Video tip of the week: OneZoom viewer for large phylogenetic trees
For this week’s tip, I’ve changed things up. I had something else planned, but as folks on Google+ last night were discovering and enjoying this new software, I decided to bring over this video on OneZoom, a new “cool tool” for exploration of the phylogenetic relationships of species. It’s an interactive viewer for larger phylogenetic trees.
This tool uses fractal strategies to enable users to zoom and scroll around the tree of life. You can quickly get a large overview, and then navigate down to precise and specific nodes on the tree. It’s very slick. The first video gives you an overview of the project and the theory. A second video they call a tutorial offers more specifics on how to interact with the software.
There are two reasons I’m glad to see this: 1) we definitely need new visualization and organization strategies with all the “big data” coming our way. And 2) they make that case that I keep making:
Much of the difficulty with phylogenetic tree visualization (and with data visualization more generally) is that we all too often constrain ourselves to the “paper paradigm”—the practice of displaying data in ways that are optimized for printing on paper.
Beyond the paper paradigm. Or, as I keep saying, the data is not in the papers anymore. It’s in the software and you have to use the software tools to explore it and take it further. And often (as was the case with ENCODE) the data is available to you long before publication–but unless you know the way in, you’ll miss out on great opportunities by waiting for the papers to come out.
In this case they assess the state of other phylogenetic visualizations as well. They describe what drove them to the solution they’ve come to–something like Google Earth for species evolutionary relationships. You can use the software to scroll around and zoom in, but there’s also a search function to go right to places of interest. Currently there are over 5000 species of mammals, and their “coming soon” section says 5000 amphibians are on the way. The goal by 2014 is approximately 2 million species.
This second “tutorial video” gives more specifics on how to interact with the software:
It is a very cool tool described on the community page at PLoS Biology. They say it’s the first in a series of a new “Cool tools” section. Excellent–I love cool tools! It’s a bit funny to me though that the YouTubes aren’t embedded in the paper as figures. Go figure….
From the Software page (http://www.onezoom.org/software.htm ) you can access both the mammal tree, and a bacterial tree with over 400,000 species. And there you’ll also see instructions for viewing your own data.
I think it will be a very engaging educational tool. What’s not as clear to me is if this will drive discovery and enable people to go further. Slick displays are great–but they are always not enough to enable further work and analysis to ensue. That may be the case here, and their planned directions will also take it further. In the meantime, it’s probably enough to have creationists minds blown…heh.
Follow them on twitter for updates: https://twitter.com/OneZoomTree @OneZoomTree
Rosindell, J., & Harmon, L. (2012). OneZoom: A Fractal Explorer for the Tree of Life PLoS Biology, 10 (10) DOI: 10.1371/journal.pbio.1001406