EteRNA – RNA Folding Game Used for Research

Folding and crowd-sourcing projects for research have been springing up for a number of years. Folding@Home became a household name due to its integration with the PlayStation 3 as a screensaver. The algorithms used for these projects are often inefficient, requiring massively complex computations for seemingly simple tasks. EteRNA; a project from Carnegie Mellon and Stanford Universities, is a new breed of computation system; instead of performing these complex calculations, it gives you the ability to interact with the simulation and solve problems yourself.

Ever looked at a folding project and thought to yourself “I could do that”? Well, now’s your chance. EteRNA is a game that puts you in control of the folding, matching up nucleotides to form RNA or ribonucleic acid – DNA’s unstable cousin. Expressing RNA in a 2D format; comprised of 4 different colored nucleotides, you can configure them to form patterns, from simple crosses to elaborate trees. You don’t need to understand the biology behind it to play the game, the rules are very simple and a large collection of challenges exist for you to practice on.

The human brain is much better equipped for pattern recognition than computers, from repeating numbers to image comprehension, so why not take advantage of this? Various projects such as Foldit and Galaxy Zoo have used this crowd sourcing method before, and in the case of Galaxy Zoo, used to great effect, processing over 50 million images of stars and galaxies within a year, with the help of 150,000 people.

Creating these simulations and solving puzzles is all well and good, but this is when EteRNA does things a little differently. After you have completed the tutorial and earned enough points from challenges, you can enter the ‘RNA Lab’. A folded shape is presented and it’s up to you to find the best way to solve it, or vote for an existing solution. Each week, the 8 highest voted solutions are taken to the lab and folded for real, with the results published a few days later. This then gives you and the community, the opportunity to see how well the computational model holds up, allowing for changes to the system to be made. The shapes are simple to begin with to allow for fine tuning of the model. As the weeks progress, more exotic RNA will be presented for simulation.

This real world part of the project is what really sets it apart from the others, seeing the results of your actions, but it does bring a few things to attention. RNA is used in various biological processes, from cellular control to protein synthesis. Creating new forms of RNA through simulation and then in the lab for study does make one wonder if it is at all safe, since we have no way of knowing what this new RNA will do. The other important point is, who will be responsible and claim ownership of these new RNA samples since this is publicly generated research.

The project is still in development with a number of bugs and feature requests already made. If you are not interested in participating in the research element, then the game itself is still fun to play. I have already put a fair few hours in, solving the numerous challenges. various help guides and tutorials have already started to appear. The game is flash based and runs inside your browser and includes a built-in chat system. Hit the source link to participate yourself.

[Currently due to popularity, the servers are feeling the strain and will be rather slow]

By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!