Lab

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.

Introduction

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 Format

Target Structures

Previous labs have focused exclusively 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.

Schedule

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 Submission

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.

Scoring

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. A synthesized design may be viewed via "Review Submitted Designs" and a representation of the <a title="SHAPE" href="/wiki/index.php5/SHAPE">SHAPE</a> data may be viewed via "Color sequences based on experimental data" in addition to base colors as in the game. A colorized graduated scale representing the <a title="SHAPE" href="/wiki/index.php5/SHAPE">SHAPE</a> data for each base may be viewed by turning on the game option: "Use continuous colors for the exp. data".

Rewards

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.

Reward History: On Mar 22, 2013 a "News Item on new scoring method" in EteRNA news announced a new scoring system due to the large increase in synthesized solutions allowed by Cloud Lab. The new Design reward = lab_score*4, and Vote_reward = lab_score*2. Prior to that the rewards calculation was Design reward = lab_score*20, and Vote_reward = lab_score*10.

Strategies

Main Article: Lab Strategies

Player-Created guides: Lab Guides

Boosting

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 Ratio

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 Tools

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 Etiquette

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.

Overview of Lab Rounds

Here is a table for showing which batch a lab belongs to. It is useful knowing which round a lab belongs to because of the error rates of the lab data.

Each synthesis round will have its own characteristics with respect to error rates. Each round is different. Sometimes, this is on purpose, as the lab tries to improve their process, and some times it is accidental, such as having reagents go bad for an unknown reason. Unlike the SHAPE values, the reported error rates are not normalized between rounds. So when comparing error rates between labs, it's important to know what rounds each of the labs were synthesized in. (Omei)

Round	Comments	Labs
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0000/ETERNA_R00_0000.rdat">R0</a><a href="https://docs.google.com/document/d/1ga8v6GoJxuHcs0LwNkljOLXX9VZWZLwsZmfWJfseYhA/edit"></a>	First batch of Player Projects	Project : Thicker Zigzag Project : Test of RNAfold (5) Project : Test of RNAfold (4) Project : Test of RNAfold (3) Project : Test of RNAfold (2) Project : Test of RNAfold (1) Project : Multiloop: Two Pairs of Adjacent Stacks Project : Testing various loop designs Project : Hard Lab Fragments: Kudzu Arm Project : Hard Lab Fragments: Kudzu Neck Project : Hard Lab Fragments: Making it Up As I Go Multiloop Project : Hard Lab Fragments: Water Strider Arm Project : Neck Length 2 - 4 branch multiloop Project : Bulge Sampler: 4-nt Project : Bulge Sampler: 3-nt Project : Bulge Sampler: 2-nt Project : Bulge Sampler: 1-nt Project : 3 single nucleotide bulges Project : Isolated Base Pairs: 2-2 Loops Adjacent to Multiloop Project : Isolated Base Pairs: Adjacent 2-1 Loops (1) Project : Isolated Base Pairs: Adjacent 2-1 Loops (3) Project : Isolated Base Pairs: Adjacent 2-1-Loops (4) Project : Zigzag: 1-Nucleotide Bulge (4) Project : Zigzag: 1-Nucleotide Bulge (3) Project : Zigzag: 1-Nucleotide Bulge (2) Project : Zigzag: 1-Nucleotide Bulge (1) Project : GU-pin shape test Project : comparison series: 2-10 Project : comparison series: 2-9 Project : comparison series: 2-8 Project : Crossroads test Project : comparison series: 2-7 Project : comparison series: 2-6 Project : comparison series: 2-5 Project : comparison series: 2-4 Project : comparison series: 2-3 Project : Fisker - 2-2 loop energy challenge Project : comparison series: 10-2 Project : comparison series: 9-2 Project : comparison series: 8-2 Project : comparison series: 7-2 Project : comparison series: 6-2 Project : comparison series: 5-2 Project : comparison series: 4-2 Project : Mat - comparison series: 3-2 - D1 Project : comparison series: Hairpin loop with 15 nts Project : comparison series: Hairpin loop with 14 nts Project : comparison series: Hairpin loop with 13 nts Project : comparison series: Hairpin loop with 12 nts Project : comparison series: Hairpin loop with 11 nts Project : Mat - comparison series: Hairpin loop with 10 nts Project : Mat - comparison series: Hairpin loop with 9 nts- D1 Project : Five Branch Multiloop Project : comparison series: Octaloops Project : comparison series: Heptaloop Project : comparison series: Hexaloop Project : comparison series: Pentaloop Project : comparison series: Triloop Project : Multiloop: 4 Branches Separated by Single Unpaired Bases Project : Multiloop: 3 Branches Unevenly Spaced (2) Project : Multiloop: 3 Branches Unevenly Spaced (1) Project : Multiloop: 3 Branches 12 Unpaired Bases Project : Multiloop: 3 Branches No Unpaired Bases Project : 3-4 and 1-2 loops Project : Chain length and loop size series 1-10 Project : chain lenth and loop size series 1-9 Project : chain length and loop size series 1-8 Project : chain length and loop size series 1-5 Project : chain length and loop size series 1-4 Project : chain lengh an loop size series 1-3 Project : comparison series: 1-15 Project : comparison series: 2-15 Project : comparison series: 3-15 Project : comparison series: 4-15 Project : comparison series: 5-15 Project : comparison series: 6-15 Project : comparison series: 7-15 Project : comparison series: 8-15 Project : comparison series: 9-15 Project : comparison series: 10-15 Project : comparison series: 11-15 Project : comparison series: 12-15 Project : comparison series: 13-15 Project : comparison series: 14-15 Project : comparison series: 15-1 Project : comparison series: 15-2 Project : comparison series: 15-3 Project : comparison series: 15-4 Project : comparison series: 15-5 Project : comparison series: 15-6 Project : comparison series: 15-7 Project : comparison series: 15-8 Project : comparison series: 15-9 Project : comparison series: 15-10 Project : comparison series: 15-11 Project : comparison series: 15-12 Project : comparison series: 15-13 Project : comparison series: 15-14 Project : comparison series: 15-15 Project : comparison series: 14-14 Project : comparison series: 13-13 Project : comparison series: 12-12 Project : comparison series: 11-11 Project : comparison series: 10-10 Project : comparison series: 9-9 Project : comparison series: 8-8 Project : comparison series: 7-7 Project : comparison series: 6-6 Project : comparison series: Project : comparison series: 4-4 Project : comparison series: Project : comparison series: 2-2 Project : comparison series: 1-1 Project : Two stacks Project : Lab design for newer players Project : Sample puzzle for lab Project : Pseudoknot 2: Biotin-Binding Pseudoknot Project : Pseudoknot 1: Minimal Project : Half of The Branches Project : Saccharomyces Cerevisiae Loop Structure Project : 30 Nucleotide Loop 3 - Bulge Internal Loop Project : Two bulges and a 1-2 loop (reverse) Project : 30 Nucleotide Loop 2 - Asymmetric Internal Loop Project : 30 Nucleotide Loop 1 - Symmetric Internal Loop Project : Sharklike V-2 (SHAPE data Exp-2) Project : Sharklike V-1 (SHAPE data Exp-1) Project : S&E5 Modified Project : Reshiram Zekrom Kyurem Project : All red and blue Project : Bulge test Project : Guanine Reduction Project : Uracil Reduction Project : Large Isolated Hairpin Project : Isolated Closing Pairs 3 Project : Alternative Mismatches Project : Adenine Reduction Project : Internal Loops: 5-2 Project : Internal Loops: 6-3 Project : FMN-RNA aptamer complex lab Project : Tobramycin Aptamer Project : Hairpins: Heptaloop Project : Hairpins: Hexaloop Project : Hairpins: Pentaloop Project : Hairpins: Tetraloop Project : Hairpins: Triloop Project : Chesterfield s-The Mousekateer Project : Plain Hooked Project : Nupack s Finger Revisited Project : Large Loop Project : Hooked Project : Multiloop Isolated Closing Pairs Project : Cytosine reduction Project : Loop Heavy Project : Fractal RNA Project : Isolated Closing Pairs 2 Project : Repetitive Structures Project : Isolated Closing Pairs 1 Project : 4-4 loop Project : JerryP s winning design without tetraloop boost Project : 2-2 loop Project : Example project 2 Project : Example project Shape Library 101: The Finger Project: mRNA structure Project: helix stacking Project: all non-canonical pairs Project : miRNA hairpin robustness Project: metal ion pseudoknots Project: VAI protein kinase R inhibitor Project: unbound aptamer structures Project: Parin s favorite motifs therm1
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0001/ETERNA_R00_0001.rdat">R1</a>	Second batch of Player Projects Tested with four different SHAPE reagents: NMIA DMS CMCT 1M7 Signal-to-Noise Averages not currently available
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0002/ETERNA_R00_0002.rdat">R2</a>	Third batch of Player Projects Tested with four different SHAPE reagents: NMIA DMS CMCT 1M7 Each design was tested with each reagent twice, the second time with a different barcode Signal-to-Noise Averages not currently available
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R69_0000/ETERNA_R69_0000.rdat">R69</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R70_0000/ETERNA_R70_0000.rdat">R70</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R71_0000/ETERNA_R71_0000.rdat">R71</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R72_0000/ETERNA_R72_0000.rdat">R72</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R73_0000/ETERNA_R73_0000.rdat">R73</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R73_0001/ETERNA_R73_0001.rdat">R73.0001</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R74_0000/ETERNA_R74_0000.rdat">R74</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R75_0000/ETERNA_R75_0000.rdat">R75</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R76_0000/ETERNA_R76_0000.rdat">R76</a>
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R76_0001/ETERNA_R76_0001.rdat">R76.0001</a>

You can get an idea about the average error rate for a lab here.

<a href="https://docs.google.com/spreadsheets/d/16D7h8pY_tqPnegawl1puDkwjNOtFR8FDrPmE-eNKF4Q/edit#gid=1636220653">Signal to noise averages</a> by Meechl

==See Also==