CS 420/594 — Biologically Inspired Computation
NetLogo Simulation


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The applet requires Java 1.4.1 or higher. It will not run on Windows 95 or Mac OS 8 or 9. Mac users must have OS X 10.2.6 or higher and use a browser that supports Java 1.4. (Safari works, IE does not. Mac OS X comes with Safari. Open Safari and set it as your default web browser under Safari/Preferences/General.) On other operating systems, you may obtain the latest Java plugin from Sun’s Java site.  General information on the models, including instructions for running them on your own computer, is available from the NetLogo Simulation Information Page.  To download this page, do not use "Save As," but right-click (or on Macs control-click) on this link.  You also need to download the NetLogo program, which you can do by right-clicking or control-clicking this link.

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view/download model file: SlimeSpiral.nlogo


This program simulates waves of motion and chemical relaying in the cellularslime mold Dictyostelium discoideum. When Dictyostelium amoebae are starvedon an agar surface they begin to aggregate, forming complex spatial patternsas they do so. Aggregation leads to the formation of a multicellular organism,called a slug, consisting of about 10,000 to 100,000 cells, that can moveabout on the substrate for some time. Eventually, the slug develops into afruiting body, a spherical stalk with a cap on top that contains spores.Under the appropriate conditions the spores can be released and germinate,thus completing the cycle.

The amoebae coordinate their movement by secreting cyclic adenosinemonophosphate (cAMP) and by moving up the resulting cAMP gradient. Thisprogram ignores the cell motion because it is several times slower thanthe cAMP wave propogation. Accordingly, the rules governing the cells'behavior are as follows:

- if a cell senses a concentration of cAMP above the relay threshold (which is believed to be higher than the movement threshold), the cell emits 100 units of cAMP and enters a "refractory" state for a specified number of time steps

- cells that are in the refractory state are insensitive to cAMP, thereby disabling cAMP secretion; instead, these cells gradually break down the cAMP in their locality, by means of an enzyme called phosphodiesterase

With each time step, patches share 50% of their cAMP content with the eightneighboring patches.


The SETUP button prints a color key in the command window and creates arandom distribution of slime mold cells, some of which release a pulse ofcAMP into the environment.

The GO button runs the simulation according to the rules outlined above.

The DENSITY slider specifies the initial density of slime mold cells.

The NUMBER slider indicates how many cells will release cAMP at the startof the simulation. In reality, these cells might be starved more severelythan the others, thus prompting them to start initiate the chemical signal.

The THRESHOLD slider specifies the amount of cAMP needed in a patch for thecell to relay the signal by releasing more cAMP.

The PERIOD slider controls the length of the cells' refractory period.


Spirals of cAMP form as wave fronts are broken by density perturbances;accordingly, the threshold and density sliders affect the extent of wavepropogation.


Modified by B. J. MacLennan Sep. 2003 for Java StarLogo 2.0.2 and Aug. 31, 2007 for NetLogo from version by Bill Thies on Scott Camazine's "StarLogo Simulations of Self-Organized Phenomena" <http://www.scottcamazine.com/personal/selforganization/starlogo/starlogo.htm>.

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Last updated: 2007-09-17.