Goodbye 2013!

Retrospective blog post time, again! 2013 was a fine year. I was lucky enough to go to Bolivia:

…and to the Everglades in Florida to see manatees and gators, and to Knoxville, Tennessee for the AAPA meetings and the Great Smokey Mountains. With a bunch of great collaborators, I coauthored a papers on RADseq in primates, protein-protein interactions, and the use of phylogenetics in primate behavior. In our lab, data collection kicked into (relatively) high gear by prepping and sequencing about a dozen “next-gen” libraries full of primates. Amazingly, they all worked!

A big change in 2013 for me outside of the lab was to restart learning Spanish using the site, italki and to begin to learn halting French using Duolingo. The Spanish certainly came in handy in Bolivia (and Florida) and I hope the French will be equally useful if I ever work in Francophone Africa.

This here blog is just over a year and a half old. A bunch of folks (almost 30,000) visited this site from all over the world this year which always makes me happy. C’mon, though, Greenland! You’re STILL a lot of grey in this map projection.

Happy 2014!

New Year’s Resolutions

When I was still taking courses, plenty of resolutions arose during the interstitial spaces between semesters. Naturally, I failed at many life changes in spite of my determination, but such is the nature of grad school. Now in the nebulous time post-classwork and pre-thesis writing, a marginally wiser version of myself comes up with the following, more modest goals.

  1. Write better code

    This is actually two interconnected goals: write code that works better and code that looks better. To improve my chops I’m working through the bioinformatic problems at Rosalind and slowly reading up on the topics covered by “What every computer science major should know”. But elegant code that others can easily build upon also requires the use of conventions and standard practices, which often are absent in the TMTOWTDI world of Perl. For that I’m finally reading Perl Best Practices. (I am already uncomfortable about their suggestion to put “else {” on its own line, for the record.) Better code is better used, which leads to…

  2. Publish more code

    I’m always so happy when people use code I’ve written, but so many of my scripts languish in disuse, written for a single problem and squirreled away somewhere on my hard drive. Publishing scripts under an open source license forces me to clean up and generalize the scripts. Plus transparency makes for good, reproducible science. I resolve to make more public, even if the scripts aren’t the prettiest and a wee bit embarrassing. May my long list of bug fixes in the code repository inspire others to publish code without shame. Speaking of which…

  3. Use version control more frequently

    I am embarrassed to admit how late I started using version control, but now I use it religiously for big coding projects (with Google Code for open source works and Assembla when I want to hide my dirty laundry). I’d like to use it more for non-code documents, like CVs. This means throwing off the shackles of Word more often, which leads me to…

  4. Write more in LaTeX

    Again, a technology I came to later in the game, I’ve written my CV and one forthcoming paper so far using LaTeX. I love having the paper grow alongside the scripts in the SVN repository, which was encapsulated by this visualization around the time I was writing the last paper. This lets you avoid this problem, a major pet peeve of mine. I hope to write my thesis in it, and deal with people who require Word format by converting it with pandoc.

  5. Set up rsync backup

    I’d like to roll my own Time Machine replacement using the Unix utility rsync, mainly because you can’t exclude folders from Time Machine. I often eject it in frustration when it tries to backup some multi-gig file in the middle of my workday. Redundant off-site backup for essential files is important, and daily backups of less important items are nice, especially if they take place at 5 AM. A smarter person would have used the time spent writing this post to set that up.

  6. Improve math ability

    It’s fading fast, after about a decade outside of a math class. Hopefully this online course will help. Finally…

  7. Collaborate/Network more

    Viewing the Ph.D. project as a solitary pursuit hinders collaboration and is at odds with how the best scientists operate. I’d like to bug colleagues more with questions about their work or proposed collaborations or just to introduce myself. To steal a quote from a good friend who’s helped me immensely in the past:

    “It is undoubtedly the case that the best scientists are the people who know what questions to ask, first and foremost. And secondarily, but almost as important is knowing who to ask for help with addressing the questions.”

Goodbye 2012!

Retrospective blog post time! 2012 was a fine year. I coauthored a paper, made some progress on a few more, started this here blog, went to the Congo, wrote a lot of code, and hopefully secured funding for my Ph.D. project. A bunch of folks visited this site from all over the world which always makes me happy. C’mon, though, Greenland! You’re a lot of grey in this map projection.

Here’s the highlight reel of the most popular pages, the top 13 in honor of 2013. Thanks for visiting and Happy New Year!

  1. Geometric Line Designs in R
  2. Similar Image Mosaic
  3. Lesula, New Monkey Species
  4. Preparing an Academic CV in LaTeX
  5. Repetition Code Demonstration
  6. Darwin Primate Mosaic
  7. Drawing Hats on a Monkey with Mechanical Turkers
  8. Primate Pet Legality Map
  9. ISIS Map of Mammals in Zoos
  10. World Map of IUCN Primates
  11. Markov Text Generation
  12. Chromosome Ideograms
  13. 3D Map of Global Treecover