Example 5 - Procedural semantic zoom

This section provides examples of usage of construction of procedural semantic zoom.

Procedural semantic zoom

Click here to download the example map that when uploaded will generate a procedurally-generated semantic zoom. Please, note that on the highest zoom level only one compartment - cell is visible. After zoom-in, two grey areas become visible, describing functional areas in the map. After another zoom-in, nucleus and synapse compartments become visible. See also the manual for adding a project.

Example Warnings

If during adding a new project, you check the bottom box: Split semantic zoom into separate layers, in the left panel in Overlays tab, you will see additional overlays, named Pathways and compartments-No. Each overlay is a single view of zoom level generated by semantic zoom. See image below:

Left panel single layers

This option is used mostly for debugging of the procedural generation of the semantic zoom, and should not be used by default.

Customization of the procedural semantic zoom

Coloring the CellDesigner areas

In MINERVA, you can customize areas drawn in CellDesigner. By default they are grey, and the only customization that CellDesigner allows is changing of the font size and color. In MINERVA, you can change the color of the area by inserting BackgroundColor command in the name of the overlay. The first line will be treated as a name, second and later will be treated as commands. For instance, an area named:
Your area
will have a name Your name and a color #5bb257.

Find out more about semantic zoom and how to draw the layers in CellDesigner here.

Overriding the order of appearance in the semantic zoom

In MINERVA, you can customize the order, in which the elements, interactions, compartments and areas appear in the semantic zoom.

  • SemanticZoomLevelVisibility controls at what zoom level the object becomes visible, applies to elements, interactions, compartments and areas.
  • SemanticZoomLevelTransparency controls at what zoom level the object becomes transparent (shows the contents inside it). Applies to compartments, areas and complexes (elements containing other elements).

These commands should be provided in <notes> block of elements (species), interactions (reactions) and compartments. For CellDesigner areas, they should be provided in the name, similarly to the Background command, as described above.

Click here to download the map with customized semantic zoom, drawn in CellDesigner. The file has the following properties:

  • Area SNCA degradation and elements in them are not modified; MINERVA displays them with the default semantic zoom calculation

  • Area SNCA translation is displayed in green
    • BackgroundColor:#5bb257
  • Area Lewy-body formation
    • SemanticZoomLevelVisibility: 1
    • SemanticZoomLevelTransparency: 1
  • Elements SNCA, NO, ROS SemanticZoomLevelVisibility: 3

  • Element SNCA misfolded SemanticZoomLevelVisibility: 2

  • Compartment Lewy-body
    • SemanticZoomLevelVisibility: 1
    • SemanticZoomLevelTransparency: 3

Upload the the map with user’s defined layers to MINERVA and examine how particular areas are displayed. After, for a comparison, upload to MINERVA the map with default semantic zoom. It has same content as the map above, but without the custom semantic zoom.

Note: In CellDesigner, layers (groups of areas) can be set to visible or invisible. Depending on this, the area names are displayed differently in MINERVA. See image below, on the left a map with layers set to invisible, on the right a map for which the CellDesigner file was saved with visible layers: CellDesigner layers visible/invisible