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This article is an overview of the RNA lab. For the lab FAQ, click here

Labs are type of puzzle in EteRNA where player solutions are synthesized and scored on their ability to fold properly. In each lab, players vote on their peers' designs to determine which are synthesized. A player must earn 10,000 points to submit and vote on lab designs.

IntroductionEdit

In lab puzzles, players are presented with an target structure which must be solved. Each player may submit three lab designs and vote per round. Once submitted, the player's design is reviewed by other players, and voted on. The EteRNA team then synthesizes the most popular designs and performs experiments to determines their secondary structure and other chemical properties.

Lab FormatEdit

Target StructuresEdit

Previous labs have focued exlcusively on satisfying a secondary structure, with many the target structures synthesized designed by players. Recently, EteRNA has moved to the design of aptamers and riboswitches.

ScheduleEdit

Labs are organized into rounds, with new rounds beginning every one to three weeks. A lab may continue for several rounds until a winner is found. Though synthesis and voting has stopped on old labs, players may continue to review old lab data and solve old lab puzzles.

Voting and SubmissionEdit

A player may submit 3 sequences and vote on 8 sequences per round. Sequences that were not synthesized in previous rounds may be resubmitted. Players may vote on their own designs, but may only vote once on a given sequence.

ScoringEdit

Lab designs are scored on a scale of 0-100 based on how well they satisfy the target structure. Scores of of 94 or higher are considered winning. A player's synthesized designs and their scores are visible on his or her player profile.

RewardsEdit

Players are awarded points for their submissions and votes, regardless of whether the sequences designed and voted on are synthesized. For designs that are synthesized, the number of points awarded depends on synthesis score. For designs that are not synthesized, the reward is calculated based on the similarity of a sequence to those that have been synthesized.

StrategiesEdit

Main Article: Lab Strategies

BoostingEdit

The value of boosting in lab is unclear. Previous winners have included both boosted and unboosted designs. Certain special loop sequences with very low free energy appear strongly base paired, however.

GC/AU/GU RatioEdit

GC pairs are more stable than AU or GU pairs; however, designs with very high GC content are difficult to synthesize and likely to misfold. Designs contining exclusively GC pairs are unlikely to be voted for or synthesized. Likewise, designs that are very rich in AU or GU pairs are unlikely to be selected for synthesis.

Computational ToolsEdit

The EteRNA lab interface contains two computational tools that provide insight into the stability of the RNA being designed: the dot plot and the melt plot. Additionally, many secondary structure prediction programs are available on the web. The utility of these tools remains unclear.

Cooperation and EtiquetteEdit

Most experienced players are eager to help others design sequences. Design strategies are openly discussed in chat, on the forum, and in the wiki. The use of other players' designs as starting points is common. Newcomers to lab may find it especially helpful to modify an existing design rather than start from scratch.

Players are encouraged to acknowledge the original designer the sequence being modified. Asking for votes is considered impolite.

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