There are many ways to create iPad app prototypes, there are tools like OmniGraffle, and Visio which you can easily create a mockup in, but you might want to create something interactive.
Or you might be dealing with non-programmers with a great idea who has difficulty expressing how they would like their app to look and run.
I found out about a great resource especially for this purpose which I mentioned in my iPad Development Tutorial and Resources Collection, but felt the creator deserved some further attention for creating something so useful.
The resource is from Amir Khella and he has created a terrific keynote theme with many iPad user interface elements along with a great step-by-step guide on how to use it. You can see an impressive video of one of his prototypes in action below:
You can find the guide and download here:
How To Prototype Interactive iPad Applications In 30 Minutes Or Less
I hope you like it.
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