Gecko

Try It
Java 1.1 browsers (for example, the Windows versions of Netscape 4.5+, Internet Explorer 4+) can run these models over the web:
MooseWood	Climate change on Isle Royale, Lake Superior. Based on Forksa.
GrassWorld	Three-level food chain: plants, herbivore grasshoppers, carnivore spiders. Plant competition. The Gecko model 101.
ScaredyWorld	Version of GrassWorld focusing on predation effects - grasshoppers evading spiders.
Woods	Northeastern forest growth simulator, based on Sortie.
BacSim	Individual-based bacterial growth simulator. See BacSim page for details.

Gecko is a spatial individual-based simulator for modeling ecosystem dynamics. Individual agents are modeled as free-moving Spheres (animated gif). (Non-animated picture for modem users.) Allometry, energetics, and spatial constraints are stressed. Within the overall Gecko framework, many different ecosystem models (2d and 3d) can be realized. The stress on physical constraints makes Gecko models unusually suited to field calibration as well as theoretical modeling. An online Swarm Gecko paper explains the basic GrassWorld model in detail, with pictures.

The latest version of Gecko is written in Java, built on CourseWare, a Java 1.1 toolkit for web-based interactive simulators. Gecko can run either over the web, or as a local graphical or batch application. New simulator models are written by adding or extending a few Java agent and landscape classes.

The current version of Gecko is Gecko2. The first production version of Gecko was based on the Swarm framework. An earlier prototype was based on John Holland's Echo models.

Gecko has been extended into the world of microbial ecology. BacSim is an individual-based simulator based on Gecko, for modeling bacterial colony and biofilm growth.

For more information on Gecko, please email Ginger Booth.

Booth, G. (1997) Gecko: A continuous 2-D world for ecological modeling. Artificial Life Journal 3:3 147-163. Text Postscript (174k) and figures Postscript (423k).
Schmitz, OJ (2000) Combining field experiments and individual-based modelling to identify the dynamically relevant organizational scale in a field system. Oikos 89:471-484.
Schmitz, OJ (2001) From interesting details to dynamical relevance: toward more effective use of empirical insights in theory construction. Oikos 94:39-50.
Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001a) Individual-based modelling of biofilms. Microbiology 147: 2897-2912. Abstract in HTML. Paper (1 Mb pdf.)
Kreft JU, Wimpenny JWT (2001b) Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth. Wat Sci Tech 43(6): 135-141. Preprint as pdf (1.4M) with correct and high quality figures;
Abstract in html; full paper in pdf (100k) as published with figure problems..
Kreft JU, Wimpenny JWT (2001c) Modelling biofilms with extracellular polymeric substances. In Biofilm Community Interactions: Chance or necessity? (Contributions made at the 5^th Meeting of the Biofilm Club, Gregynog Hall, Wales, September 13-15, 2001), pp 191-199. Gilbert P, Allison D, Brading M, Verran J, Walker J (eds). BioLine, Cardiff.

Biofilm club website.

van Loosdrecht MCM, Heijnen JJ, Eberl HJ, Kreft JU, Picioreanu C (2001) Mathematical modelling of biofilm structures. Anthonie van Leeuwenhoek 81: 245-256.

Kreft, J-U., G. Booth, and J.W.T. Wimpenny (2000) Applications of individual-based modelling in microbial ecology. In Microbial Biosystems: New Frontiers (Proceedings of the 8th International Symposium on Microbial Ecology, Halifax, Canada, August 9-14, 1998), pp 917-923. Bell CR, Brylinsky M, Johnson-Green M (eds). Atlantic Canada Society for Microbial Ecology, Halifax, Canada.
Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (1999) Individual-based modelling of biofilms: Why? In Biofilms: The Good, The Bad, and The Ugly (Contributions made at the 4^th Meeting of the Biofilm Club, Gregynog Hall, Wales, September 18-20, 1999), pp 257-262. Wimpenny JWT, Gilbert P, Walker J, Brading M, Bayston R (eds). BioLine, Cardiff.

Biofilm club website.

Kreft, J-U., G. Booth, and J.W.T. Wimpenny (1998) Bacsim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144:3275-3287. Abstract. Paper (pdf).
Schmitz, O.J. and G. Booth (1996) Modeling food web complexity: the consequence of individual-based spatially explicit behavioral ecology on trophic interactions. Evolutionary Ecology 11: 379-398.

	Toolsmith.
	Microbiologist and toolsmith on BacSim.
	Ecologist, principal investigator on Gecko.
	Ecologist, principal investigator on Gecko Woods.
	Microbiologist and modelling enthusiast.