Game helps scientists fight ash disease
By David Szondy
August 14, 2013
Playing video games and feeling virtuous may seem almost like a contradiction in terms, but the Sainsbury Laboratory in Norwich, UK has turned gaming into a way to advance science and help protect the environment. The Fraxinus game is a Facebook app that uses player participation to figure out the structure of a fungus genome, as part of a crowdsourcing effort to combat a disease that threatens Britain and Europe’s ash trees.
The frightening thing about diseases is that they have a habit of popping up out of nowhere. Ash dieback is one such disease. The Chalara fungus (Hymenoscyphus pseudoalbidus) first surfaced in Poland in 1992 and wasn't even described until 2006. However, during that time the disease had already spread across northern Europe to the British Isles, where it threatens to destroy up to 95 percent of Britain's ashes.
The Open Ash Die Back project includes the Sainsbury Laboratory, the Genome Analysis Centre, and the John Innes Centre, and is funded by the Biotechnology and Biological Sciences Research Council (BBSRC). It's looking at how the fungus kills and how to combat it by studying the nucleotide sequences that make up the fungus genome.
“Understanding tree diseases at the genetic level could provide a chance of recovering from this epidemic, as well as other threats to our native populations, in a way that was not available when we experienced Dutch elm disease,” says principal pathologist at Forest Research Dr. Joan Webber.
Unfortunately, this is an extremely difficult task to carry out directly because DNA analysis can only deal with very small strands and the process destroys those strands. Therefore, the team’s approach is to generate models of the fungus genome and then compare these models to the actual nucleotide strands to see how closely they match.
There’s another “unfortunately” at work here, because this matching is itself an extremely large task involving 60,000,954 nucleotides. That means it needs to be outsourced or, to be more precise, crowdsourced.
Crowdsourcing experiments has come a long way since the SETI project released its screensaver in 1999, to help process data in the search for intelligent life in the Cosmos. Recently, the approach has been used to plot the genome for a new strain of E. Coli that broke out in Germany, as well as many other projects. Most of these have been requests for people to donate time on their computers via screensavers or similar software that does calculations when the machines are otherwise inactive, but that’s not what’s needed to fight ash dieback.
“Computer power alone is not the answer to making the most of our data,” says Dr. Dan MacLean from the Sainsbury Laboratory, who came up with the Fraxinus game. “An awful lot of human expertise and knowledge has to be poured on top and with this game we can start to include the non-specialist.”
The Fraxinus game is named after the ash tree (Fraxinus Excelsior) and has been under development since December 2012 by the firm of Team Cooper. What’s different about it is that it doesn't use the computer to solve the problem at hand, but the player. That’s because humans are very good at pattern detection, so Team Cooper came up with a game that is both addictive and competitive as a way of getting eyes on the screens.
The game consists of a small genome segment and underneath this are the actual strands for comparison. The game provides an approximate match and it’s the player’s job to improve this by moving the sequence right or left and swapping or removing bits. The player with the best match can “claim” the sequence, though higher scorers can take it away. To improve the competitive angle, the player can invite friends to play along. The highest scorers will earn a credit in publications of results.
“Each play of the game will contribute a small but useful analysis,” says MacLean. “The more people who play it, the more accurate the results will be for us and the quicker we can generate the information needed to help our woodlands recover from the current epidemic.”
The game can be found on Facebook.
The BBSRC video below introduces the Fraxinus game.