EteRNA

From EteRNA WiKi
(Redirected from What is EteRNA)
Jump to: navigation, search

 

Contents

 

EteRNA

See also: An overview of EteRNA

EteRNA is a collaboration between scientists at Carnegie Mellon University and Stanford University that crowdsources the computationally challenging tasks of RNA design and structure prediction. The EteRNA game consists of puzzles, lab activities, player projects, strategy design, and community support.

 

Puzzles

Main Article: Puzzles

Puzzles consist of a target structure that players attempt to satisfy by the placement of different nucleotides. An additional degree of difficulty and/or realism is afforded by a variety of restrictions placed on player solutions.

 

Lab

Main Article : Lab

The RNA Lab is a section of the game where player-designed RNAs are synthesized and scored according to their folding accuracy. In lab, players design sequences to fold into a given target structure. The EteRNA community then votes on player solutions to determine which are ultimately synthesized. In each lab, computer-designed RNAs are synthesized as well. The performance of players frequently surpasses that of state-of-the-art RNA design algorithms.

 

Scoring

Players are awarded points for the successful completion of puzzles and, eventually, their contributions to lab. At 10000 points, players unlock the ability to contribute to lab. At 20000 points, players unlock the ability to design their own puzzles. Players can also track their rank in the EteRNA community as they continue to gain points.

 

Why are we designing things?

Basically no one knows how 'best' to make particular shapes in RNA so if you need a particular shape which bases go where is a puzzle. The Eterna game is a simulation which lets us try to solve the puzzle. First you learn how the Eterna simulation works (tutorials and simple puzzles) then you try to push the boundaries of the simulation (solving and creating player puzzles) then you go to the labs and try to solve the real world puzzles (still within the Eterna simulation) Then those solutions that are voted most interesting/likely to succeed actually get made in a real world lab and then the results come back to us (the players) and can be interpreted (this is actual real science!) to try and work out for next time which solution is most likely to actually succeed, then feeding back into the player knowledge improving designs and eventually the eterna simulation itself.

 

What are Vienna and Rnassd?

They are programs that try to give you an idea of how well your design will work. Rnassd is one simulation program, Vienna is another simulation - if you put your current suggested solution from the Eterna simulation into that simulation you get a second view of how likely it is to work Note that is just a model too - and some ideas outside the models may also be equally likely or unlikely to work). Just that if it works in all the simulations then it's probably going to work in the real lab some of the time. If you want to check out the vienna program there is a link to a guide for it here

External links

Personal tools
Main page
Introduction to the Game