Look at DPS and Mag+, but keep in mind that both are quite expensive if you want to get your publication in front of people...
Both of these systems "hack" an indesign file... placing elements on certain layers give them different properties. I am not a huge fan of the idea overall, as indesign is not a great tool to create these types of interactive experiences IMO.
Also, keep in mind that the compiling process involves taking all the content in indesign and making it all into static, non-searchable graphics! Think Microsoft encarta from back in the day... The resulting files are huge... It is hard to convince users to download a 4gb magazine.
Consider also iBooks author. It is terribly documented, but with some work you can make a very custom template. it supports a lot of widgets and uses a similar layout engine to keynote. Files are also huge however.
We did a ton of research on this and wound up deciding that developing a dynamic and responsive website with lots of multi-touch and swipe support was a far more cost effective option...