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One slight drawback is that you can't go back in the exercise (eg to check some earlier data). If you stop for some reason, you have to start all over again.
I found that the students generally enjoyed the exercise. but for some it became a bit of a competition. Some tried to get through the exercise as fast as possible without really thinking about what they were doing. In this regard it would be helpful to have a page at the end of the exercise which reviewed and quizzed the students the important concepts. Of course, this could be accomplished with a writing assignment for the class upon completion of the exercise.
This is one of the best virtual geology lab exercises I've seen. I highly recommend it.