One essential element is the need to be able to comment on work. Students may peer-review each other's work, and certainly the teacher would like to be able to do the same. I was brainstorming this problem this week because, as it turns out, I have to figure out how to create eportfolios for the fall semester. Our old software is going poof.
By serendipity, I saw a blog at blogged.com called Academic Productivity. Lo and behold, there was an article about a "web highligher and sticky notes" application--exactly the sort of thing I'd been brainstorming about. The service is seen as a competitor for delicious.com, which I use religiously to maintain my bookmarks. It's called diigo.com, and it allows you to bookmark a page, add tags, organize into folders, mark as read or unread, and--best of all--highlight portions of text within a web page and add comments. These can be public, private, or restricted to within a particular group. The image below, snipped from a New York Times article, illustrates such a comment. If you browse to that page with your Diigo account activated, you should be able to see the note I left, since I made it public. (Note: the "Readers' Comments" box on the left has nothing to do with Diigo--it's the usual bloggish comments allowed in NYT.)Diigo comes with a Firefox plug-in that makes it easy to do your markups. The menu bar is shown below.

An "open" portfolio of the type I've described could have a home base in a public blog, which is a nice way to host content, with built-in commenting and RSS feeds. Plus, many kinds of media can be directly embedded, like graphics, sound, video, and anything that runs on Flash or Silverlight.
Clearly, even with markups, the loss of a built-in gradebook may be too much to suffer for some instructors. Perhaps Gary Brown's harvesting gradebook will come to the rescue there. In the meantime, I think it's worth trying out the markups as a pedagogical tool.
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