Much of my research involves developing agent-based models (ABMs) of microbes. These models can be quite complex and I always struggle to communicate them beyond my research group. Towards this, we are developing scaled-down versions of our models that can illustrate the main ideas of the full models. We use the NetLogo framework and publish the models as applets that can be run in a browser.
NOTE that starting on January 2014, when Oracle shipped Java Update 51, which disables support for unsigned applets by default, these applets can no longer be run in your web browser. See the details here. However, you can still run download and run the applet on your computer. Simply click on a link below. Then follow the “NetLogo” link on that page to download and install NetLogo, and the link to download the model file. Send me an email if you run into any problems.