Ingeneue Tutorial: the first general purpose program designed to construct and analyze models of genetic networks. This is a link to the Ingeneue tutorials and documentation page. These tutorials are bundled with the current version of Ingeneue, but may be viewed online as well (Kerry Kim).
Morphogenesis Tutorial: an online tutorial demonstrating how local differences in contractility in groups of adhering cells give rise to global shape changes, in 2D. Instructions are included to download a jarfile to run the code and modify various parameters from the simulation window, and to create input files to specify various initial geometries. (Sherrard and Munro)
Sim2D: a starting point for 2D agent-based biological simulations. The basic code is a very simple 2D predator-prey model (formerly known as "Muttons and Gluttons"). Learn Java by modifying these behaviors to create more complex dynamics. Extend this code into a model of your interest. (Alberts)
Sim3D: a starting point for 3D agent-based biological simulations. The basic code is a very simple 3D predator-prey model; learn Java, and Java3D, by modifying these behaviors to create more complex dynamics. This code makes a good starting point for complex 3D models, and has been successfully used this way at the CCD. (Alberts)