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I just finished my 7 part series about software and internet resources for research.
Part 1, “Inspiration for an Idea,” can be found here

part 2, “Literature Review,” can be found here,

part 3, “Research,” can be found here,

part 4, “Transcription”, can be found here,

part 5, “Analysis,” can be found here,

part 6, “Write up,” can be found here,

and part 7, “Publishing,” can be found here.

I hope to make the seven parts into wiki pages so that I can add resources as I learn about them and so that others may add their resources as well.

There are a few themes in almost each entry that I wanted to reiterate one last time. I mention the use of wikis and mind maps in many stages as a tool for organization, as well as maintaining PDFs in Yep.
Organization in research is very important and there are a lot of software and online tools that can help!

Related posts:
GTD – anthropology style
How to “network” as an (online) anthropology student