October 20, 2014

Sci + Tech | October 17, 2011
Computer game contributes to science
Just this one though. Sorry.

Researchers in McGill’s Computer Science department have turned thousands of hours of procrastination into scientific data that could eventually advance our knowledge of genetic disorders.

As a result of conversations with an office mate at Massachusetts Institute of Technology, Professor Jérôme Waldispühl had the idea, while doing post doctoral research, of harnessing the power of humans to solve scientific problems in the form of a game. Could a game be created that would allow everyone – even people who don’t know any biology – to contribute their efforts to solving complex biology problems?

Waldispühl returned to the idea after coming to McGill in 2009. He teamed up with Mathieu Blanchette, a comparative genomics specialist and, together, they hired two students – Alex Kawrykow and Gary Roumani – to design such a game over the summer. The culmination of their efforts resulted in Phylo, the game that allows users to contribute to science by aligning genetic sequences. Launched last November, Phylo will soon be available as an app on cellphones and tablets.

Scientists arrange sequences of D.N.A, R.N.A, or protein in order to find similarities and learn more about how genomes have evolved over time. By locating where mutations may have occurred and where parts of genetic code have been conserved, scientists can learn more about the spread of genetic diseases in humans and other species. “To infer which regions of the genome are important, we need to compare them,” explains Waldispühl. Finding similarities in a region helps scientists identify the functional part of a genome. This is the goal of comparative genomics.

While computers can align the sequences, they don’t always succeed in finding the optimal alignment. The process is also time-consuming and very expensive. Humans, however, are better able to solve these visual puzzles, and they do so more efficiently. However looking at raw genetic data can be confusing, even for trained researchers, and would probably be akin to reading ancient Sanskrit scroll for most of us. That’s where Phylo comes in.

The idea behind Phylo is that players align coloured puzzle pieces vertically on a screen, essentially re-arrange regions of genomes. This fun game takes some of the burden away from geneticists. Players are essentially doing the grunt work for these researchers, giving them the data they need to make scientific discoveries.

One of Phylo’s best features is that anybody can play it; there is no scientific knowledge required. This is what sets Phylo apart from games like Foldit, a protein-folding game from the University of Washington that made the news recently after some of its players solved a puzzle that had plagued scientists for years. However, Foldit requires knowledge of some scientific principles, while Phylo does not.

Phylo has more than 16 000 registered users who have worked to solve over 300 000 puzzles. On high-traffic days, the site gets over 15 000 submissions, but on low days, only 300 to 400. Increasing Phylo’s popularity is the next step. Waldispühl and his colleagues hope to use Facebook to find more players and get them playing for longer periods of time. “The success of the project is only valid if we build a large and strong community where everybody participates,” Waldispühl said.

Phylo already has a Facebook group, where players can talk about the puzzles, interact with the developers, and even suggest potential game improvements. Once the game establishes a larger connection with Facebook, users will be able to compete and share puzzles with their friends. “The idea behind that is to integrate and use the social network as a base to grow… step by step we’ll be able to grow the network of people and have a community that communicates around this and continues to work on these puzzles,” Waldispühl said.

There are many groundbreaking principles built into the fundamental concept of Phylo: the transformation of a hard and complex science into a fun game for all, human computing, and most importantly the open and encouraged involvement of the general public in scientific research. Phylo and multiple-alignment sequencing could very well be one of the first of many biology games that lead to important discoveries down the road.

As for the gamers themselves, they’re a diverse bunch. Some play once; others spend hours solving puzzles that are more and more difficult. Phylo’s top user has completed over 6000 levels. “It’s pretty impressive,” Waldispühl laughs.

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