I'm looking for a site to help my middle school students do digital notecards when they work on research papers.

In the past, I have required them to keep physical notecards of all their sources and information so that I could check to make sure they were organizing their material correctly and also synthesizing it as the wrote it.  Many would ask if they could do their notes in MS Word, but I was afraid they would just copy and paste material from the internet, not discern it or read it carefully, and then potentially end up plagiarizing.    They are getting familiar with wikis.  I have considered having them use a wiki to collect all their notes in one place.  But, again, I don't want them copy and pasting large blocks of information without putting it into their own words.  I also am afraid they'd collect a long "list" of info that would be difficult to sort through and find the information they needed.

If there was a way to create digital notecards, they could mark them in someway similar to how they would paper notecards, and then organize them in a sensible way to quickly find the information they needed.

I'm trying to teach them high-tech ways of taking notes and collecting research.  At the same time, I'd like to go as paperless as possible.  I have them saving their work on google docs so we don't have to print reams of rough drafts, but the notecard process I'm still tweaking.

Any site suggestions?

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I think Google Docs is your best choice. There might be dedicated note programs like Microsoft's NoteOne, but a doc seems to accomplish the same thing. Very accessible too.
I wonder if using Diigo and having students tag, annotate & share bookmarks along with using the highlight and/or sticky note feature might be a good alternative to notecards. They could highlight the portion of the page that they think would be useful & then have to add a recap in the annotation.

Here are a few other links about digital notecards:

And since they're already using Google Docs, Google Docs could be their note taking tool too as Alan said - use a document or set up a template in a Google Presentation with each slide being a notecard.

None of these solutions solves "copy and paste" though - that's a different issue. However, if you require that all sources are cited as information is added to whatever the online notecard is, it's easy to check if something was directly copied.
I use Noodle Tools for my own research, but I think there is a small fee (covered by my university). www.noodletools.com

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