Java Tutorials

Links to Ingeneue tutorial page

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).


Links to 
Morphogenesis Tutorial

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)

Links to Sim2D

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)



Links to Sim3D

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)


Links to SimFil

SimFil: demonstrates a simulation of flexible cytoskeletal filaments with biophysically appropriate deflection, relaxation time-constant, and thermal writhing. The code incorporates an html tutorial that presents background theory and tips for implementation (Alberts)

Mac Application Executable Jar