In the first part of the tutorial we will learn how to set up a simple cell and export it for later use with the Simulator. After you have started the application it presents an empty workspace.

The left part of the workspace contains all elements that are used to modify the properties of the compartment and cells. The right part displays the compartment corresponding to the settings on the left.

Click the New Cell button to add a new cell to the compartment. Several new buttons and input fields will appear, the cell will be visible at the origin of the coordinate system in the 3d view . Clicking Center Cells will move the cell to the center of the compartment. Dragging withing the 3d view while keeping the left mouse button (LMB) pressed changes the perspective.

The new set of input fields is divided in two parts; the first part governs settings pertaining to the whole cell, while the second part controls individual "Protrusions". Drag the size slider under the "Protrusion" heading to the right or enter a number in the text field to increase the size of the cell.

The most important component in both parts is the set of sliders. They control the overall position of the cell and the position of the individual protrusions respectively. Click the New Protrusion button. A new set of sliders will appear in the section controlling the protrusions. You might have to scroll down using the scrollbar between the buttons and the 3d view, before it becomes visible. Move the second protrusion by slowly dragging the slider labeled x Position or by entering a number in the adjacent field. Note that only the second protrusion is moving. Now move the sliders in the section pertaining to the whole cell. Both protrusions will move. An other difference between the two type of movement is that when individual protrusion are moved the change of the slider position is reflected by changes in the number fields. Moving the whole cell does not affect the values of the positions of the protrusions as these are positions relative to an imaginary anchor point of the whole cell. Use the Size slider to adjust the size of the protrusions. Keep the slider in the right half of it's range otherwise the protrusion will have a negative size and thus be invisible. Keep adjusting the sizes and positions of the protrusions till you get a feel for the interaction of the protrusions. When the cursor is over a set of buttons controlling a protrusion the parts of the cell influenced by that protrusion will be highlighted.

If you have a created cell similar to the one pictured above, the next step will be setting up "regions" of the cell that can be used to map a model of biochemical interactions to the geometry. Change the Edit Mode from Geometry to Regions. Editing regions is similar to editing protrusions except that regions do not overlap. Scroll back to the to of the buttons and click the New Region twice to create two regions and move them relative to the cell by dragging the sliders or entering numbers in the text boxes. Use the Name text field to assign descriptive names to the regions.

Now all geometry information required to run a simulation is set. However the size of the compartment - as indicated by the coordinate axes - is larger than the cell, wasting time and memory during the simulation. Reduce the size of the compartment using the Width, Length, and Height fields and recenter the cell with the.Center Cells button. If the cell does not fit into the compartment it will be cropped ensuring that the cell used in the simulation has a well defined membrane. Save the cells using the Save. If the SimCellDesigner warns about the cell having an unusual shape this typically means that there is a cavity inside the cell or that it has the shape of a torus. If the cell is made up of more than one connected component you will have to connect the components of the cell before saving by either moving or adding protrusions.

We begin this tutorial with an empty workspace. Create a cell with a diameter of 10-15 volume elements, the precise number does not matter as long as the cell fills at least half of the compartment. Center the cell in the compartment using the center button.

Now create a second cell, and move it close to the first cell without changing it's size. Then increase the size of the second cell until it touches the first.

Uncheck the check box labeled Cell. The second cell will become invisible. This makes it possible to view the interface between two cells as the invisible cell is still exercising it's influence on the compartment. Tick the check box again to enable viewing and editing of the cell. Now increase the it's size till the cells radius is approximately 4 volume elements.

Make the cell invisible again. Now it should be apparent that the second cell in in contact with the first. there should be a visible deviation from the unperturbed shape of the first cell.

Repeat the process of increasing the second cells size and inspecting the contact surface to get a good understanding how the cells interact.