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The last thing to do, obviously, is to pull it all together and actually write the paper. This is where the word processor gets very high marks from people who remember "correctional fluids." Spellers are also very high on my list, anyway, of the software products that have made research writing easier. It is also the part where a good sense of the paper's structure becomes invaluable.
A good bibliographic program that you've integrated into your research habits can also be invaluable - at the very least, it is going to be a big improvement over fumbling with styleguides (assuming you can even find the style guide) looking for the correct way to write a footnote for a book originally published in 1857 or the 3rd edition in a series. Or going back online to try to find the correct bibliographic information to cite the perfect quote on an index card that just has "Barns, Ethan, 1999" written at the top. Documenting the sources for the evidence you include and providing expert support for positions you've taken in the discussion are absolutely critical to good research writing, so you can't skip this part, however much of a headache it may give you. But if you've been using a program like Citation as an integral part of your research process, at this point, the tedious work of citing sources is finished. You'll just have to put keys (linking to bibliographic records) in your document to cite sources, insert the quotes where your outline indicates they need to be placed - and then "ask" the program to write your references for you.
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