tools Menu	Tools Menu provide access to Directed Acyclic Graph Engine and Querying Language GUI.

Table 4-1: Menu Options in BiologicalNetworks

The toolbar contains the shortcuts for some of commonly used menu option like open, save, print, help etc which are activated by clicking on the corresponding icons.

4.3.1 Node Editor

In any model the Node may be one of the Bioentities:Gene, Protein, Cell Object, Enzyme, mRNA, Pathway, Complex, Small Molecule etc. For easy identification each category has a different icon associated with it as shown in Figure 4-2-5 . The Node Editor is a pane which is located at the right of the main window. Figure 4-4 shows a snapshot of the Node editor. Following information can be entered through the Npde editor:

Figure 4-4: Node Editor

Label	Name displayed on the model workspace
Full Name	Full Name
Concentration	Concentration specified in Moles/litre
Volume	Volume of the compartment to which the bioentity belongs. Volume is entered through the project properties tab ( 4.1).
Total Quantity	Number of moles of the bioentity
No. of Molecules	Number of molecules of the bioentiy
Value Fixed	Check this check box for keeping the concentration fixed during simulation
Notes	Annotation of the bioentiy

Only one of concentration and number of Molecules need to be entered. The rest is calculated using formula:

Total Quantity = Concentration x Volume	Equation 4-1
No. of Molecules = Total Quantity x Avogadro’s Number	Equation 4-2

4.3.2 Process Properties

An in-silico model of a biological system is abstracted as a network of bioprocesses or chemical reactions. Section 3.3 describes steps to be followed for constructing a model on the model workspace.

Process Properties is an interface (Figure 4-5) for viewing and changing the properties of a bioprocess or a reaction such as stoichiometry, rate laws etc.

The Process editor consists of two tabs:

Process : Through this tab the process/reaction name, reversibility and stoichiometry and other properties can be entered. Stoichiometry can be entered through the drop down list of positive integers prefixed to each bioentiy involved in the process/reaction. Also a quick view of the properties of bioentity, which form the reaction, can be obtained by pressing the View Bioentity Details button as shown in (Figure 4-5: Process Properies Editor).

Kinetics : The kinetic law associated with the process/reaction and the associated rate constants are entered through this tab. In this version only Mass action rate law is supported.

Figure 4-5-1: Process/Reaction Editor - Process/Reaction Tab

Figure 4-5-2: Process/Reaction Editor - Process/Reaction Tab

4.3.3 Compartment Editor

Chemical reactions may take place in different compartments. Compartment Editor is an interface ( Figure 4-6 ) for changing the properties of a compartment.

Figure 4-6: Compartment Editor