Isaac's room is ridiculously neat - you'll notice that there's nothing out of place and nothing looks cluttered. You can find most of his belongings in his trunk, though all the items he wanted to keep are in the closet. There are some notes laid out on his desk as well, addressed to the other people here (and one other person).

Those might not be the first things you see though, since there are the designs painted on two of the walls. You'll find yourself staring at a map of Amestris with certain cities labeled. Ishval is circled in red. Some of them have paper duct-taped nearby with Isaac's handwriting, written in code of course.

The second wall has a map of Central City with a familiar alchemical array painted through it in red. Three specific points are marked on this map and once again there's duct tape and paper containing notes on whatever it is this one's supposed to represent.

Inside the desk you can find an alarming amount of notes - they're written in Amestrian and coded in a cipher that involves numbers, letters, and mathematical equations. If you're able to figure out the cipher you're certainly welcome to read them! Otherwise these are coded to look like research notes on his alchemy.