The Gecko family of individual-based simulators were my main research thrust at Yale. I've presented Gecko at a number of scientific conferences, mostly to those interested in individual based modeling, but some interested in the ecosystem dynamics. I authored and co-authored a number of papers. I've taken a very different approach than most to 'spatial' modeling - Gecko entities have extent and volume and mass, not just grid position.
Woods is the one usually used for teaching, at Yale and beyond.