there are many good systems out there. i do flood and drain hydroponics with 3'x6' trays, and lumatek 600 watt ballasts with cooltube hoods. i use 6''x6'' grodan cubes as my medium, and gh nutes w/ b-cuzz bloom for the flower period. and run 20 600 watt lights in a 20'x20' room. and yield quite well. for a 12'x12' room i would use 2 4'x8' trays with 6 600 watt light setups. i would air cool them with a 6'' fan. i would have a 10'' fan exausting the room, and an 8'' fresh air intake. i would also have at least 4 oscelating fans. it would be good to insulate with r-13 for walls, and r-30 for the ceiling if there is no insulation currently. you will also need a 100 gallon reservoir 2 water pumps, a 8 light controller, a 60 litre dehumidafier, co2 and climate controller are optional but if you have the doe they are well worth it i would get the sentinal for climate control
I would consider the Ebb n Gro system for that much space. It comes with 12 units but is expandable to 50 and they all can be run off a single reservoir and controller. You should be thinking about 6k watts. The Ebb n Gro you can rotate plants very easily. Cleanup is simple. If your looking for a blueprint check out SugarDaddie . he's running about 5k with 48 buckets. You could load it up with trays but I wouldn't want to manage 15 or so trays. Plus with the Ebb n Gro your only talking about expanded clay so you won't need to buy rockwool or w/e. Just wash the clay between uses. here is the ebb n gro Ebb & Gro 12-Plant Hydroponic Grow System - Plantlighting Hydroponics and here is sugardaddie's thread http://forum.grasscity.com/advanced-grow-journals/523232-5000-watt-ebb-n-grow-show.html