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They are going to run together topically. So when the OCW materials address loops, for instance, you'll do the loops exercises on Codecademy. They won't line up precisely, but it will be like having two different people explaining something to you, hopefully both with useful perspectives.
Will the course materials specify exactly which examples need to be done, or would you just be expected to browse around and find them? That's what I was doing, and it wasn't obvious to me which examples to do with each session of the course. The course materials I have don't mention it.
Yes, each week there will be an e-mail specifying which exercises on Codecademy correspond to which sections of the 6.189 content. We'll also be linking to some video lectures from 6.00SC on MIT OCW as well, again with a rough correspondence to the content in the other sources.