3.2 Creating Pathway/Model

To create a pathway/model in BiologicalNetworks, there are several means to do it. User can load ready-made pathways/models from pathway databases or SBML files (will touch them in next chapters) or manually create a new pathway/model from scratch. Hereby, we’ll describe the manually creating of a pathway/model.

Creating a project - Use the New Project button

to open a new project workspace. Click on the button to create a new project. A new modelling canvas will be automatically generated.

Creating a species - Use the Species buttons

to create new species in the Palette Pane. Click on the species button once and then click on the modelling canvas where you want to place the new species.

Creating a reaction node - Use the Reaction button

to create a new reaction in the modelling canvas. Click on the button once and click in the modelling canvas where you want the new reaction created.

Creating a reaction - Use the Linking Tool ReactionFlow/Binding button

to links the species to the reaction node. Click on the tool once and click on the species you want to link with the reaction node, hold the left mouse button and drag the arrow to the reaction node.

Creating a compartment - Use the Compartment button

to create a new compartment in the modelling canvas. Click on the workspace and drag the mouse to the desired region which covers all the reactions taking place in the same compartment.

You can easily explore all the species in the model tree viewer by its category and edit any of them.( Figure 3-2).

Figure 3-2: BiologicalNetworks Project Browser