At the top of the Main Simulation Window, just below the window header, is the menu bar, with the menu headings: 'File', 'Tools', and 'Help'.
The File menu deals with the functions you are used to in most menu-driven programs: Exit the program, make a new document (here: a simulation), and open and save.
The Tools menu shows all the various tool windows you can open in the simulation. Such windows will let you view a particular aspect of the colony and let you interact with it in detail. There are function key shortcuts for each of these tool windows listed to the left of each item.
The Help menu sports this Tutorial and the Guide. You can browse the guide after you have finished this tutorial to get more in-depth information on how Mars Simulation Project works.
Directly below the menu bar is the Toolbar, which features icons to quickly access some of the functions available in the menus. Hover your cursor over them to see a tooltip indicating which function they perform.
Click this link to go forward to Step 4, or this link to go back to Step 2.