Mad Prime: Tag programming

ExploreTree update

Madeleine Ball — Thu, 18 Feb 2010 16:45:00 -0500

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!

ExploreTree & pretty flowers

Madeleine Ball — Tue, 08 Sep 2009 23:13:00 -0400

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.

Evolutionary Time

Madeleine Ball — Tue, 05 May 2009 02:44:00 -0400

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. ;-)