EteRNA
 | |
| Developer(s) |
Carnegie Mellon University Stanford University Rhiju Das Adrien Treuille Jeehyung Lee Peter Kinney Snehal Gaikwad Minjae Lee Daniel Cantu Ming Yao Travis Mandel Chris Vanlang Te (Ford) Hu Alex Limpaecher Ann Kladwang Noah Fishel Sophie Wang Jackie Gu Elyse Kelly Matt Baumgartner Stephanie Federwisch Skanda Mohan Jonathan Ciscon Benjamin Bethurum Kyle Beauchamp David Klionsky Eric Butler Aarti Singh Ranqi Zhu Martin Azizyan Caleb Geniesse |
|---|---|
| Initial release | 2010 |
| Development status | Active |
| Available in | English |
| Type | Game with a purpose, Puzzle |
| Website | http://eternagame.org/ |
EteRNA is a browser-based "game with a purpose", developed by scientists at Carnegie Mellon University and Stanford University, that engages users to solve puzzles related to the folding of RNA molecules.[1] The project is funded by the National Science Foundation.[2]
Similar to Foldit—created by some of the same researchers that developed EteRNA—the puzzles take advantage of human problem-solving capabilities to solve puzzles that are computationally laborious for current computer models. The researchers hope to capitalize on "crowdsourcing"[3] and the collective intelligence[1] of EteRNA players to answer fundamental questions about RNA folding mechanics. The top voted designs are synthesized in a Stanford biochemistry lab to evaluate the folding patterns of the RNA molecules to compare directly with the computer predictions, ultimately improving the computer models.[2][4]
Ultimately, EteRNA researchers hope to determine a "complete and repeatable set of rules" to allow the synthesis of RNAs that consistently fold in expected shapes.[5] EteRNA project leaders hope that determining these basic principles that may facilitate the design of RNA-based nanomachines and switches.[6] EteRNA creators have been pleasantly surprised by the solutions of EteRNA players, particularly those of nonresearchers whose "creativity isn't constrained by what they think a correct answer should look like".[7]
As of 2016, EteRNA has about 100,000 registered players. [8]
Gameplay
Players are presented with a given target shape into which an RNA strand must fold. The player can change the sequence by placing any of the four RNA nucleotides (adenine, cytosine, guanosine and uracil) at various positions; this can alter the free energy of the system and dramatically affect the RNA strand's folding dynamics. In EteRNA, different restrictions, such as those on the number of certain bases and the number of the three base-pair types, as well as locked bases, are sometimes imposed. A molecule is occasionally also included, which binds with the RNA and has critical effects on the free energy of the system. In some more advanced puzzles, players may be presented with two or three different target shapes at the same time; the single sequence the player produces must fold in the respective shapes under different conditions (presence or absence of a binding molecule).
EteRNA puzzles are roughly classified into three types: Challenges, Player Puzzles, and Cloud Lab. Challenges are the puzzles prepared by the game-makers to introduce players to the workings of EteRNA as well as to provide series of pre-set puzzles for players to attempt. Player puzzles are generated by players, and Cloud Lab is where the active, proposed and archived laboratory projects are presented for players to review, vote or attempt.
Once players have completed a sufficient number of RNA puzzles, they unlock the chance to generate puzzles for other players. These puzzles can be selected as future synthesis candidates if they fit certain rules and prove interesting. Other more complex puzzles are not currently lab synthesis candidates.
Accomplishments
- As of August 2011, approximately 26,000 players have contributed RNA sequence designs and over 306 designs have been synthesized for in vitro testing.[9]
- In January 2014, the results from EteRNA have been published in the PNAS journal, with "EteRNA participants" listed as co-authors in the paper.[10][11]
- The EteRNA gamers beat the supercomputer-powered algorithms in solving all the 100 RNA secondary structure design challenges while the best score of the six algorithms used is 54. By manipulating the chemical sequences of RNA the gamers created stable forms of desired shapes. The strategies designed by the players identified specific structural features that make inverse RNA folding difficult. The EteRNA researchers hope that by integrating their strategies into algorithms, improvement in automated RNA secondary structure design can be achieved. The results of the challenges were published in the Journal of Molecular Biology on February 2016. [8][12]
See also
References
- 1 2 "RNA Game Lets Players Help Find a Biological Prize", John Markoff, New York Times, January 10, 2011
- 1 2 "Rebooting science outreach", Alan Chen, American Society for Biochemistry and Molecular Biology, June 2011
- ↑ "RNA research EteRNA gets its game on", Erin Allday, San Francisco Chronicle, January 17, 2011
- ↑ "Play a game and engineer real RNA", John Roach, MSNBC, January 11, 2011
- ↑ "Treuille On EteRNA - A Game Played By Humans, Scored By Nature":Interview with Adrien Treuille, Byron Spice, Faculty & Staff News, Carnegie Mellon University, January 22, 2011
- ↑ About EteRNA
- ↑ "Will NIH Embrace Biomedical Research Prizes?", Michael Price, ScienceInsider, Science 19 July 2011
- 1 2 Taylor, Nick (18 February 2016). "Gamers crush algorithms in RNA structure design challenge". fiercebiotechit.com. Retrieved 23 February 2016.
- ↑ "The Public, Playing a Molecule-Building Game, Outperforms Scientists", Rachel Wiseman, Wired Campus blog, The Chronicle of Higher Education, August 12, 2011
- ↑ EteRNA Team. "Eterna results published in PNAS". Retrieved 19 July 2014.
- ↑ Lee, Jeehyung; Kladwang, Wipapat; Lee, Minjae; Cantu, Daniel; Azizyan, Martin; Kim, Hanjoo; Limpaecher, Alex; Yoon, Sungroh; Treuille, Adrien; Das, Rhiju; EteRNA participants (Jan 17, 2014). "RNA design rules from a massive open laboratory" (PDF). PNAS: 1–6. doi:10.1073/pnas.1313039111.
- ↑ Das, Rhiju; et al. (17 February 2016). "Principles for Predicting RNA Secondary Structure Design Difficulty". Journal of Molecular Biology (Elsevier). doi:10.1016/j.jmb.2015.11.013.