2. Part Two: Building a Spatial Compartment with a Cell
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2. Part Two: Building a Spatial Compartment with a Cell

  1. Start the Simmune CellDesigner

  2. Click "New Cell".

  3. Click "Center Cells".

  4. Deselect "Show Ruler" and increase the size of the cell by moving the "Size" slider below "Protrusion". Note: Cells in the CellDesigner are composed of "Protrusions". A cell contains at least one, the fundamental protrusion determining the spatial origin of the cell. This protrusion can only be modified in size. Modifying its position means moving the cell. Additional protrusions can be moved relative to the fundamental protrusion to permit creating (almost) any (simply-connected) cell shape.

  5. Click "New Protrusion".

  6. By moving and resizing the protrusion generate a shape that looks approximately like this.

  7. Select "Show Ruler" again and draw a line anywhere in the compartment to place the ruler.

  8. By moving cell and ruler position the ruler in such a way that its end coincide with the centers of the cell faces.

  9. Enter 10 in the field next to the "Rescale Ruler length to" button, then click the button. Note how the cell volume changes.

  10. Switch the "Edit Mode" to "Regions".

  11. Click "New Region".

  12. Move/resize the Region until it cover the entire cell.

  13. Save the geometry into a file (e.g. "Cell.geo").

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G protein Signaling Tutorial Home | ToC 3. Part Three: Simulating the Model