A "separate instance" is a completely different install of moodle. Our portfolios are set up on a different server, in fact. Students have the same ids and usernames (although they do have to log in twice if going from the instructional moodle to the portfolio moodle). Having two different moodles allows me some latitude--for example, you COULD turn off all the "teaching" things, like quizzes/gradebooks/assignments, on the portfolio moodle. You would certainly NOT want to do that on the main moodle used for instruction.
Since Moodle does not have licensing restrictions, you can have as many as you want. We have quite a few--a faculty space, a portfolio space, an instructional space, and old moodles kept as archives. There are some tricks to running more than one on the same server (not difficult), or you can have them on different servers. If you set up the same external authentication method (we use LDAP) and upload the same usernames, there is little problem for the students going back and forth between systems. We do try to make them look different!
Teaching with Moodle
Students Building their own Study Course
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