Tuesday, August 7, 2012

TeX Stack Exchange: preview-latex does not function

I have previously mentioned Preview-Latex and AUCTeX. I was trying to set it up on the work computer, but the previews weren’t showing up properly. I thought I had had the problem before, but it was a different problem. This TeX Stack Exchange question had the answer, though: disable SAFER for Ghostscript. I do not know why this works.

Wednesday, December 14, 2011

Allow me to recommend latex-diff and latexbatchdiff

I do almost all of my technical writing in LaTeX, and I do revision control on everything with git. Unfortunately, tracking changes in revisions is very difficult in LaTeX. Maybe I make a change to a single word in a paragraph: a naive diff on the .tex file shows the entire line as being changed, and, even worse, then I just have the diff as plaintext, not something I could show a non-LaTeX user.

latexdiff is able to overcome this, automatically generating indications of changes, like Word’s change tracking system: new words show up as blue and underlined, deleted text is red and crossed-out. (How the changes are indicated is configurable, with several default styles to try.) latexdiff has two shortcomings, though. First, if I’m using version control to manage revisions, I have to manually save old .tex files off to the side so that latexdiff can find them. Second, latexdiff only works on single-file LaTeX documents. I like to put each section in its own file.

latexbatchdiff fixes both of these things. I just typed,

latexdiff-git 1ca0 head.tex abstract.tex acknowledgments.tex\
    introduction.tex methods.tex results.tex conclusion.tex

and it generated a marked-up PDF. (1ca0 is the start of a SHA for a previous revision.) It’s fantastic.

Friday, April 1, 2011

On “Antedisciplinary” Science

In PLoS Computational Biology, Sean R. Eddy wrote a Perspective, ["Antedisciplinary" Science](http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010006), on how to think about emerging interdisciplinary fields in science. In particular, he is concerned with the rising expectation that research groups have members from distinct disciplines, say a team with a biologist, a computer scientist, and a physicist. He contends that, in many cases, it is more effective to have teams of generalists. This is important to me because I feel like my job is a combination of numerical analysis, mechanics, computer programming, and biology: I think this is awesome. I get bored easily, and I'm delighted that I have a job in which I get to do a lot of complementary things.

Friday, November 5, 2010

Allow me to recommend AUCTeX, preview-latex, and Vincent Goulet's Emacs for OS X Modified

I am wanting to start typesetting my articles in LaTeX rather than using Pages+Endnote+Mathtype or, worse, Word. I don't like the LaTeX writing process of write, run LaTeX, run LaTeX again a couple of times to get the equation numbering correct, convert the dvi to a pdf, open the pdf, find a typo in an equation, cry, go to the bathroom, make a cup of tea, write some more. AUCTeX is a package for Emacs that makes it easier to write LaTeX with handy keyboard shortcuts and syntax highlighting, for example. Most notably, AUCTeX comes bundled with a tool, preview-latex, which presents rendered math equations in-line.

This requires a GUI-enabled Emacs. On the Mac, Cocoa Emacs is the most current. Vincent Goulet has prepared a special build of Cocoa Emacs, Emacs for OS X Modified, which includes AUCTeX as well as ESS and psvn if you're interested in those, too.

I don't know if this is a common problem, but for my installation, preview-latex didn't work properly until I disabled TeX-PDF-mode by C-c C-t C-p or adding (TeX-PDF-mode nil) to my .emacs file. I got the idea from this mailing list discussion.

Monday, May 31, 2010

Allow me to recommend Cyberduck

Price: Free

Cyberduck is a reliable, easy-to-use FTP, SFTP, S3, etc. browser for OSX. And you get a cute rubber duckie in your dock! I used to use Fugu, and I find Cyberduck to be much more pleasant.

Sunday, May 23, 2010


Check out my Buzz profile.

Thursday, May 20, 2010

Most confusing chart of the day

The most confusing chart of the day award goes to:
Ide Orientation development in thermotropic liquid 2004.pdf (page 4 of 6)
Uploaded with plasq's Skitch!

from Ide and Ophir. Orientation development in thermotropic liquid crystal polymers. Polymer Engineering and Science (2004) vol. 23 (5) pp. 261-265. Depicted are three values (tensile modulus, tensile strength, and area reduction) for five datapoints. Three scales appear on two y-axes. I think that this plot means that the tensile modulus for the extrudate decreases with increasing shear rate; I'm not sure why I should care about the other two variables because they don't look like they change very much, but it's hard to tell, because they are also on a smaller visual scale than the tensile modulus.
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