Example VAX simulation where the learner attempts to isolate an epidemic through quarantine.
VAX!
A game about epidemic prevention in ruby, javascript and d3.
Salathé Group, Penn State University. site 
Some of the concepts we teach are rather abstract, but some people in my group are working on creating standalone, interactive learning modules to bring home these concepts. Every modern browser now supports amazingly rich interactions, and it would seem like a wasted opportunity not to make use of those capabilities. It's somewhat disturbing that in 2013, there is still a huge niche for good, interactive learning tools, but at the same time this presents us with a great opportunity too. blog
Update Dec. 17: This was Vax!, which turned out to be hugely popular beyond the MOOC. It was developed by grad student Ells Campbell.
Before Vax, the extent of my web development experience is encompassed by this amazing Ruby on Rails tutorial. Therefore this web application is minimalist by-design. I've employed a few libraries, such as d3.js, jquery, and jqueryui. I've also employed a few gems to handle cookies, errors, and styling. github
See also Sand Avalanche with updates after reading the sample chapter from Salathé's Nature in Code. leanpub