Systems biology - manual model construction

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Building from scratch

Creation of a new diagram

The model development process is initiated by creation of the model network or Type-diagram-icon.png diagram. A new diagram can be made in the Work Space by two methods:

  1. via Control Panel → New Diagram (Note: please select the correct folder for a new diagram in your project area):

    Model fromscratch Fig1.png

  2. via the Tree Area by a single click with the right mouse button on the corresponding folder of the project:

    Model fromscratch Fig2.png

The platform will ask you to select the Type-diagram-icon.png diagram type and specify the Type-diagram-icon.png diagram name you want to create in the work space. In the following, the creation of a new “SBML model in SBGN notation” will be described.



Model fromscratch Fig3.png

Upon selecting the type of a diagram and clicking Ok button a new node New Diagram will appear in the Tree Area and the corresponding tab is opened in the Work Space to start the diagram creation.



Model fromscratch Fig3 1 18 03.png

A pathway diagram opened in the work space has a tool bar as shown below:

Model fromscratch Fig4.png

Adding a new element to the diagram

Building from BioModels Repository

To analyze developed and published model or use this one as a basis for modification/extension, you can employ BioModels repository the folder of that is represented under Databases tab in the Tree Area. Select the Biomodels repository by a single click with the left mouse button, then double-click will open the subdirectory (Diagrams→Curated).


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Figure 1. BioModelsDB repository in corresponding tab of the Tree Area.


To open model of interests, double-click of the left mouse button the model icon in the Tree Area or a single-click of the right mouse button on the icon and press Open in a pop-up window.


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Figure 2. Opening previously developed model from BioModelsDB in BioUML.

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