I’m currently trying to figure out how could I support the writing of a doctoral thesis manuscript with software tools. Here is what I’ve discovered so far.

The tools I currently use:

Microsoft Word. This is the basic workhorse for typing in text. I’ve used it so many years that escaping it is difficult, even though I’ve several bugs and problems with it. I manage to author my work with it in a quite productive manner, whence, I don’t see a reason to learn a new word processor at the moment (I’ve experienced quite many issues with the Open Office too, and the LaTeX based processors feature a steep learning curve).

Bookends. This is the software I use for references. I like it (despite it is not free), because I can manage the files and references locally. I used to use the free JabRef, but the exporting of the references in a proper format was not as smooth as I would like it to be. Bookends does much better work in integrating to Word, although, there are even better ones, such as EndNote, but it is way too pricey (~$250).

My current experiments include:

Mendeley. This is a reference manager, which appears quite simple and attractive. The issue with me is that I want to store my research articles (the PDFs) locally. I may develop a way to use this that takes advantage of the cross-referencing capabilities of the software. It shows effectively what is related to a particular article. This is the core feature I’m missing in Bookends.

Zotero. This is a free application, which functions as Firefox plugin. It integrates neatly to word. What I especially like is the way that it installs shortcut keys in Word that makes it easier to add citations and bibliography.

CiteULike. I found this handy for exploring connections, where different articles are related.

PS. I found handy instructions on how to make the short cut keys for the Scripts menu in Word. Check here how you can create the much needed feature in Word to paste without formatting (the example is for Macs).