I wish to explore new design concepts in an application which break the traditional WIMP desktop metaphor. How can I guide the user through an app like this without using a manual?
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Three ways come to mind about how to go about doing this:
Provide a Tutorial or Virtual Tour Guide
This doesn't have to be a separate document or video, though the details will depend on the interface you're building.
For example, many video games make the first couple of levels basically a tutorial. It introduces mechanics, usually one at a time, and presents you with ways to use them. When done well, it hardly feels like a "noob tour," because it also moves you through the storyline. As you gain mechanics later in the game, these new items may be highlighted in some way to make you aware of them (one good example of this is in World of Warcraft - once you reach level 10, you unlock talents and specializations; the talent button is highlighted on your bar until you acknowledge it by opening the talent window). Once you've gone through the tutorial or acknowledged the new mechanic, the system removes the highlight and allows you to move on to other things.
Likewise, Windows XP will highlight the menu entries in the Start menu for newly-installed applications, so that you can find them. Once you've found them and opened them, they are no longer highlighted. Additionally, on new profiles, it will call your attention to the Start button, prompting you to interact with it. Office 2007 and newer will make the menu button in the upper left glow the first time you use the application, until you interact with it (or, I think, until it eventually times out).
The biggest downfall to this is that if a new user approaches the interface after the guide has been gone through, that new user may have a difficult time learning the interface. This is often dealt with by encouraging the use of user profiles, whereby the new user would have their own environment, and would have the opportunity to see the introductory material.
Make the Interface so Intuitive, A Guide is not Needed
This is far easier said than done, and many complexe interfaces only partially implement this (hence the option for some combination of both). This can be done in a number of ways and depends largely on the system you're building. Obviousness and discoverability are key when building a completely new interaction system.
The biggest drawback to this is that what is obvious to one person won't necessarily be obvious to another, and discoverability will depend greatly on the user's background.
For example, Windows (as far back as Vista, believe it or not), Mac OS, and Gnome-based Linux operating systems all have the ability to pull up their respective launch menus (Start, Launchpad, Applications Pane, respectively) with a single button press (the "Windows" or "Super" key for Windows and Linux) or short key combination (Mac actually requires this to be configured to work close to the same way the others do, but after that, it works the same). You can also immediately start searching, without specifically focusing on the search field, by simply typing after you've pulled the launch menu up. This is easily discoverable by anyone who knows about this in one of the other operating systems. I, personally, found out that this works even in Windows 7 after being used to running Ubuntu and Fedora. However, someone who's never used a similar paradigm before (including myself, when I initially switched from Windows XP to Ubuntu), will have a hard time finding it, if they ever do.
A good example of where a new paradigm works for most people is swipe gestures on a touch screen. The lack of navigation controls, coupled with an indication that there is more off-screen, prompts the user to try to reach those other items. The swipe gesture is often sensitive enough that a reaction happens with even a small swipe-like movement from the user. This reinforces the behavior very quickly, and encourages the user to try other, similar behaviors to see what else will happen.
What you do, or what your specific combination ends up being, will greatly depend on the interface you're trying to build. The best way to find the right method or combination will largely be to simply put a prototype of your system in front of people and see how they interact with it. Find the weak points and improve them by doing something such as one of the above two things and retest. Also, study your target demographic and see what they're used to doing. You can then provide various responses based on what they're already likely to do.
The Windows 8 interface encourages people to explore the UI by moving the cursor over various elements (largely also because their flat design). There are many examples of applications, both desktop and web that encourage users to explore new features by creating a first-time popup, highlight certain UI elements, or having a general window in the help section that highlights new features in the form of tutorial videos, quick guide or just tips. I am sure that users wouldn't mind if you introduced these things as long as it is easy for them to close or opt out.