Before you start playing with all the options, it might be a good idea to determine what this computer model is based on. Remember this is a simulation of the activated sludge in a wastewater treatment plant. Most of the activity we are worried about takes place in the aeration basins. A typical arrangement might look something like this:

Since the guys at Clemson wanted to simulate such a situation, they decided they could model this setup as a chain of three completely mixed reactors like so:
The program is setup so that we can model a chain of up to nine reactors. Then we specify the flow scheme, the reactor volumes, flow rates to each reactor, and the solids retention time (SRT). We can also adjust the concentrations of everything in the feed stream, and the kinetic parameters of the heterotrophic and autotrophic organisms used. More about all this in a moment.
For more detailed information about the model, check out pages 11-19 in the manual. Pages 13-18 give descriptions of all the components that make up the feed stream. The rest contains information about the simplifying assumptions that were made for this model. This information will make more sense to you once you start using the program; so let's do that now.