Thursday, February 7, 2013

Using Genetics and Google to Change How We See the Common Grunge

It's that time of year again: flu season. Everyone hates it. Countless stores stock up on cough suppressant and cough drops as customers buy them out. So it's at this time of year that great research, like that of professor of bioinformatics  Dr. Daniel Janies becomes necessary. Utilizing gene sequencing and algorithmic shortcuts, Before coming to UNC Charlotte Dr. Janies and his team at Ohio State University created a digital mapping of the flu around the world, known as Supramap.

Tasked by DARPA, Dr. Janies' research group worked to create a mapping of pathogens to display evolutionary biology over time and space. The team utilized homemade computers to create evolutionary trees of the pathogens. These trees are diagrams to explain the  evolution and relationship or organisms. Typically very large and hard to compute, Dr. Janies' complex trees required a significant amount of bioinformatic innovation: he and his team worked with computer engineers to create custom computers as well as to calculate shortcuts within the algorithms in order to speed up the process.

Dr. Janies and a colleague showing off Supramap
So why the flu virus?

"We wanted to make it relevant to the public, so we chose a pathogen that is well known," he says. The research started a few years ago, when genetic data on pretty much every organism was not only hard to obtain, but expensive to create as well. "We chose influenza because there was a lot of good data for it already available. It's easy to sequence and easy to compare sequences and we can get a lot of strains from all over the world." This data includes the location and time of the virus' emergence and spread as well as the host data, whether it was in a human or animal (remember bird flu?).
A Screenshot of the Supramap software
After obtaining all of this data, the team needed a framework to help display the time and space component in a logical, yet friendly interface, so as to bring the data out of academia and into everyone's hands.

"So we took these evolutionary trees and put the data into Google Earth. This helped us to create a weather map of the disease," says Dr. Janies. Using Google Earth visualization, the path of this virus could be mapped around the globe, showing how different strands move across space and time and allowing a user to see how it changes over time. Though originally starting with H5N1 -- the rarely documented bird flu strain, the team eventually tackled H1N1, one of the common human flu viruses. "Our diagrams looked like we had thrown spaghetti on the screen, so it became a challenge to rethink the visualization."

The Supramap framework is not only made for the flu. Dr. Janies hopes that the service-oriented framework will be utilized for other diseases as well. "We've put the software out there for people to download and run," he says. "We've also put it into a service-oriented architecture so that others can write to it. Or they can use our client. Supramap is now just a client to a web-service that runs these calculations." He adds, "our vision is that someone will use it for something we wouldn't have thought about."
The Supramap Workflow
Supramap is actually on display at the American Museum of Natural History.The link is here.

So what's next for Dr. Janies now that he's here at UNC Charlotte? Well he hopes to add some more to Supramap, expanding it utilizing the wet labs of the university's Bioinformatics building. Though appreciative to all those who helped with his previous projects, Dr. Janies says "it's nice to be able to create your own samples where you are rather than asking around." Dr. Janies is also working on the Tree of Life project, a program that works to create evolutionary tree groups for all organisms. He's currently working on the part that deals with echinoderms -- starfish and their relatives. "Echinoderms are some of our closest relatives among the invertebrates, and they have some amazing abilities," Dr. Janies notes. "Some can regenerate. So by digging into these trees we might be able to help better ourselves." There's going to be a lot more to be seen as Dr. Janies continues his work here at UNC Charlotte.

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