EteRNA
Encyclopedia
EteRNA is a browser based game
, developed by scientists at Carnegie Mellon University
and Stanford University
, that engages users to solve puzzles related to the folding of RNA
molecules. The project is funded by the National Science Foundation
.
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
" and the collective intelligence
of EteRNA players to answer fundamental questions about RNA folding mechanics. The top player 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.
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. EteRNA project leaders hope that determining these basic principles that may facilitate the design of RNA-based nanomachines and switch
es. 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".
As of August 2011, approximately 26,000 players have contributed RNA sequence designs and over 306 designs have been synthesized for in vitro
testing.
s (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.
Once players have completed a sufficent 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.
Browser game
A browser game is a computer game that is played over the Internet using a web browser. Browser games can be created and run using standard web technologies or browser plug-ins. Browser games include all video game genres and can be single-player or multiplayer...
, developed by scientists at Carnegie Mellon University
Carnegie Mellon University
Carnegie Mellon University is a private research university in Pittsburgh, Pennsylvania, United States....
and Stanford University
Stanford University
The Leland Stanford Junior University, commonly referred to as Stanford University or Stanford, is a private research university on an campus located near Palo Alto, California. It is situated in the northwestern Santa Clara Valley on the San Francisco Peninsula, approximately northwest of San...
, that engages users to solve puzzles related to the folding of RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
molecules. The project is funded by the National Science Foundation
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
.
Similar to Foldit
Foldit
Foldit is an online puzzle video game about protein folding. The game is part of an experimental research project, and is developed by the University of Washington's Center for Game Science in collaboration with the UW Department of Biochemistry...
—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
Crowdsourcing
Crowdsourcing is the act of sourcing tasks traditionally performed by specific individuals to a group of people or community through an open call....
" and the collective intelligence
Collective intelligence
Collective intelligence is a shared or group intelligence that emerges from the collaboration and competition of many individuals and appears in consensus decision making in bacteria, animals, humans and computer networks....
of EteRNA players to answer fundamental questions about RNA folding mechanics. The top player 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.
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. EteRNA project leaders hope that determining these basic principles that may facilitate the design of RNA-based nanomachines and switch
Switch
In electronics, a switch is an electrical component that can break an electrical circuit, interrupting the current or diverting it from one conductor to another....
es. 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".
As of August 2011, approximately 26,000 players have contributed RNA sequence designs and over 306 designs have been synthesized for in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
testing.
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 nucleotideNucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s (adenine
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
, cytosine
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
, guanosine
Guanosine
Guanosine is a purine nucleoside comprising guanine attached to a ribose ring via a β-N9-glycosidic bond. Guanosine can be phosphorylated to become guanosine monophosphate , cyclic guanosine monophosphate , guanosine diphosphate , and guanosine triphosphate...
and uracil
Uracil
Uracil is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine, cytosine, and guanine. In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine.Uracil is a common and...
) at various positions; this can alter the free energy
Thermodynamic free energy
The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering and science. The free energy is the internal energy of a system less the amount of energy that cannot be used to...
of the system and dramatically affect the RNA strand's folding dynamics.
Once players have completed a sufficent 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.
See also
- Citizen scienceCitizen scienceCitizen science is a term used for the systematic collection and analysis of data; development of technology; testing of natural phenomena; and the dissemination of these activities by researchers on a primarily avocational basis...
- FolditFolditFoldit is an online puzzle video game about protein folding. The game is part of an experimental research project, and is developed by the University of Washington's Center for Game Science in collaboration with the UW Department of Biochemistry...
- Game with a purpose
- List of crowdsourcing projects
- Serious gameSerious gameA serious game is a game designed for a primary purpose other than pure entertainment. The "serious" adjective is generally prepended to refer to products used by industries like defense, education, scientific exploration, health care, emergency management, city planning, engineering, religion,...