ExploreTree, a processing program I’ve made for displaying and browsing tree data structures, has been rewritten and features have been added. New features include:

• Two modes of drawing: “slanted” and “radial” (see pics below)
• Two methods of avoiding overlapping node names: “nudge” and “hide”
• Dotted lines indicating more of the tree lies beyond an outer node
• Dynamic tree depth: adjusts depth so that there is never more than N nodes visible

Old features still there are:

• Search for organism & path highlighting
• Click to move to a node
• Forward and backwards movement with arrow keys
• Font adjustment & tree depth adjustment
• Right-clicking on a node (or control-click for Macs) opens up the corresponding Wikipedia page

The main version of the tree, a manually created tree I’ve made, is on the main site www.exploretree.org. Here is an image of it as a “slanted” tree with “nudged” nodes, near “rose” (to which the path is highlighted):

The original version of the program had no ability to display branching distances, but the new version does. You can see this when the it’s used to display a tree downloaded from Interactive Tree of Life website. Here is an image of this as a “radial” tree with overlapping nodes “hidden”, within Metazoa (aka. “animals”) and the path highlighted to Homo sapiens (aka. “human”):

In addition to the new features, part of the motivation for this update was that I can envision a lot of adaptations of this program for specific uses. The original version’s code was all entangled, making it extremely difficult to modify. This re-write has attempted to modularize the code a fair amount. At the very least this will make it easier for me to create spin-off programs from it in the future. Maybe a version that can read in “GEDCOM” genealogical data to make family trees — the age of the parent at birth can be used to determine branch lengths!

People often note how the internet enables hypochondria, by allowing you to see a multitude of conditions — some exceedingly rare — that happen to match your symptoms. But if you don’t abuse it I think it’s actually quite helpful.

I did a lot of walking today and this evening I noticed my left foot had a sore spot. I described it to Chris (verbatim, this is cut-and-paste from chat): “around my toes, on the left foot like… the joint where the knuckles are on the hand, around my third and fourth toes”.

I kept poking at it, wondering if it was bruised inside, trying to remember if I’d stumbled and banged it earlier in the day. So I tried the net….

It turns out this is an spot-on description of the localization of Morton’s Neuroma — weird scary name, but really a very common foot problem. My case is quite mild, I’ll take it easy and let the irritated nerve & inflammation relax. It can be caused by bad arch support — I’ve been told before that I should use arch-support inserts, so I should get a pair for these shoes.

Hah! It looks like there’s a protocol for DNA hybridization in blots using 5% Irish cream liquor! I kid you not. Here’s a sample quote from the methods of Yamamoto et al. 1993:

Hybridization was carried out overnight at 65°C in a solution containing 6 × SSC, 5% Irish cream liqueur (Original Irish Cream, R & A Bailey’s), 20 mM Na₂HPO₄, 20 μg/ml heat-denatured salmon sperm DNA, and 2 μCi/ml of the ³²P-labelled probe.

The original source appears to be Elbrecht, A. 1987, “Lab Hints: Irish Cream Liqueur as a Blocking Agent for DNA Dot Blots.” BM Biochemica, 4:12-13. BM = Boehringer Mannheim, it appears to be a newsletter. It’s too obscure for my cursory searching to turn up a copy of the original, I wonder what the motivation was! Maybe this way you can order liquor using grant money? This idea has a lot of potential…!

The New York Times has a nice article on flower evolution today.

If you enjoy looking at evolutionary trees to see how closely related different living things are, you might enjoy playing with ExploreTree. I’ve added features that make it a lot more fun: the zooming in and out is animated, you can search for an organism and follow a path. Plus now, with a little help from Chris, it runs on a webpage (feel free to show it to friends & family). Give it time to load, though.

Here is a snapshot of the location illustrated in the NYTimes article:

I’ve put off posting about the program for a while since I kept hoping to improve it a little more, but here it is. It was written in processing, you can get the code if you’d like to play with it here (or improve it!) on github.

Another social hour poster illustration:

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!

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. 😉

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. 🙂

The hard copy of the Nature Biotechnology with my article in finally came out, so here’s a pic of me posing with it. I designed the cover too, it’s an abstract representation of padlock probes capturing sites in bisulfite-treated DNA, with a color-warped photo of induced pluripotent stem cells in the background.

If you happened to stumble across this site because you’re interested in the profiling methods, please feel free to contact me. Of course, the news about 5-hydroxymethyl-cytosine kind of throws a wrench into the gears of any DNA methylation profiling studies.

Today I produce things of questionable value to society. Five cheezburgers pleez, kthxbai.

moar funny pictures