INTERFACE

CYCELL is composed of five tabbed sections.

Before we get to them, let's agree on some terminology. We'll call the left side of the screen the Console. The right portion -- where your cells live -- will be called the Petri Dish.

The Petri Dish is zoomable with the mousewheel. And, holding down the right mouse button will allow you to pan your Petri Dish.

The Petri Dish is set up like a torus, with vertical and horizontal wrap-arounds.

Blue/Yellow

The Blue/Yellow tab opens the cell sorter interface.

Every simulation you run will always have three built-in cell types called Default_Blue, Default_Yellow, and OBSTRUCTION. When you write your own Rules, even though you don't declare these three states, they will always be present.

The bottom part of this tabbed panel allows you to directly -- in real-time -- adjust the adhesions and sizes of these two special types of cells. You can place a random grid of Blues and Yellows by clicking Place X by Y grid. The QUICK START section gives some more details.

The top part is a more general control panel for all the simulations.

Clear will erase all the cells in the Petri Dish. Iterate will begin your simulation; the radio buttons next to Iterate control the nature of the button.

Fancy Graphics will draw the cells in a prettier (albiet, slower) manner.

Draw Vectors and Draw Gradient will display the directional vectors and the gradient in your Petri Dish. Once again, displaying these will slow down the simulation a bit.

Use Field tells CYCELL to have the cells sense fields and, if checked, will give you the option to actually see the Fields.

The Speed slider indicates how frequently the screen will be re-drawn; the lower the number, the more frequently. And, the Flux slider controls the degree of randomness inherent in the system, as described in more detail in Overview. The default value of 10 usually works well for most simulations.

Monitor

The Monitor tab opens an interface that allows you to place and monitor your cells.

The most important tool is the Manual Placement widget. The drop-down list contains all the STATEs of your cells. If you load or write your own Rules, all the declated STATEs will be in here. Even if you haven't loaded any Rules, Default_Blue, Default_Yellow and OBSTRUCTION will always be in the list. To place a cell, use the drop-down to select a cell state. Then click the checkbox to the left. You will then be able to draw your cell on the Petri Dish. If you wish to place several cells of the same type, you can hit Enter and draw at a different spot.

After drawing your cells, pushing Iterate will bring them to life.

While the simulation running, you can press Space while your cursor is over a cell, and you will be able to monitor the values of all the variables in that cell as the simulation proceeds. Moreover, by clicking Debug Monitored Cell, a window will pop up which will allow you watch the monitored cell process the Rules, step by step.

Manipulate

What's the point of growing artifical flatworms and the like if you can't cut them in half and see what happens?

The control planel under the Manipulate tab is pretty self-explanatory. At any time, you can tab over to it, select some cells to kill or move.

If you wish to move a group of cells around, select them and then click Move Selected Cells. You will then be able to drag the selection around. Note that you can't place a bunch of cells on top of other cells; the selection will be turn green or red depending on whether there is an obstructions.

Field Editor

Fields can be complicated. In fact, the subject has its own page.

But, the Field Editor itself is a snap.

You have the ability to draw 4 different Fields. Each Field has its own color and number. (Field No. 0 means the absence of a field.)

The Brush Size slider controls the brush size.

Each cell has a default Presumed Location when it is first crated. The Adjust Default Presumed Location checkbox will allow you to alter this default presumed location (represented by the littel white dot.)

Likewise, each cell has a presumed orientation... this too can be altered using the knob.

(As discussed in the Field section, there is also a presumed scale; this will always be set to 1.0 by default and can't be changed through the Field Editor.

Finally, the Load Field and Save Field buttons will bring up a load/save dialog.

(The CYCELL Fields are saved as simple .PNG files and, technically, they can be edited in other software. Keep in mind, though, that the color values have to be exact and the Presumed Location pixel is specially marked. Unless you really know what your are doing, we'd recommend sticking with the CYCELL editor.)

Rule Editor

The Rule Editor is where all the magic happens. You can write your own little program to control your cells.

The Load Rules and Save Rules buttons will bring up a load/save dialog. (The extension for Rules is .cyr. But, they're just simple text files. If you wish to write rules in a different editor, be careful with the line breaks... CYCELL doesn't like hard-returns.)

Once you have loaded or written your Rules, press the Compile Rules button to compile them and store them in your cells. If there errors, the lower text box will display them, along with some suggestions as to how syntax.

The middle text-box in the diagram will open if you press Syntax Guide. It's a handy reference guide to the Rule Syntax. For the complete syntax, of course, check out Rule Syntax.