Before I get to work on writing of a substantial means, I would really like to have a good system in place for handling things. All I really want is:
- A way to mark up the document into sections
- A way to easily cite references (ideally drag & drop)
- A way to format that document similar to how XHTML and CSS work together
So in my browsing, I’ve found out that LaTeX is exactly what I was looking for in terms of separating the document content from the design. Unfortunately LaTeX has all kinds of ugly codes that are used in-text for doing this, which makes it sort of hard to read, and difficult to share with other not familiar with LaTeX. Generating a file in BibTeX format (which integrates citations and automatic bibliography generation with LaTeX) is easy, Papers does it… and so do BibDesk and JabRef (both free!). After a couple of hours playing around with LaTeX using TeXShop (part of the MacTeX bundle, or try MiKTex if you’re on Windows) and the wonderful “The Not So Short Introduction to LaTEX 2e” I was able to generate most of the document content I need.
Being in education, we’re required to follow American Psychological Association format for most journals, and therefore I absolutely adore the apa template (although it’s still following 5th Ed. APA style). I just recently discovered LyX, which is the closest thing to what I’ve been searching for. It generates the LaTeX underneath, leaving only the editable content visible, and offering a nice GUI interface for marking up the document. Sadly I haven’t yet been able to get the apa template to generate references properly, everything comes out as a “?” Once I track this down I’ll be happy with working in LyX.
Thinking ahead to the dissertation, I doubt I will be able to convince anyone on my committee, or my advisor, to start using LyX in order to review my writing. That got me to thinking about other places where I had seen working citations and the ability to easily comment/edit… Wikipedia! I need to check and find out if anyone else has written a script to convert wiki markup to LaTeX. That would be the ideal situation for collaborative writing as wikimedia has versioning, citations, commenting, and collaboration all baked in. Even better if the wiki citations could pull from a BibTeX file or BibTeX-formatted page.
I have to believe that someone else has gone down this road!

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Update: 12/17/2009
I found the wonderful Bibwiki extension for Wikimedia that comes awfully close to what I was looking for.
http://www.plaschg.net/bibwiki/
This will require me to keep a copy of my master bibtex file in the wiki, and perhaps go back through and wrap citations after cutting/pasting, or do a find/replace. But this is pretty close to what I was looking for, and the references can be hyperlinked if the DOI is available on the bibtex entries.
Giving it a try and will follow up with an update in the future