The most important such format is Flash SWF format. Therefore, movie formats with vector-graphics frames would be a natural choice for embedding into PDF. But PDF is a format that can display both vector and raster graphics, where the big advantage of vector graphics is its resolution-independence. Traditional movies are essentially sequences of resolution-dependent (rasterized) images, with additional information on how fast to play the frames. In particular, I included some links to LaTeX-based PDF presentation tools that can do almost anything that Keynote can do, based on the power of Adobe Reader.
If you have looked at my suggestions for doing scientific presentations using Apple's Keynote, you should be convinced by now that LaTeX is an essential ingredient for any computer-based talk with mathematical content. The context of this page is the problem of how to prepare scientific/technical documents. But if you go through my example on this page, it will be clear that PDF all by itself at this point in time has (almost) all the features a multimedia author could ask for. In fact, since Adobe has acquired Macromedia, some convergence of PDF and Flash might be expected in the future. While printable documents are thought of as static, PDF can be dynamic and interactive, see for example these interactivity demos.
The Portable Document Format (PDF) is much more than just a substitute for paper. PDF with animations Including animations in PDF using LaTeX
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