Going paperless is a challenge but I've had a lot of success using dropbox and Google Apps as well as one note.
Free atomic learning on creating eportfolios with Adobe Acrobat X from Atomic Learning.
One of the things I have as my "big three" this year is the concept of a paperless portfolio using adobe acrobat pro. I'm a member of Adobe ed exchange and am using it to find all kinds of great resources. This page has links to best practices for eportfolios, digital assessment, as well as streamlining admin tasks. Useful resources. The cool thing is you can annotate with video, audio, an text and pdfs move very well onto ipads and devices like that.
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