Hi Chris,
I'm not sure there is a right way...yet. I've seen people coding entire algos in Research and then port them, and also seen people just do research in Research and then write their algos in the IDE. The IDE has some nice benefits with the debugger, and is required for entry into the Quantopian open, but I understand how nice it is to work in IPython.
We are planning to get the code more similar, so copying and pasting between the two will become easier, but for now it's a bit of whichever works best for you.
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