LaTeX

ByMatt

 

p' = \frac{w_{AA}p^2 + w_{Aa}pq}{w_{AA}p^2 + w_{Aa}pq + w_{aa}q^2}
 

This semester, one of my classes has required me to turn in all of my assignments in LaTeX. LaTeX (la-tek) is built on TeX, a typesetting language meant to produce beautiful documents reminiscent of the days when papers were printed from engraved plates. Typesetting was an art that got lost in the digital age.

When I first got the news that assignments were to be handed in using LaTeX, I admit I was a bit worried. The assignments were already going to be difficult enough since it is a bioinformatics class working with data types I have not been used to dealing with. On top of that, I’d have to learn a new system for typing up my homework. It has been a pain in the butt, but it has also been fun and pretty useful. One of the big advantages of LaTeX is its typesetting of mathematical formulas. It is easy and elegant, once you get used to the syntax. Anyone who has used the Microsoft equation editor that comes with Office knows it is a pain to work with. The point and click interface is slow and clumbsy. The LaTex looks ugly, but it also makes sense. The formula above reads as follows in LaTex:

p’ = \frac{w_{AA}p^2 + w_{Aa}pq}{w_{AA}p^2 + w_{Aa}pq + w_{aa}q^2}

The second advantage of LaTeX is that it can be completely integrated with R, the programming language that I use to analyze data. Natively, R outputs to plain text. But LaTeX integration with Sweave lets me run R code along with the TeX document and output data tables and graphics in a printable format, integrated with text. Plus, if I need to alter the R code, I can do so right in the Sweave document.

Lately, I discovered a LaTeX plugin for wordpress that allows me to make mathematical formulas in LaTeX’s math mode. There’s currently no math typesetting for html, yet the internet is a great resource for learning about math topics. Unfortunately, the LaTex doesn’t integrate as selectable text, but instead is output as an image, but it’s a good start for now. Perhaps I can make some future posts that involve some mathematical modeling of biological topics.

Since I have been using LaTeX for bioinformatics class, I have been using it to turn in assignments for other classes. It has been a useful medium for typing up Quantitative Genetics problem sets, and the presentation that I’ll be giving at Evo-Wibo in two weeks will be made using LaTeX. At some point, I’ll have to install Lilypond, a typesetting language for producing music notation.

I’m a nerd, and proud of it.

By the way, extra props if you understand the equation at the top of the page.

Similar Posts

  • 5000 feet

    It snowed in Moscow for the first time this season on Thursday. And although the accumulation didn’t amount to much in town, the mountains were turned white the next day. But two days of sunshine, and evidence of the snow is all but gone. The mountains around Moscow are back to their baren self. But at 5000 feet, winter has begun. Today I drove up to the Bald Mountain lookout tower on Palouse Divide, mostly to find a geocache, but also to enjoy the view, hike in the forest, and see just how much snow may have fallen at higher…

  • Gardening

    I can’t believe it’s July already. Time is flying by this summer. June has been a mixture of hot and dry with cold and rainy, and that has been good for my garden. Last year, I built two raised beds, each 8′ x 4′, but I only got one bed filled with dirt. It yielded some nice tomato plants that I had started from seed, until the goat got in and ate them down. This year, I got the second bed filled with dirt and built two more 8′ x 2′ beds which I filled with strawberry plants. The two…

  • December Update

    When I started this site, I never expected to make daily posts. Weekly? Maybe. Monthly? Less desireable. I’m kind of ashamed that it’s been three months with no updates, but there hasn’t been much of excitement to talk about. There haven’t been any big adventures this fall. I’m just plugging away at the Ph.D. thing, which has also made me uninspired to write here. So, here’s my update for now. It’s snowing. We had our first snowfall that actually stuck, and though it’s only a few inches, it’s enough to put on our boots and snow gear and go out…

  • |

    The Birds at our Feeder

    We get lots of birds in our trees in the front yard. This could be contributed to the source of food we are supplying to them. The list of winter birds is less than the summer residents. For example, I haven’t seen a bluebird in months, and most of the woodpeckers have left the yard too. And of course, the hummingbirds have gone since they don’t have the proper gear to tolerate the cold. But even with the few remaining species, watching the feeders has been a delight. In Idaho, we have the possibility to see four different kinds of…

  • Let it Snow

    Winter has made a comeback here on the Palouse. After several weeks of warm weather into the 50’s, the temperatures have cooled down, but the precipitation remains. The snow began Monday night, giving us only an inch or two, not much to worry about. But the snow continued throughout Tuesday dropping another two inches on Moscow. However, for every inch of snow that Moscow gets, Deary gets 2-3 times that, and so we had about 6 inches on our driveway when I got home Tuesday night. I got to use our new snow blower for the first time to clear…

  • Small World

    Harvest Moon, originally uploaded by Matthew Singer. Beth, one of the photo club members and employee at the Prichard Art Gallery downtown, mentioned at our last meeting that a student was in town with the current exhibit at the gallery. He didn’t know anyone and was desperate to hang out with people his own age. So we got a group together last night and hung out around the town. I thought the visiting student was an art student, but it turns out he’s actually studying conservation biology and had spent some time working environmental education. And, he’s from Maine. Well…