Research Profile – Gaming for Science

McGill researchers are developing online computer games to help analyze large amounts of genetic data.

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Can thousands of online computer gamers help scientists solve complex genetic puzzles?

Genetics research often involves looking for similar patterns in huge amounts of genetic data, according to Dr. Jérôme Waldispühl, assistant professor of computer science at McGill University and head of the Computational Structural Biology group.

“We can design computer programs to do this, but they tend to be slow and don’t always give the best solution,” says Dr. Waldispühl. “Adding in human brain power helps with this type of task. People-power and computer-power are complementary.”

Researchers who are trying to match certain aspects of genes need to sift through vast amounts of information. Simply assigning a handful of scientists to do the matching isn’t very practical and wouldn’t get very far, according to Dr. Waldispühl.

This is where online gamers could prove incredibly useful. By turning tasks like pattern matching into online computer games that can be played by tens of thousands of people, researchers can get results fairly quickly. It also helps free up scientists so they can work on other aspects of the research.

"We start with a big problem in biology, we cut it into a lot of small pieces, and we can distribute it all over the world into video games," he says. This sort of ‘crowd-sourcing’ approach to doing science is becoming more common, with existing projects relating to astronomy, physics, environmental science and more already online.

Dr. Waldispühl’s team has already launched one such computer game, called Phylo. It went online in 2010 and currently has about 30,000 registered players. Dr. Mathieu Blanchette, assistant professor of computer science is co-supervisor of the project.

“Not all problems can benefit from this divide-and-conquer approach. But the problem we address works,” says Dr. Waldispühl.

The game was developed to find similar patterns between sequences in DNA, RNA and proteins in different living creatures. The matching of these sequences is referred to as multiple sequence alignments (MSA). Learning where similar regions are helps researchers better understand the structure of genes, and how they work.

Players don’t need to understand any science to play Phylo; they simply have to match brightly coloured squares to other squares of the same colour. Since the game’s launch, researchers have received close to 600,000 solutions to MSA problems. The information is helping identify the genetic roots of a wide variety of diseases, ranging from Alzheimer’s disease to cancer.

"You can take whole genomes and compare them to each other. There are sequences in humans, fish and [other] animals that are conserved [the same] and have functions," says Dr. Waldispühl. The research can also shed light on how genetic sequences have evolved.

Sections of genetic material that line up show "regions that have been conserved during evolution between species. If some regions are identical between all species, there is probably a reason for that. One possibility is that these regions are functionally important and that a mutation in these regions may create a metabolic disorder,” he says.

The researchers are now starting work on developing games that will use the same crowd-sourcing concept to solve other genetics-related issues, such as identifying regulatory regions in the genome and more.

"Games are a natural interface between people and computers. Such scientific games have terrific potential to solve complex problems arising in molecular biology," says Dr. Waldispühl. Better yet, people playing the games not only contribute to science but have fun.

“We start with a big problem in biology, we cut it into a lot of small pieces, and we can distribute it all over the world into video games.”
- Dr. Jérôme Waldispühl, McGill University