An important step in the Lean UX process is continuous validation of design ideas, especially early in your process. We are lucky enough to have a UI Engineer (shout out to Dan Hahn!) on our team who builds high-fidelity prototypes, but sometimes it is best for the designer to spend a few hours cobbling together that prototype and not ask the engineer to code and recode a prototype several times if testing the first design iteration.
The best prototypes seem the most real and finished to the test subject. If the user thinks your prototype is not live, the data is fake, he/she may be more forgiving and less critical. It is important that a table of data has numbers that look real, not a series of #### and that your text is not lorem ipsum. The best prototypes are built with HTML/CSS and JS, but as a designer, I do not code often enough to be able to churn out a full-fledged prototype for a complex feature in a few hours. Earlier on in your design process, when you need to validate your hypotheses and your general design direction, something more lightweight built from your design file or a paper prototype is sufficient.
In Prototyping: A Practitioner’s Guide, Todd Zaki Warfel does a fantastic job of covering the why and how of prototyping within the UX design process. He spends several chapters walking through prototyping with various tools: Powerpoint, Keynote, Visio, Fireworks, Axure RP & HTML. What he misses is OmniGraffle Pro. It is mentioned briefly, but never fully explained.
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