"Add mode", accessed by pressing the 'a' key, allows you to click within the grey rectangle to add chromatophores. To create a link between two chromatophores, click and hold within the first cell and drag to the second. You may also create a link when adding another chromatophore by dragging to the connected cell before releasing. To toggle display of connections, press 'n'.

"Move mode", accessed by pressing the 'm' key, allows you to relocate chromatophores by clicking and dragging.

"Graph mode", accessed by by pressing 'g', allows you can graph the radius of a single chromatophore vs time. Click on the desired chromatophore. Remember to leave graph mode (press 'a' or 'm') before clicking on another chromatophore, otherwise the graph will represent the last chromatophore clicked.

"Query mode", accessed by pressing 'q', allows you to read out the activation, radius, chroma number, cordinates, and connections of any clicked chromatophore.

"Layer mode", accessed by pressing 'L', allows you to change the color of the chroma you are about to add. Press number 1 for red, 2 for yellow, and 3 for brown. In layer mode, keys 1-3 do not adjust simulation variables (see below) - first press 'L' to leave layer mode in order to use these adjustments.

Holding the ALT key (OPTION on macs) and clicking on a chromatophore deletes that chromatophore. Holding ALT while dragging from one chromatophore to another deletes the connection between those chromatophores.

Each chromatophore has an internal activation value, which is expressed by its radius. You can stimulate a cell (i.e. increase its activation value) by holding SHIFT while clicking within the cell's boundaries. You can inhibit a cell by holding SHIFT and CONTROL while clicking it. If this cell is connected to other cells, the activation (or inhibition) will spread around the network. A cell loses activation each time step, but may lock into a stable positive activation state due to its connections with other cells (who are providing positive input activation). Cells also undergo a period of 'inactivation' following strong activation, during which they become more difficult to stimulate.

You can adjust three simulation variables as the simulation is progressing. First press the key corresponding to the variable you would like to adjust ('s', 'd', or 'c'), then press the number key of the number to which you would like to set that variable - odd numbers 1-9 (for 0.1-0.9), 0 (for 1.0), or the up or down arrows (to increment the variable by 0.01). Press 's' to adjust the strength of stimulation (both excitatory and inhibitory) delivered with each click. Press 'd' to adjust the decrement of activation during each time step (1.0 equals no decrement, 0.1 equals quite a lot of decrement). Press 'c' to adjust the coupling between cells, or the synaptic weight of each connection (1.0 equals strongly connected cells, 0.1 weakly connected cells). You can adjust the weights between the various layers by clicking within the colored circles along the bottom of the window. Hold down the mousebutton as you drag away from the circle - the straight-line distance you drag sets the weight for that layer pair.

The activations of all cells can be set to zero by pressing 'e'.

Every cell can be connected to every other cell by pressing 'f' (fully connected).

A premade circular network can be loaded by pressing 'l'.

The 'r' key will remove an edge from each chromatophore currently displayed on the screen.

The cells twichiness ('warbling') currently has nothing to do with their activation state. In the future, the size of the cells may affect the warble rate. Warbling can be adjusted by pressing 'w'.

KEY ---------------- FUNCTION

a --------------------- add mode

c --------------------- adjust global corelation (in distance-based weighting mode)

d --------------------- adjust decrement

e --------------------- erase all connections

f ---------------------- fully connect all cells

g --------------------- graph mode

l ---------------------- toggle layer mode

m -------------------- move mode

n --------------------- show/hide connections

o --------------------- open premade network

q --------------------- query mode

r ---------------------- remove one edge from each chroma

w --------------------- adjust warble rate

x ---------------------- adjust inactivation window

z ---------------------- toggle distance-based weighting

1-9 ------------------- set simulation variable to 0.1-0.9

1-3 ------------------- select layer type if in layer mode

0 ---------------------- set simulation variable to 1.0

UP ------------------- increment simulation variable by 0.01

DOWN ------------- decrement simulation variable by 0.01

shift ----------------- stimulate on click

shift & control --- inhibit on click

alt -------------------- remove chroma on click