Following up the initial release, version 1.1 brings toxic plumes, several new types of organisms, slightly increased performance, a clearer interface, and more information about what's happening in the simulation. The new organisms showcase some new abilities and behaviors and there are the beginnings of mod and extension support.
The easiest way to get started is to open the web Applet (first link) or download the executable .JAR and run like a program. You can also download the source code here or on github to complie on your own. The introduction and features pdf outlines the basic functions and features of each part of the program and the How to Brew Beer tutorial lists the exact steps you need to simulate brewing beer in the program.