Monday, 25 March 2013

The genome game

We've made an HTML5/Javascript educational game for teaching children about bioinformatics. You can try out the game on our webserver, or download it, fork it and develop it for your own purposes.

The idea is that we have 4 binary digits controlling 4 aspects of a cute creature's phenotype (eye colour, head colour, body colour and number of legs). The binary digits are big clickable buttons, which toggle the bit value and correspondingly change the creature. We can use this initial button-clicking exercise to talk about combinatorics and binary numbers: how many different creatures can be made by changes to 4 bits?

Then we show the underlying rules. These are the equivalent of "if-then-else" rules, defining how the bit values control the phenotype. The rules can be changed, so the children can choose which bit controls which characteristic, and also choose colours and leg numbers.

The genome game at National Science Week

Finally we can "Make population". This creates a random population of 5 creatures, all generated from the current set of rules, and it hides the rules. Now the game is to have a friend who didn't see the rules guess what the underlying rules were. They can see the 5 creatures and the genomes of each creature. Sometimes it's easy to work out the rules, and sometimes the rules can't be completely determined. It depends on the random 5 creatures. Sometimes all the creatures with blue eyes also happen to have 6 legs, and then we just can't tell which of the 4 bits is responsible for which characteristic.

We finish up the discussion by asking how many genes the children think are in baker's yeast (approx 6,000, easy to get hold of a bag of yeast, and they can guess what it is and what it does). They'd guess at "1? 2? 4? millions?" After this we asked them to guess how many genes in a human (approx 20,000). And describe how about 16 genes are actually responsible for your eye colour, not just one. And finally, ask how many genes in wheat (current estimate approx 100,000 or more). The look of astonishment at the complexity of wheat was a common reaction, quickly followed by "Why?". So we tell them that's what scientists are currently trying to find out: what do all our genes or the genes in yeast or wheat actually do? How many representatives of a population would scientists need to determine what the 100,000 genes in wheat do? And we tell them that if they want to work in bioinformatics when they grow up, then they could find out the answers for themselves.

Wheat and yeast: how many genes do they have?

How did this game come about? We have a BBSRC funded project on the application of multi-relational data mining to the problem of finding which parts of an organism's genotype are responsible for its phenotype. This problem is often called GWAS (genome wide association studies) or marker-assisted selective breeding. As part of the application for funding, we said that we'd do some public outreach activities, making a bioinformatics game for children that could be used as part of the Technocamps activities, and represented the research problem that we were working on. The game is obviously a highly simplified view of the research, but still does give an idea of how hard the problem is!