Visual modeling

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Visual modeling in BioUML

Fig 1.BioUML interface for visual modeling

Visual diagram editing interface is represented on fig.1. It consists of 5 main parts:

  1. Repository tree.
  2. Pane for selected diagram.
  3. Toolbar for new elements adding to the diagram. Type of available elements depends on the diagram type.
  4. Editor pane for selected element on the diagram.
  5. Set of tabs for current diagram.

Adding new elements

Fig 2.Adding new species to the diagram. Select element on the toolbar and edit properties in the appeared dialog.
Fig 3.Adding new species to the diagram. Species is now added. Select it and change its role (mathematical variable) properties

Visual instruction on how to add species see on figs 2 and 3. To add object to the diagram user should perform next steps:

  1. click on the correspondent icon on the toolbar
  2. click on the place for new element on the diagram pane
  3. edit object properties in the appeared dialog
  4. press enter

After element is added user may define its additional properties in the editor pane.

Variable properties editing

Fig 4.Variables tab.
Fig 5.Parameters tab.

For model variables editing, BioUML presetn two tabs:

  • Variables (see fig. 4) - for variables which are associated with species, compartments or other elements on the diagram.
  • Parameters (see fig.5) - other variables.
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