Monthly Archives: May 2009

Harvard Genetics Retreat 2009

Was kind of sad this year having a “retreat” in a slightly different building in the same city. I amused myself by constructing a genetics “buzzword bingo” list.

  1. Slide showing a signaling pathway with >= 15 proteins named
  2. Messing with this gene causes cancer
  3. Anything involving stem cells
  4. Microarray data
  5. High throughput / deep sequencing
  6. RNAi
  7. Animal model vaguely resembling a human disease
  8. GWAS
  9. Messing with this gene makes this tissue/organ look funny
  10. Epigenetics
  11. Mass spec data
  12. FACS
  13. Evolution
  14. A photo that makes you lose your appetite
  15. Apoptosis is mentioned
  16. HAIRBALL (aka. “interaction network“)
  17. Anything related to sex (eg. chromosomes)
  18. RNA splicing
  19. Bacteria
  20. Yeast
  21. Plant
  22. Worm
  23. Fly
  24. Fish
  25. Mammal

Although silly, I found this actually helped keep me paying attention to talks. I applied it to the last session and almost got a BINGO, but Norbert Perrimon’s signaling pathway slide only had 13 proteins. So close!

Evolutionary Time

This last Saturday Chris and I participated in a code jam organized by a friend using processing, a programming language oriented towards enabling interactive visualization and graphics. I used processing to create all of the graphs in the recent Nature Biotechnology paper – I came to it because I was frustrated with an inability to create exactly the graph type I wanted. In the end each of my graphs is created by a small program, but I’m happy with putting in that effort to get something that looks great.

For the code jam I had been wanting to create a browsable tree of life akin to the fractal-like tree of life comic I made a while back. To this end I created a Newick format tree, working my way back from humans. I filled in only organisms and names that were familiar to me, reasoning that obscure organisms only serve to make a tree confusing, cluttered, and unapproachable. So far I’m only as far as unikonts, you can get a copy of it here if you like. (Please consider this as licensed under CC-by-SA if you’d like to use it.)

Chris found and applied some java code for interpreting a newick format file and creating a tree data structure, and I worked out a simple recursion for drawing the tree out to a given depth from a given node. Clicking on a node redraws the tree from that location; pressing any key zooms back out by one level. Here is a screenshot of the base:

One of the nice aspects of processing is that visualizations should be portable to java applets. Although we haven’t done it yet, hopefully we’ll be able to do that. If you have processing installed, you can download a copy of what we wrote. (You’ll need to fix the file path in the source code to point at the tree.) Other improvements I’d like to do: to make zooming smooth rather than jumping (this can be disorienting when a large change occurs) and add the ability to search and choose an organism, then color the tree according to distance from that organism so you can click “warmer” colors to get closer to it.

The theme of the event was “clocks” and although I had intended to work on this anyway, it did fit into the theme fairly well: we called the program “Evolutionary Time”. We were thrilled to be awarded the “wealth” prize by processing founders Ben Fry and Casey Reas: a gift certificate to the MIT Press Bookstore, which I intend to spend on a reference or two for processing, hopefully to further improve our program. ;-)

YouTube meme becomes scientific study!

You may have seen him before: Snowball the Dancing Cockatoo. ScienceNOW Daily News reports on a Current Biology study – a neurobiologist went to study the bird and sees dancing as a phenomenon connected to the ability to imitate sounds. A companion paper looks for dancing ability in a number of animals, but only found it in animals that were able to vocally mimic sounds.

If you haven’t watched the video you definitely have have to. If you have… it’s worth watching some again. :-)