May. 1st, 2008

fyfer: (Default)
I like my Mac for many reasons. Life is so much better now that I can run analyses in a terminal window and work on a Word document at the same time. I wrote the first chunk of my thesis in Word quite happily. But when it came time to deal with inserting references and figures, I made a big last-minute decision.

My thesis is now in LaTeX. I've always enjoyed writing LaTeX, and I always assumed I'd write my thesis in it. But once I had so much written in Word, it seemed like a hassle to switch.

Not so! Almost everything was plain text, with no equations and very little text formatting. Copying it into emacs was trivial. With some help (and moral support) from Nick, I found the MacTeX package. Now life rocks. I write in my shiny native emacs that verges on wysiwyg in tex mode (superscripts are super!), I save my pretty figures as pdfs in Illustrator, and then I just run pdflatex on the commandline. Everything is where I want it and looks clean and professional. And even better, a friend gave me "thesis in a box", a set of templates and configuration files for University of California theses. Now I don't have to worry about the title page format or any of that.

And as for references... I've used EndNote before and liked it, but no one had a copy I could "borrow", which is part of why I gave up on Word. I've never used BibTex. It's always scared me. But then I discovered BibDesk. This is amazing. It can do everything EndNote does (in particular, search PubMed remotely) and I just paste the citation strings into emacs. I even found some bst files to make the references section look like I want.

This is working so well that it makes me sad that most biology journals don't accept LaTeX submissions.


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December 2010

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