| In this section, the steps for building a model would be described. Every model requires a project space. To define a new model the first step is to open a new project by using the icon in the toolbar or the menu option (File->New). This creates a model workspace on which the model network is built. Following sections describe how to define Nodes, Processes and edit their properties. Free text details or references for the model can be entered in the description window (4.2). Other specific information like User Name, Date, Species Name, etc can be entered in the project properties tab mentioned in 4.2.
5.1.1 Adding Biological Components
After creating the model workspace, the next step is to define different species in the network. Steps for adding new specie in the model are as follows:
- Click on the icon of specie category, i.e. gene, enzyme etc, in the Palette Panel. This will change the mouse pointer inside the model workspace to the icon of the selected category.
- Place the new specie on the model workspace.
- Change the properties of the specie by invoking the Figure 4-4 Species editor. By default a name would be assigned to the specie and its concentration would be set to “1” if it is a reactant and to “0” if it is a product. On moving the mouse pointer to a specie icon a tool tip is displayed with its name, volume and concentration.
5.1.2 Adding Prcesses/Reactions
The next step after creating the bioentities in the model is to define the processes/reactions and the associated kinetics. In BiologicalNetworks a reaction is graphically represented by a bioprocesses/reaction icons (Figure 4-3 ) and linking arrows. The steps for defining a bioprocess/reaction are as follows:
- Select the bioprocess/reaction icon from the Palette Panel
- Place the bioprocess/reaction link icon on the workspace by clicking on the workspace
- Choose the bioprocess/reaction arrow from the Palette Panel and link the bioprocess/reaction link with the bioentity in the bioprocess/reaction by clicking and dragging the mouse. If bioentity is a source/reactant, the arrow should originate from it with the arrowhead at the bioprocess/reaction link. To indicate destination/product the arrowhead should point to the bioentity and tail should be on the bioprocess/reaction link.
- Go to the Figure 3-4: Bioprocess/Reaction Editor window by double clicking on the bioprocess/reaction icon and see/change the properties, enter the stoichiometry, rate law and other information as explained earlier. On moving the mouse pointer to a bioprocess/reaction icon a tool tip is displayed with its name, bioprocess/reaction equation, rate law and rate law parameters etc.
5.1.3 Adding Compartments
In BiologicalNetworks a compartment is graphically represented by a compartment icon (Figure 4-3)
The steps for defining a compartment are as follows:
- Select the compartment icon from the Palette Panel
- Click on the workspace and drag the mouse to the desired region, which covers all the reactions taking place in the same compartment.
- Change the properties of the compartment by invoking the Figure 4-6: Compartment Editor. By default a name would be assigned to the compartment and its volume would be set to “1.0E-14”. On moving the mouse pointer to a compartment a tool tip is displayed with its name, and volume.
5.1.4 Editing Model
The model network definition is complete with the creation of all the species and reactions on the workspace, and entering their properties through the Species and Reaction editor. To better organize and aesthetically enhance the components on the workspace the following can be done:
- Move the components on the workspace. This can be done by first switching to the selection mode and then choosing the component on the workspace. The component can be moved around and resized. During all these process, the network topology will be preserved.
- Change the colour of the components. A component may be given any color from the colour palette in the Palette Panel.
- Add text to the model workspace. To enter on any section of the model free text may be added by selecting the annotation icon from the model click and placing a text box on the workspace. Also font and colour of the text may be changed by using the colour and fonticons in the Palette Panel.
- Cut, Copy, Paste and Delete component. These standard operations can be done on any component on the model workspace – specie, reaction arrow, reaction link, text box – through the Edit menu or standard key strokes.
- Undo and Redo operations. Up to 10 operations can be undone and redone using the icons in the toolbar.
- Zoom in /out/fit and Zoom in selected region. This feature becomes useful when the model size becomes big. The zoom in, zoom out, zoom to fit and zoom in selected region icons in the toolbar implement this functionality.
- Resize component. The species and reaction icons can be resized by selecting them and dragging one of the control points.
- Layout component. BiologicalNetworks incorporates two intelligent layout algorithms for automatically creating an aesthetically pleasing network layout of the model on the drawing workspace. These are:
- Force Directed algorithm: This algorithm is more suitable for layout of networks with many loops in it.
- Hierarchical algorithm: This algorithm gives better results when used for laying out networks with less loops e.g. linear cascades.
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