Lab

From Eterna Wiki

This article is an overview of the RNA lab process.

Labs are type of puzzle in Eterna where player solutions are synthesized and scored based on experimental data. In each lab, players vote on their peers' designs to determine which are synthesized.

A player must complete the progression puzzles to submit and vote on lab designs.

Lab Steps Overview

Scheduled Rounds

Labs are organized and scheduled into rounds.  Each round may last from a week to several months. A lab may continue for many rounds until a goal has been achieved. Alhough synthesis and voting has stopped on old labs, players may continue to review old lab data and work on old lab puzzles.

Analysis

The lab archive is a treasure trove of data on what RNA designs were most successful in the labs. Review successful past designs to find winning strategies that get you more points!  Select a lab which has the "Results Posted" indicator then scroll down to the conclusions section.  Most labs have a leaderboard which helps to find the best designs. The Forum is a great place to find suggestions made by other players and to ask questions. Each round of a lab usually has its own Forum topic.

Design

In lab puzzles, players are presented with a goal which varies by lab.  In the early labs, the goal was always to design a RNA which would fold into the target structure.  Later, Eterna moved to the design of aptamers and riboswitches. More recently, goals have varied and may involve designing RNA with the lowest degradation or the best activity. The goals of a lab are described in the Lab Details. Ask questions in the Discussion area or in the Forum.

Submission

The number of designs which a player may submit varies by lab.  This is given in the lab info to the right of the lab details.

Voting

All designs are reviewed by other players, and votes are placed. Players may vote on their own designs, but may only vote once on a given sequence.  Voting is usually simultaneous with submission.  Votes may be withdrawn and changed up until the deadline.

Laboratory Synthesis

The Eterna team of scientists at various laboratories then synthesizes the most popular designs in a real laboratory. This is where the real science happens!

Design Scoring

The synthesized designs for the labs are given Lab scores as follows:

  • If the lab result is a SHAPE score, then the Lab score is the SHAPE score, which ranges from 0-100. If the lab results give another attribute, such as iSAT, degradation, or protein expression, then the researchers determine how to convert the measured value(s) to Lab score. The range should remain 0 – 100.
    • After the lab is complete, the Lab score of a synthesized design is included in Design Details when the design is opened.
    • All designs which were not synthesized are given a Lab score equal to that of the closest synthesized design. Closeness is determined by the number of matching bases between the two designs. These Lab scores are not included in the Design Details since they are only approximations but are used in awarding points.

    Player Rewards

    Points are awarded as follows:

    • Design points are awarded for a player’s highest scoring design for each puzzle of a lab (whether synthesized or not). A player will receive points for only 1 design per puzzle.
    • Design points = 4 x Lab score
    • Voting points are awarded for the highest scoring synthesized design for which a player voted. A player will receive points for only 1 design per puzzle.
    • Voting points = 2 x Lab score
    • A player may find their awarded points as follows: Click on Latest Activity (Bell Icon), then on the Open (square with arrow) icon, Click on Labs on the menu on the right.  A player’s lab points will be listed.
    • 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.

     Cooperation and Etiquette

    Most experienced players are eager to help others design sequences. Design strategies are openly discussed in chat,  and on the forum. 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.

    Types of Labs

    1. Classic Eterna - Early labs without barcodes
    2. FMN Aptamers - Early FMN aptamer labs
    3. Player Projects - Cloud lab beta
    4. Switches - Early switch labs
    5. Cloud Labs - Labs with barcodes 
    6. OpenCRISPR - Discover design patterns for guide RNAs to make gene editing more precisely controllable
    7. OpenTB - Design RNA sensors to detect active TB
    8. OpenRibosome -  Generate customized ribosomes able to synthesize diverse polymers and materials (launched 2019)
    9. OpenVaccine - Improve the stability of mRNA vaccines (launched 2020)

    Strategies for Labs

    These strategies are for labs where the goal is to design a RNA which folds into a target structure, analyzed by SHAPE data.

    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.

    Overview of Lab Rounds (prior to 2015?)

    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)

    Each round number is connected to an rdat file and most rounds have spreadsheets with extracted data. The data is taken from RMDB (RNA Mapping Database). 

     

    Round  Comments Labs  Signal-to-noise average

    R0

    12/21/2012

     

    First batch of Player Projects

    R0.xlsx

    R0.googlesheet

    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
     1.583

    R1

    4/9/2013

    Second batch of Player Projects
    Tested with four different SHAPE reagents:
    Signal-to-Noise Averages not currently available  
     

    R2

    3/7/2013

    Third batch of Player Projects
    Tested with four different SHAPE reagents:
    Each design was tested with each reagent twice, the second time with a different barcode
    Signal-to-Noise Averages not currently available 

     
    R69

    R69.xlsx

    R69.googlesheet

    Cloud Lab 1 - Aires by wateronthemoon
    Cloud Lab 2 - Triangle of doom version 2 by dstea
    Cloud Lab 3 - A Simple Zigzag by janelle
    Cloud Lab 4 - Random by theravin
    Cloud Lab 5 - The Nonesuch by rnjensen45
    Cloud Lab 6 - Cross by firedrake969
    Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux
    Cloud Lab 8 - Stellar Crossbow by jmf028
    Cloud Lab 9 - Final Countdown by Tesla sDisciple
    Cloud Lab 10 - Random Shape 2 by ElNando888
    Cloud Lab 11 - Little bug by JR
    Cloud Lab 12 - Anchor by ribonucleic
    Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl
    Cloud Lab 14 - Easy loop sizes by Edward Lane
    Cloud Lab 15 - Triloop Buffet by jandersonlee
    Cloud Lab 16 - Section from lab Water Strider by Brourd
    Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies
    Cloud Lab 18 - Anaconda About to Poop by SpaceFolder
    Cloud Lab 19 - Big Hairpin Loop by Eli Fisker
    Cloud Lab 20 - Random4 by mat747
     6.998
    R70

    Switch Cloud Labs  

    LabPuz02 by JR
    Bistable 3 by jnicol
    Hair Trigger by space_miser
    Will It Bind? by jmf028
    Stratospheric by Dennis9600
    Phase II - 1 by ElNando888
    LS2 by c-quence
    Anchor 2.0 by ribonucleic
    Day 2 by wateronthemoon
    Alive and kicking by Eli Fisker
    Laydown and Jump by rnjensen45
    McSwitch by Meechl
    Water Snake Redux by jruaya
    My Screw-Up Corrected? by SpaceFolder
    Nincompoop by hoglahoo
    Lines by starryjess
    Bound state has a zigzag by stevetclark
    Chirality by kcabral28
    Switch Test 1 by Brourd
    Top Notch by jmf028
     

    R71

    5/10/2013

    R71.xlsx

    R71.googlesheet

    My Screw-Up Corrected? by SpaceFolder
    Cloud Lab 1 - Aires by wateronthemoon
    Cloud Lab 2 - Triangle of doom version 2 by dstea
    Cloud Lab 3 - A Simple Zigzag by janelle
    Cloud Lab 4 - Random by theravin
    Cloud Lab 5 - The Nonesuch by rnjensen45
    Cloud Lab 6 - Cross by firedrake969
    Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux
    Cloud Lab 8 - Stellar Crossbow by jmf028
    Cloud Lab 9 - Final Countdown by Tesla sDisciple
    Cloud Lab 10 - Random Shape 2 by ElNando888
    Cloud Lab 11 - Little bug by JR
    Cloud Lab 12 - Anchor by ribonucleic
    Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl
    Cloud Lab 14 - Easy loop sizes by Edward Lane
    Cloud Lab 15 - Triloop Buffet by jandersonlee
    Cloud Lab 16 - Section from lab Water Strider by Brourd
    Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies
    Cloud Lab 18 - Anaconda About to Poop by SpaceFolder
    Cloud Lab 19 - Big Hairpin Loop by Eli Fisker
    Cloud Lab 20 - Random4 by mat747
     3.698

    R72

    6/11/2013

    R72.xlsx

    R72.googlesheet

    Ball & Chain by Krobar
    Simplify by Tesla sDisciple
    An Arm and a Leg 1.0 by kcabral28
    Huffman by hotcreek
    QRNAL0 by Quxwozing
    Riboswitch-based by jruaya
    1-X bulge testing   by Omei
    EzFold by space_miser
    Thursday by DHammond
    TEBOWNED mutation - BH
    TEBOWNED mutation - U
    TEBOWNED mutation - B
    Flu Virus
    TEBOWNED reloaded
    MedLoop
    Ball & Chain by Krobar
    Simplify by Tesla sDisciple
    An Arm and a Leg 1.0 by kcabral28
    Huffman by hotcreek
    QRNAL0 by Quxwozing
    Riboswitch-based by jruaya
    1-X bulge testing by Omei
    EzFold by space_miser
    Thursday by DHammond
     4.272

    R73

    7/30/2013

    R73.xlsx

    R73.googlesheet

     

    1-1-1-1-1-1 Multiloop
    2-2 and 3-3 loops
    A-U Closing Base Pairs
    caulobacter_ncrna_lists
    Hex-a-Stripe
    Magic  boosts in 2-2 loops
    Magic boosts in 2-2 loops revised  thanks starry
    Permuted loops
    Probing the 3D motif atlas
    Quad Loop test
    RNA Bridge
    RNA Bridge (Updated)
    RNA Strength
    Short Stacks
    Single state - Switch state
    Single to Switch try  2
    The GAAA loop
    Tighter Two Stacks for 3-way Multi-Loop testing
    Tribute To Satellite Kepler
    Two stacks
    Two Stacks - Triloop hairpin variation
    Variations on a theme of 1-0 loops and short stack hairpins
     3.775

    R73.0001

    R73.0001.xlsx

    R73.0001.googlesheet

     3.881
    R74

    R74.xlsx

    R74.googlesheet

    A-U Closing Base Pairs 2
    Tetraloops and 0-0-0-0 Multiloop Phase 1
    Tetraloops and 0-0-0-0 Multiloop Phase 1 Version 2
    Lonely Base Pair - 1-1: Multiloop
    Lonely Base Pair - 2-2: Multiloop
    Lonely Base Pair - 3-3: Multiloop
    FMN Switch 2.0 - First State with Locked Bases
    Can We do it in 10? - FMN Switch 2.0
    Triloop with multiloop core phase 1
    Two Bulge Zigzag - Variation 1
    Two Bulge Zigzag - Variation 3
    Two Bulge Zigzag - Variation 4
    G-U Closing Base Pairs
    G-U Closing Base Pairs 2
    Reversed G-C Multibranch Loop Closing Base Pairs
    Probing for tertiary structure
    Modeled Impossible: 31+ Nucleotide Internal Loops
    RNA windows pilot project - 16s rRNA (3I1M)
    Caulobacter ncRNA discovery
    Tristable RNA
    Hammerhead Ribozyme Wildtype Mutate and Map
    MedLoop V2
    Hammerhead Ribozyme G12A Mutate and Map
    Entoplea bizarre tRNA 2D structure mt tRNA-Arg
     4.442
    R75

    R75.xlsx

    R75.googlesheet

    Short Stacks 2
    SARS coronavirus structure test
    FMN Binding Site Chemical Footprint
    Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V1
    New Frontier
    Frog leg - Electric
    ZigZag and ZagZig
    Chicken leg
    Chicken leg - Splayed
    Motor Protein - Step 1
    Motor Protein - Step 2
    Motor Protein - Step 3
    Intrinsically unfolded RNA
    Probing the structure of  poly-A loops by mutation
    PSTVd probing
    Improving the Nearest Neighbor Energy Model Using EteRNA  Pilot
    TCF21 3 UTR
    MedLoop redux
     5.621

    R76

    8/23/2013

    R76.xlsx

    <a href="/wiki/Now I found">R76.googlesheet</a>

    Find Z - Here It Is!
    Two Bulge  Zigzag  - Both Conformations
    Two Bulge  Zigzag  - Variation 2
    Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V2
    TinkerToy Retread
    Frog leg - relaxed
    Frog leg - Stretched toe
    Intersecting stacks 2
    Is RNA directional 1 of 2
    Semicircle - 2 bends
    Semicircle - 5 bends
    Location Dependent Chemical Footprints Part 1
    Location Dependent Chemical Footprints Part 3
    Location Dependent Chemical Footprints Part 4
    Location Dependent Chemical Footprints Part 5
    Location Dependent Chemical Footprints Part 6
    Teeny tRNA
    P5abc Mutants to Affect Folding Transitions
    Testing 3D structure prediction of G/G mismatches (boosts!)
    Testing for crazy conformations of tandem G/A and A/G pairs
    A codon riboswitch
     3.692
    R76.0001

    R76.0001.xlsx

    R76.0001.googlesheets

     3.389

    R77

    9/23/2013

    R77.xlsx

    R77.googlesheet

    Intersecting stacks investigation
    Is RNA directional 2 of 2
    Semicircle - 3 bends
    Semicircle -  4 bends
    Location Dependent Chemical Footprints Part 2
    Could Curves Survive?
    Adding some sweet tetraloops
    Palindromes part one
    Dimer B
    Dimer A
    Robot serial killer 1 - Lab killer too?
    Robot serial killer 2 - Lab killer too?
    Short Stacks 3
    Relaxed multiloop 2
    New Frontier 2
    Five Adjacent Stem Multibranch Loop
    crRNA
    tracrRNA
    sgRNA89_NGS
    sgRNA67
    sgRNA48
    Repeat hairpins v1
    Codon riboswitch [repeat of tryptophan]
    Codon riboswitch [arginine]
    Class I ligase
    MedLoop resurrected
    Un-stable
    M-stable
    EteRNA R45-46 FMN Aptamer with Single Binding Site
    EteRNA R43 the Backwards C
    Codon riboswitch [histidine]
    Reproducibility Lab 1
     1.714
    R78

    R78.xlsx

    R78.googlesheet

    Example project..
    G-U GAGA Tetraloop Boost
    Repetitious sequences
    Robot serial killer 3 - Lab killer too?
    FMN Shape Test- 1st State
    FMN Shape Test- 2nd State
    Wobble Quad Stability 1
    SHAPE Profile - U-U Mismatch - Pilot Run
    SHAPE Profile - C-U Mismatch - Pilot Run
    SHAPE Profile - U-C Mismatch - Pilot Run
    SHAPE Profile - C-A Mismatch - Pilot Run
    SHAPE Profile - A-C Mismatch - Pilot Run
    SHAPE Profile - G-A Mismatch - Pilot Run
    SHAPE Profile - A-G Mismatch - Pilot Run
    Unmodified tRNA sequences
    Chicken Leg - Reversed
    Reversed motor - step 1
    Double 1-3 Loop
    SHAPE Profile - C-C Mismatch - Pilot Run
    Large GU stack
    Neck strength analysis 3 of 3 - Weak - AUs + GUs.
    Hexaloop Kd and SHAPE test
    P5abc Mutants to Affect Folding Transitions 2
    MedLoop Double Mutants - Shape 0
    MedLoop delta Double Mutants - Shape 0
    Bistable double mutants - Shape 0
    M-stable double mutants - Shape 0
    Un-stable double mutants - Shape 0
    Bistable hairpin mutate and map - Shape 0
    Un-stable alternative mutate-and-map - Shape 0
    RPL11a Pseudouridylation Site Mutate and Map - Shape 0
    TEF1 Pseudouridylation Site Mutate and Map - Shape 0
    RPL11a Mutant Pseudouridylation Site Mutate and Map - Shape 0
    Permuted Loops - Shape 0
    Permuted Loops - Shape 1
    Permuted Loops - Shape 2
    Permuted Loops - Shape 3
    Permuted Loops - Shape 4
    Permuted Loops - Shape 5
    Permuted Loops - Shape 6
    Permuted Loops - Shape 7
    Permuted Loops - Shape 8
    Permuted Loops - Shape 9
    Permuted Loops - Shape 10
    Permuted Loops - Shape 11
    Permuted Loops - Shape 12
    Permuted Loops - Shape 13
    Permuted Loops - Shape 14
    Permuted Loops - Shape 15
    Permuted Loops - Shape 16
    Permuted Loops - Shape 17
    Permuted Loops - Shape 18
    Permuted Loops - Shape 19
    Permuted Loops - Shape 20
    Permuted Loops - Shape 21
    Permuted Loops - Shape 22
    Permuted Loops - Shape 23
    Permuted Loops - Shape 24
    Permuted Loops - Shape 25
    Permuted Loops - Shape 26
    Permuted Loops - Shape 27
    Permuted Loops - Shape 28
    Permuted Loops - Shape 29
    Permuted Loops - Shape 30
    Permuted Loops - Shape 31
    Permuted Loops - Shape 32
    Permuted Loops - Shape 33
    Permuted Loops - Shape 34
    Permuted Loops - Shape 35
    Permuted Loops - Shape 36
    Permuted Loops - Shape 37
    Reproducibility Lab Another Round - Shape 0
    Reproducibility Lab Another Round - Shape 1
    Reproducibility Lab Another Round - Shape 2
    Reproducibility Lab Another Round - Shape 3
    Reproducibility Lab Another Round - Shape 4
    Reproducibility Lab Another Round - Shape 5
    Reproducibility Lab Another Round - Shape 6
    Reproducibility Lab Another Round - Shape 7
    Reproducibility Lab Another Round - Shape 8
    Reproducibility Lab Another Round - Shape 9
    Reproducibility Lab Another Round - Shape 10
    Reproducibility Lab Another Round - Shape 11
    Reproducibility Lab Another Round - Shape 12
    Reproducibility Lab Another Round - Shape 13
    Reproducibility Lab Another Round - Shape 14
    Reproducibility Lab Another Round - Shape 15
    Reproducibility Lab Another Round - Shape 16
    Reproducibility Lab Another Round - Shape 17
    Reproducibility Lab Another Round - Shape 18
    Reproducibility Lab Another Round - Shape 19
    Reproducibility Lab Another Round - Shape 20
    Influenza PB2 mutant sequences - Shape 0
    Influenza PB2 mutant sequences - Shape 1
    Single strand barcodes - Shape 0
    Single strand barcodes - Shape 1
    Single strand barcodes - Shape 2
    Single strand barcodes - Shape 3
     2.604
    R79

    R79.xlsx

    R79.googlesheet

    Test of locking loop bases in a ribozyme-like structure
    Relaxed multiloop 1
    Relaxed multiloop 3
    Reversed motor - Step 2
    Reversed motor - Step 3
    Reversed motor - Step 4
    A-U Closing Base Pairs 3
    A-U Closing Base Pairs 4
    T.thermophilise16S Hammerhead
    Alien partial glasses - Mirror version
    Single to Switch try  2 - Mirror version
    Let s break the barcode
    Don Quixote
    Mummiebrain s M2
    Impossible Folding II - The Intramolecular G-quadruplex
    PB2elem2_MR_syn - Shape 0
    GNRA/receptor project - Shape 0
    GNRA/receptor project - Shape 1
    GNRA/receptor project - Shape 2
    GNRA/receptor project - Shape 3
    CR4-5 domain of human telomerase - Shape 0
    CR4-5 domain of human telomerase - Shape 1
    CR4-5 domain of human telomerase - Shape 2
    CR4-5 domain of human telomerase - Shape 3
    CR4-5 domain of human telomerase - Shape 4
    CR4-5 domain of human telomerase - Shape 5
    CR4-5 domain of human telomerase - Shape 6
    CR4-5 domain of human telomerase - Shape 7
    CR4-5 domain of human telomerase - Shape 8
    CR4-5 domain of human telomerase - Shape 9
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    CR4-5 domain of human telomerase - Shape 11
    CR4-5 domain of human telomerase - Shape 12
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    CR4-5 domain of human telomerase - Shape 16
    CR4-5 domain of human telomerase - Shape 17
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    CR4-5 domain of human telomerase - Shape 19
    CR4-5 domain of human telomerase - Shape 20
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    CR4-5 domain of human telomerase - Shape 22
    CR4-5 domain of human telomerase - Shape 23
    CR4-5 domain of human telomerase - Shape 24
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    CR4-5 domain of human telomerase - Shape 28
    CR4-5 domain of human telomerase - Shape 29
    CR4-5 domain of human telomerase - Shape 30
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    CR4-5 domain of human telomerase - Shape 42
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    CR4-5 domain of human telomerase - Shape 54
    CR4-5 domain of human telomerase - Shape 55
    CR4-5 domain of human telomerase - Shape 56
    CR4-5 domain of human telomerase - Shape 57
    RF01020 mutate-and-map - Shape 0
    RF01020 mutate-and-map - Shape 1
    RF01020 mutate-and-map - Shape 2
    RF01020 mutate-and-map - Shape 3
    RF01020 mutate-and-map - Shape 4
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    RF01020 mutate-and-map - Shape 15
    RF01020 mutate-and-map - Shape 16
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    RF01020 mutate-and-map - Shape 19
    RF01020 mutate-and-map - Shape 20
    RF01020 mutate-and-map - Shape 21
    RF01020 mutate-and-map - Shape 22
    RF01020 mutate-and-map - Shape 23
    RF01020 mutate-and-map - Shape 24
    RF01020 mutate-and-map - Shape 25
    RF01020 mutate-and-map - Shape 26
    RF01020 mutate-and-map - Shape 27
    RF01020 mutate-and-map - Shape 28
    RF01020 mutate-and-map - Shape 29
    RF01020 mutate-and-map - Shape 30
    RF01020 mutate-and-map - Shape 31
    RF01020 mutate-and-map - Shape 32
    RF01020 mutate-and-map - Shape 33
    RF01020 mutate-and-map - Shape 34
    RF01020 mutate-and-map - Shape 35
    RF01020 mutate-and-map - Shape 36
    RF01020 mutate-and-map - Shape 37
    RF01414 mutate-and-map - Shape 0
    RF01414 mutate-and-map - Shape 1
    RF01414 mutate-and-map - Shape 2
    RF01414 mutate-and-map - Shape 3
    RF01414 mutate-and-map - Shape 4
    RF01414 mutate-and-map - Shape 5
    RF01414 mutate-and-map - Shape 6
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    RF01414 mutate-and-map - Shape 8
    RF01414 mutate-and-map - Shape 9
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    RF01414 mutate-and-map - Shape 11
    RF01414 mutate-and-map - Shape 12
    RF01414 mutate-and-map - Shape 13
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    RF01414 mutate-and-map - Shape 17
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    RF01414 mutate-and-map - Shape 19
    RF01414 mutate-and-map - Shape 20
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    RF01414 mutate-and-map - Shape 24
    RF01414 mutate-and-map - Shape 25
    RF01414 mutate-and-map - Shape 26
    RF01414 mutate-and-map - Shape 27
    RF01125 mutate-and-map - Shape 0
    RF01125 mutate-and-map - Shape 1
    RF01125 mutate-and-map - Shape 2
    RF01125 mutate-and-map - Shape 3
    RF01125 mutate-and-map - Shape 4
    RF01125 mutate-and-map - Shape 5
    RF01125 mutate-and-map - Shape 6
    RF01125 mutate-and-map - Shape 7
    RF01125 mutate-and-map - Shape 8
    RF01125 mutate-and-map - Shape 9
    RF01125 mutate-and-map - Shape 10
    RF01125 mutate-and-map - Shape 11
    RF01125 mutate-and-map - Shape 12
    RF01125 mutate-and-map - Shape 13
    RF01125 mutate-and-map - Shape 14
    RF01125 mutate-and-map - Shape 15
    RF01125 mutate-and-map - Shape 16
    RF01125 mutate-and-map - Shape 17
    RF01125 mutate-and-map - Shape 18
    RF01125 mutate-and-map - Shape 19
    RF01125 mutate-and-map - Shape 20
    RF01125 mutate-and-map - Shape 21
    RF01125 mutate-and-map - Shape 22
    RF01125 mutate-and-map - Shape 23
    RF01125 mutate-and-map - Shape 24
    RF01125 mutate-and-map - Shape 25
    RF01125 mutate-and-map - Shape 26
    RF01125 mutate-and-map - Shape 27
    RF01125 mutate-and-map - Shape 28
    RF01125 mutate-and-map - Shape 29
    RF01125 mutate-and-map - Shape 30
     3.046

    R80

    2/5/2014

    R80.xlsx

    R80.googlesheet

    Wobble Quad Control 2
    Wobble Quad Control 3
    Wobble Quad Control 4
    SHAPE Profile - G-G Mismatch - Pilot Run
    Reversed G-C Multibranch Loop Closing Base Pairs 2
    SHAPE Profile - U-U Mismatch - Pilot Run 2A
    SHAPE Profile - U-U Mismatch - Pilot Run 2B
    SHAPE Profile - A-G Mismatch - Pilot Run 2A
    SHAPE Profile - A-G Mismatch - Pilot Run 2B
    Tetraloop Competition Series - GAAA
    Tetraloop Competition - UUCG
    Tetraloop Competition Series - UACG
    Tetraloop Competition Series - GAGA
    SHAPE Profile - A-A Mismatch - Pilot Run
    Repeatability - Melted Helix Variation 1
    Repeatability - Melted Helix Variation 2
    SHAPE Profile - Most Likely Base Pair C/G
    Really big loop coil - Classic science toy
    Intrinsical - Frequency 1
    Intrinsical - Frequency 8
    Impossible Folding I
    Poly (A) Structure Analysis 1
    New Frontier 3
    Cobalamin Riboswitches  - Shape 0
    Cobalamin Riboswitches  - Shape 1
    Cobalamin Riboswitches  - Shape 2
    Cobalamin Riboswitches  - Shape 3
    Cobalamin Riboswitches  - Shape 5
    Cobalamin Riboswitches  - Shape 11
    Cobalamin Riboswitches  - Shape 12
    Cobalamin Riboswitches  - Shape 14
    Cobalamin Riboswitches  - Shape 19
    Cobalamin Riboswitches  - Shape 23
    Motif Assembled GAAA tetraloop binders - Shape 0
    The RFAM Mapping project - Shape 0
    The RFAM Mapping project - Shape 1
    The RFAM Mapping project - Shape 2
    The RFAM Mapping project - Shape 3
    The RFAM Mapping project - Shape 4
    The RFAM Mapping project - Shape 5
    The RFAM Mapping project - Shape 6
    The RFAM Mapping project - Shape 7
    The RFAM Mapping project - Shape 8
    The RFAM Mapping project - Shape 9
    The RFAM Mapping project - Shape 10
    The RFAM Mapping project - Shape 11
    The RFAM Mapping project - Shape 12
    The RFAM Mapping project - Shape 13
    The RFAM Mapping project - Shape 14
    The RFAM Mapping project - Shape 15
    The RFAM Mapping project - Shape 16
    The RFAM Mapping project - Shape 17
    The RFAM Mapping project - Shape 18
    The RFAM Mapping project - Shape 19
    The RFAM Mapping project - Shape 20
    The RFAM Mapping project - Shape 21
    The RFAM Mapping project - Shape 22
    The RFAM Mapping project - Shape 23
    The RFAM Mapping project - Shape 24
    The RFAM Mapping project - Shape 25
    The RFAM Mapping project - Shape 26
    The RFAM Mapping project - Shape 27
    The RFAM Mapping project - Shape 28
    The RFAM Mapping project - Shape 29
    The RFAM Mapping project - Shape 30
    The RFAM Mapping project - Shape 31
    The RFAM Mapping project - Shape 32
    The RFAM Mapping project - Shape 33
    The RFAM Mapping project - Shape 34
    The RFAM Mapping project - Shape 35
    The RFAM Mapping project - Shape 36
    The RFAM Mapping project - Shape 37
    The RFAM Mapping project - Shape 38
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    The RFAM Mapping project - Shape 40
    The RFAM Mapping project - Shape 41
    The RFAM Mapping project - Shape 42
    The RFAM Mapping project - Shape 43
    The RFAM Mapping project - Shape 44
    The RFAM Mapping project - Shape 45
    The RFAM Mapping project - Shape 46
    The RFAM Mapping project - Shape 47
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    The RFAM Mapping project - Shape 49
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    The RFAM Mapping project - Shape 53
    The RFAM Mapping project - Shape 54
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    The RFAM Mapping project - Shape 56
    The RFAM Mapping project - Shape 57
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    The RFAM Mapping project - Shape 60
    The RFAM Mapping project - Shape 61
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    The RFAM Mapping project - Shape 63
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    The RFAM Mapping project - Shape 66
    The RFAM Mapping project - Shape 67
    The RFAM Mapping project - Shape 68
    The RFAM Mapping project - Shape 69
    The RFAM Mapping project - Shape 70
    The RFAM Mapping project - Shape 71
    The RFAM Mapping project - Shape 72
    The RFAM Mapping project - Shape 73
    The RFAM Mapping project - Shape 74
    The RFAM Mapping project - Shape 75
    The RFAM Mapping project - Shape 76
    The RFAM Mapping project - Shape 77
    The RFAM Mapping project - Shape 78
    The RFAM Mapping project - Shape 79
    The RFAM Mapping project - Shape 80
    The RFAM Mapping project - Shape 81
    The RFAM Mapping project - Shape 82
    The RFAM Mapping project - Shape 83
    The RFAM Mapping project - Shape 84
    The RFAM Mapping project - Shape 85
    The RFAM Mapping project - Shape 86
    The RFAM Mapping project - Shape 87
    The RFAM Mapping project - Shape 88
    The RFAM Mapping project - Shape 89
    The RFAM Mapping project - Shape 90
    The RFAM Mapping project - Shape 91
    The RFAM Mapping project - Shape 92
    The RFAM Mapping project - Shape 93
    The RFAM Mapping project - Shape 94
    The RFAM Mapping project - Shape 95
    The RFAM Mapping project - Shape 96
    The RFAM Mapping project - Shape 97
    The RFAM Mapping project - Shape 98
    Nando s Zippers - Shape 0
    Ambiguous Bulges - Shape 0
    Ambiguous Bulges - Shape 1
    Ambiguous Bulges - Shape 2
    Ambiguous Bulges - Shape 3
     2.217

    R81

    2/4/2014

    R81.xlsx

    R81.googlesheets

    Dimer A - control
    Small Loops- v. 1
    SHAPE Profile - G-G Mismatch - Pilot Run 2A
    SHAPE Profile - G-G Mismatch - Pilot Run 2B
    SHAPE Profile - A-A Mismatch - Pilot Run 2B
    Simplify - Mirror version
    SHAPE Profile - Most Likely Base Pair G/C
    Early bulge
    Really big loop coil - control
    Intrinsical frequency
    Intrinsically Green
    Intrinsically Blue
    Very relaxed multiloop
    Intrinsical - Frequency 2
    Intrinsical - Frequency 6
    Intrinsical - Frequency 7
    TrpBoundState
    TrpAltA
    TrpAltB
    TrpAltC
    GNRA/receptor project - Shape 0
    GNRA/receptor project - Shape 1
    GNRA/receptor project - Shape 2
    GNRA/receptor project - Shape 3
    GNRA/receptor project - Shape 4
    GNRA/receptor project - Shape 5
    GNRA/receptor project - Shape 8
    GNRA/receptor project - Shape 12
     2.620

    R82

    2/5/2014

    R82.xlsx

    R82.googlesheet

    Improving the Energy Model: Competing Tetraloops  Part 1
    Ziggy 25 (aka Multiloop Test)
    Reversed G-C Multibranch Loop Closing Base Pairs 3
    SHAPE Profile - A-C Mismatch - Pilot Run 2A
    SHAPE Profile - G-A Mismatch - Pilot Run 2B
    Neck strength analysis 1 of 3 - Strong - alternating GCs.
    Neck strength analysis 2 of 3 - Medium - alternating AUs.
    SHAPE Profile - C-C Mismatch - Pilot Run 2B
    SHAPE Profile - A-A Mismatch - Pilot Run 2A
    Late bulge
    Late bulge control
    Intrinsically Red
    Intrinsical - Frequency 3
    Intrinsical - Frequency 4
    Short Neck and Split Ends
    Adding some sweet triloops
    Ribozyme 1: Hammerhead variant
    JR s Let s Break the Barcode - 2 nt Dangling End Gap
    JR s Let s Break the Barcode - 3 nt Dangling End Gap
    Improving the Energy Model: Favoring an Equivalent Structure
    Improving the Energy Model: 5-Base Hairpin Loops
    Reproducibility Lab Round 3 - Shape 0
    Reproducibility Lab Round 3 - Shape 1
    Reproducibility Lab Round 3 - Shape 2
    Reproducibility Lab Round 3 - Shape 3
    Reproducibility Lab Round 3 - Shape 4
    Reproducibility Lab Round 3 - Shape 5
    Reproducibility Lab Round 3 - Shape 6
    Reproducibility Lab Round 3 - Shape 7
    Reproducibility Lab Round 3 - Shape 8
    Reproducibility Lab Round 3 - Shape 9
    Reproducibility Lab Round 3 - Shape 10
    Reproducibility Lab Round 3 - Shape 11
    Reproducibility Lab Round 3 - Shape 12
    Reproducibility Lab Round 3 - Shape 13
    Reproducibility Lab Round 3 - Shape 14
    Reproducibility Lab Round 3 - Shape 15
    Reproducibility Lab Round 3 - Shape 16
    Reproducibility Lab Round 3 - Shape 17
    Reproducibility Lab Round 3 - Shape 18
    Reproducibility Lab Round 3 - Shape 19
    Reproducibility Lab Round 3 - Shape 20
    Motif Assembled GAAA tetraloop binders - Shape 0
    Motif Assembled GAAA tetraloop binders - Shape 1
    Motif Assembled GAAA tetraloop binders - Shape 2
    Motif Assembled GAAA tetraloop binders - Shape 4
    Motif Assembled GAAA tetraloop binders - Shape 6
    Motif Assembled GAAA tetraloop binders - Shape 7
    Motif Assembled GAAA tetraloop binders - Shape 8
    Motif Assembled GAAA tetraloop binders - Shape 10
    Motif Assembled GAAA tetraloop binders - Shape 11
    Johan s sequences
     2.989

    R83

    3/27/2014

    P4-P6 domain  Tetrahymena ribozyme was also run,
    but only in R83, not R83.2 or R83.3
    R83.xlsx
    Wobble Quad Stability 2
    Wobble Quad Stability 3
    Wobble Quad Stability 4
    Wobble Quad Control 1
    SHAPE Profile - C-U Mismatch - Pilot Run 2A
    SHAPE Profile - C-A Mismatch - Pilot Run 2B
    SHAPE Profile - A-C Mismatch - Pilot Run 2B
    SHAPE Profile - G-A Mismatch - Pilot Run 2A
    SHAPE Profile - C-C Mismatch - Pilot Run 2A
    Early bulge control
    Intrinsical - Frequency 5
    Triloop Hairpin and Stem Loop - Helix Stability
    The G Quadruplex - Round 2
    New Frontier 4
    SAM II Riboswitch
    1.946 

    R83.0002

    4/1/2014

     

    R83.0002.xlsx

    R83.0002.googlesheet

     4.907

    R83.0003

    4/3/2014

     

    R83.0003.xlsx

    R83.0003.googlesheet

     5.690

    R84

    4/21/2014

    R84.xlsx

    R84.googlesheet

    FMN Binding Site - Rotated
    SHAPE Profile - C-U Mismatch - Pilot Run 2B
    SHAPE Profile - Most Likely Base Pair U/A - Variation 1.1
    Most Likely Base Pair U/A - Variation 1.1B
    SHAPE Profile - Most Likely Base Pair U/A - Variation 1.3
    SHAPE Profile - Most Likely Base Pair G/C - Variation 2
    SHAPE Profile - Most Likely Base Pair G/C - Variation 2B
    Kinky Bits
    JR s Let s Break the Barcode - Adjacent Barcode Version
    The Donkey s Tail
    A-U Closing Base Pairs - 4.1
    A-U Closing Base Pairs - 4.2
    G-U Closing Base Pairs - 4.3
    G-U Closing Base Pairs - 4.4
    Motif study: the S-turn
    Consensus
    Pure A
    GA mismatch only
    G14A
    Alternative  C-C mismatch
    Alternative  U-C mismatch
    Alternative  U-C & A-C mismatches
    G12A
    Mad multiloop - Pentaloop 1
    Pentaloop 2
    Pentaloop 3
    Hexaloop 1
    Hexaloop 2
    Hexaloop 3
    Neck-Hairpin Spacing 3
    Neck-Hairpin Spacing 1
    Neck-Hairpin Spacing 0
    Neck-Hairpin Spacing 2
    Return of the boost
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 6
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 5
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 4
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 3
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 2
    Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 1
    Hairpin ribozyme
    Variant 1
    Variant 2
    RNA Transient Structures and pre-miRs - Shape 0
    RNA Transient Structures and pre-miRs - Shape 1
    RNA Transient Structures and pre-miRs - Shape 2
    RNA Transient Structures and pre-miRs - Shape 3
    RNA Transient Structures and pre-miRs - Shape 4
    RNA Transient Structures and pre-miRs - Shape 5
    RNA Transient Structures and pre-miRs - Shape 6
    RNA Transient Structures and pre-miRs - Shape 7
    RNA Transient Structures and pre-miRs - Shape 10
     2.725

    R85

    5/9/2014

    R85.xlsx

    R85.googlesheet

    SHAPE Profile - Most Likely Base Pair U/A - Variation 1.2
    SHAPE Profile - Most Likely Base Pair U/A - Variation 1.4
    SHAPE Profile - Most Likely Base Pair C/G - Variation 2
    SHAPE Profile - Most Likely Base Pair C/G - Variation 2B
    GGG/UCC Wobble Closing Base Pairs - Hexaloop RE
    GGG/UCC Wobble Closing Base Pairs - Heptaloop
    5  Hairpin Stem  Part 1 - Five Base Pairs + UUCG Tetraloop
    Stabilise the 1-1-1-1-1 multiloop
    FMN in zigzag
    L3-9
    L3-8
    L3-7
    L3-6
    L3-5
    L3-4
    Helix Comparison - 4x4 Loop
    Helix Comparison - 5x5 Loop
    Helix Comparison - 6x6 Loop
    Helix Comparison - Four Base Pair Stem
    Helix Comparison - Eight Base Pair Stem
    Helix Comparison - Stem 2 G-U
    Helix Comparison - Stem 1 G-U
    New Frontier 5
    Telephone
    Effect of Bulge Proximity on RNA Stability
    Effect of Bulge Proximity on RNA Stability:  More Distance
    FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 1
    FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 2
    FMN Mimic Pilot - AGUAUA/UAACA
    FMN Mimic Pilot - (GUAGUA/GAAAC & AGGAUA/UAAUU)
    FMN Mimic Pilot - (UGUAUU/GAAGG & UGGAUA/GACGG)
    FMN Mimic Pilot - (CUGAAC/GACGG & CGUUAC/GGAGG)
    FMN Mimic Pilot - (AGGAUA/UACUG & AGGAUA/UAAGG)
    FMN Mimic Pilot - (CUGAGC/GACGG & CGGAUA/GACGG)
    Unbound
    Bound - Mimic CCUAUC--GAAGG
    Bound - Mimic GUAGUA--GAAAC
    Bound - Mimic UGUAUU--GAAGG
    Bound - Mimic AGGAUA--UAAUU
    Bound - Mimic UGGAUA--GACGG
    Bound - Mimic CUGAAC--GACGG
    Bound - Mimic AGUAUA--UAACA
    Bound - Mimic CGUUAC--GGAGG
    Aptamer secondary structure - Shape 2
    Aptamer secondary structure - Shape 5
    Aptamer secondary structure - Shape 6
    Aptamer secondary structure - Shape 7
    Aptamer secondary structure - Shape 8
    Reproducibility Lab 2 - Shape 0
    Reproducibility Lab 2 - Shape 1
    Reproducibility Lab 2 - Shape 2
    Reproducibility Lab 2 - Shape 3
    Reproducibility Lab 2 - Shape 4
    Reproducibility Lab 2 - Shape 5
    Reproducibility Lab 2 - Shape 6
    Reproducibility Lab 2 - Shape 7
    Reproducibility Lab 2 - Shape 8
    Reproducibility Lab 2 - Shape 9
    Reproducibility Lab 2 - Shape 10
    Reproducibility Lab 2 - Shape 11
    Reproducibility Lab 2 - Shape 12
    Reproducibility Lab 2 - Shape 13
    Reproducibility Lab 2 - Shape 14
    Reproducibility Lab 2 - Shape 15
    Reproducibility Lab 2 - Shape 16
    Reproducibility Lab 2 - Shape 17
    Reproducibility Lab 2 - Shape 18
    Reproducibility Lab 2 - Shape 19
    Reproducibility Lab 2 - Shape 20
    Stanford Switch Puzzle
     2.295

    R86

    6/9/2014

    R86.xlsx

    R86.googlesheet

    20% Non Watson-Crick Base Pairs - Effortless
    40% Non Watson-Crick Base Pairs - Medium
    60% Non Watson-Crick Base Pairs - Heating Up
    70% Non Watson-Crick Base Pairs - Hard Mode
    80% Non Watson-Crick Base Pairs - Insanity
    Hand and Finger Remade - OFF State
    Hand and Finger Remade - Mimic
    Simple RNA Switch Remade - OFF State
    Simple RNA Switch Remade - Mimic
    Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus
    Hair Trigger - Sub 2 (Stable) by Brourd: -4.86 Kcal/mol Mimic Bonus
    Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus
    Bistable 3 - Mod of Eli by mat747: -4.86 Kcal/mol Mimic Bonus
    Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0
    Investigation of Alternative Human tRNA Structures - Shape 4
    Investigation of Alternative Human tRNA Structures - Shape 5
    Investigation of Alternative Human tRNA Structures - Shape 14
    Investigation of Alternative Human tRNA Structures - Shape 15
    Investigation of Alternative Human tRNA Structures - Shape 16
    Investigation of Alternative Human tRNA Structures - Shape 17
    Investigation of Alternative Human tRNA Structures - Shape 18
    Investigation of Alternative Human tRNA Structures - Shape 19
    Investigation of Alternative Human tRNA Structures - Shape 23
    Investigation of Alternative Human tRNA Structures - Shape 25
    Investigation of Alternative Human tRNA Structures - Shape 28
    Investigation of Alternative Human tRNA Structures - Shape 36
    Alternative structure space for human tRNAs - Shape 4
    Alternative structure space for human tRNAs - Shape 5
    Alternative structure space for human tRNAs - Shape 14
    Alternative structure space for human tRNAs - Shape 15
    Alternative structure space for human tRNAs - Shape 16
    Alternative structure space for human tRNAs - Shape 17
    Alternative structure space for human tRNAs - Shape 18
    Alternative structure space for human tRNAs - Shape 19
    Alternative structure space for human tRNAs - Shape 23
    Alternative structure space for human tRNAs - Shape 25
    Alternative structure space for human tRNAs - Shape 28
    Alternative structure space for human tRNAs - Shape 36
     3.217

    R87

    8/18/2014

    R87.xlsx

    R87.googlesheet

     

    Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - The Finger lab revisited - Gap size 2
    Lab Entry Level 2 - The Finger lab modified - Gap size 2
    Poly (A) Structure Analysis 2
    Multistate RNA Sequence - 2 Residues
    Multistate RNA Sequence - 3 Residues
    Multistate RNA Sequence - 4 Residues
    Hairpin Loop Comparison Pilot - Shape 0
    Hairpin Loop Comparison Pilot - Shape 1
    Hairpin Loop Comparison Pilot - Shape 2
    Hairpin Loop Comparison Pilot - Shape 3
    Hairpin Loop Comparison Pilot - Shape 4
    Hairpin Loop Comparison Pilot - Shape 5
    Hairpin Loop Comparison Pilot - Shape 6
    Hairpin Loop Comparison Pilot - Stem Comparison Tests
    SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 0
    SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 1
    SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 0
    SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 1
    Multistate RNA - CC/G bulge - Shape 0
    Cyanocobalamin (vitamin B12) RNA aptamer SHAPE profile - Shape 0
    Sarcin-ricin vs boosted internal loops - Shape 0
    Sarcin-ricin vs boosted internal loops - Shape 1
    Sarcin-ricin vs boosted internal loops - Shape 2
    Sarcin-ricin vs boosted internal loops - Shape 3
    Sarcin-ricin vs boosted internal loops - Shape 4
    Sarcin-ricin vs boosted internal loops - Shape 5
    Sarcin-ricin vs boosted internal loops - Shape 6
    2-2 Superboost
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 0
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 1
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 2
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 3
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 4
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 5
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 6
    Apical Loop Comparison - Dissimilar Stem Sequences - Shape 7
    Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 0
    Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 1
    Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 2
    Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0
    Alternative structure space for human tRNAs - Shape 4
    Alternative structure space for human tRNAs - Shape 5
    Alternative structure space for human tRNAs - Shape 14
    Alternative structure space for human tRNAs - Shape 15
    Alternative structure space for human tRNAs - Shape 16
    Alternative structure space for human tRNAs - Shape 17
    Alternative structure space for human tRNAs - Shape 18
    Alternative structure space for human tRNAs - Shape 19
    Alternative structure space for human tRNAs - Shape 23
    Alternative structure space for human tRNAs - Shape 25
    Alternative structure space for human tRNAs - Shape 28
    Alternative structure space for human tRNAs - Shape 36
     1.004

    R87.0001

    8/21/2014

    R87.xlsx

    R87.googlesheet

     1.731

    R87.0002

    8/21/2014

    R87.xlsx

    R87.googlesheet

    1.109

    R88

    8/27/2014

    R88.xlsx

    R88.googlesheet

    Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - The Cross lab revisited - Gap size 2
    Lab Entry Level 2 - The Cross lab modified - Gap size 2
     0.918
    R88.0002   5.627

    R89

    R89.xlsx

    R89.googlesheet

    Switch Cloud Lab: The Next Generation 4 - OFF
    Switch Cloud Lab: The Next Generation 4 - MIMIC
    Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus R2
    Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus R2
    Bistable 3 - Double Trouble by Darkfire47: -2.51 Kcal/mol Mimic Bonus
    Hair Trigger - Reresub 3 (Unstable) by Brourd: -2.51 Kcal/mol Mimic Bonus
    Pseudo-Titration Experiment: Lines - Errazaarge by ViennaUCT
    Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - Bulge Cross lab revisited - Gap size 2
    Lab Entry Level 2 - Bulge Cross lab modified - Gap size 2
    3.149
    R90

    R90.xlsx

    R90.googlesheet

    Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - Bend and Ends Sampler revisited - Frozen shape with gap size 2
    Lab Entry Level 2 - Bends and Ends Sampler modified - Gap size 2
    1.037
    R91

    R91.xlsx

    R90.googlesheet

    Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - The Asymmetry lab revisited - Gap size 2
    Lab Entry Level 2 - The Asymmetry lab modified - Gap size 2
    S1-KL1
    S1-KL1-noGU
    S1-KL-negative
    S1-KL-1S72_423
    S1-KL-new_A
    S1-KL-new_B
    S2-KL1
    S2-KL1-noGU
    S2-KL-negative
    S2-KL-1S72_423
    S2-KL-new_A
    S2-KL-new_B
    4/4 Base Pairs 5
    5/5 Base Pairs 5
    6/6 Base Pairs 5
    7/7 Base Pairs 5
    4/4 Base Pairs 3
    5/5 Base Pairs 3
    6/6 Base Pairs 3
    7/7 Base Pairs 3
    Shift 4/4 Base Pairs 5
    Shift 5/4 Base Pairs 5
    Shift 6/4 Base Pairs 5
    Shift 5/5 Base Pairs 3
    Shift 6/5 Base Pairs 3
    Shift 7/5 Base Pairs 3
    2.364
    R92

    R92.xlsx

    R92.googlesheet

    Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - The Backwards C lab revisited - Gap size 2
    Lab Entry Level 2 - The Backwards C lab modified - Gap size 2
    4 x 4 TEP Riboswitch 5
    5 x 5 TEP Riboswitch 5
    6 x 6 TEP Riboswitch 5
    4 x 4 TEP Riboswitch 3
    5 x 5 TEP Riboswitch 3
    6 x 6 TEP Riboswitch 3
    Shift 5 x 5 TEP Riboswitch 5
    Shift 6 x 5 TEP Riboswitch 5
    Shift 7 x 5 TEP Riboswitch 5
    Shift 5 x 5 TEP Riboswitch 3
    Shift 6 x 5 TEP Riboswitch 3
    Shift 7 x 5 TEP Riboswitch 3
    Structure Competition 3x3 v1
    Structure Competition 3x3 v2
    Structure Competition 2x2 v1
    Structure Competition 2x2 v2
    Structure Competition 1x1 v1
    Structure Competition 1x1 v2
    Structure Competition 0x0 v1
    Structure Competition 0x0 v2
    TEP Aptamer Chemical Mapping Footprint
    TEP Aptamer Chemical Mapping Footprint 2
    TEP Aptamer Chemical Mapping Footprint 3
    6.407
    R93 R93.googlesheet
    binary capture
    Control II - Intermolecular KL
    27.251
    R94 [1] R94.googlesheet [2]
    Three Branch Junction - AAAUAAA
    Three Branch Junction - Sequence Mutation 1
    Three Branch Junction - Sequence Mutation 2
    Three Branch Junction - Sequence Mutation 3
    Three Branch Junction - Structure Mutation 1
    Three Branch Junction - Structure Mutation 2
    External Loop Test
    Hairpin Loop Test
    Multibranch Loop Test
    88-nt
    72-nt
    Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - Chalk Outline lab revisited - Gap size 2
    Lab Entry Level 2 - Chalk Outline lab modified - Gap size 2
    Design your own Kissing-Loop
    Control I - Parallel Crossover KL
    Control II - Intermolecular KL
    Six of One Mod
    Solutions Aplenty by Mayanne
    Pentaloop by Hyphema
    Rational Design by ElNando888
    Mod of Jandersonlee s Flip Turn 6-4 - Mark IV (split further) by Jieux
    Collage by Hyphema
    Slip Loop 5-4 by Jandersonlee
    Straighten It 3 by Starryjess
    Branch Zipper by codygeary
    Can t Score This 6x6 by Jnicol
    Mod of Barely Score This 6x5 by Jnicol
    Mod of Cross Section by Starryjess
    Mod of 1x1 Loop Experiment by Jieux
    Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - Tilted picture of running man revisited - Gap size 2
    Lab Entry Level 2 - Tilted picture of running man modified - Gap size 2
    GgaC/GgaC vs GagC/GagC 1
    GgaC/GgaC vs GagC/GagC 2
    GgaC/GgaC vs GagC/GagC 3
    GgaC/GgaC vs GagC/GagC 4
    GgaC/GgaC vs GagC/GagC 5
    GgaC/GgaC vs GagC/GagC 6
    GgaC/GgaC vs GagC/GagC 7
    GgaC/GgaC vs GagC/GagC 8
    GgaC/GgaC vs GagC/GagC 9
    GgaC/GgaC vs GagC/GagC 10
    GgaC/GgaC vs GagC/GagC 11
    GgaC/GgaC vs GagC/GagC 12
    GgaC/GgaC vs GagC/GagC 13
    GagC/GagC vs GgaC/GgaC 1
    GagC/GagC vs GgaC/GgaC 2
    GagC/GagC vs GgaC/GgaC 3
    GagG/CagC vs GgaG/CgaC
    GgaG/CgaC vs GagG/CagC
    GgaC/GgaC vs GagC/GagC 1B
    GagC/GagC vs GgaC/GgaC 1B
     3.347
    R95 R95.googlesheet
    Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 0
    Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 4
    Lab Entry Level 1 - Water Strider revisited - Gap size 2
    Lab Entry Level 2 - Water Strider modified - Gap size 2
    5.067
    R96

    R96.googlesheet

    R96.fusion table

    Same State 1
    Same State 2
    Same State NG 1
    Same State NG 2
    Same State NG 3
    Exclusion 1
    Exclusion 2
    Exclusion 3
    Exclusion 4
    Brourd's Mod of Exclusion 4
    Exclusion 5
    Exclusion 6
    Sensor for hsa-mir-208a
    Sensor v2, turn-off variant
    Sensor v2, turn-off variant 2
    Sensor v3, turn-off variant 1
    Sensor v3, turn-off variant 2
     
    R97

    R97.googlesheet

    R97.xlsx

    R97.fusion table

    R97ExclusionsWithDesignerAndLink.googlesheet

    R97.Meechl's Exclusion Plus - Fusion Table

    Most Recent Fusion Table for R97 (hopefully)

    Brourd's Mod of Exclusion 4
    Exclusion 1
    Exclusion 2
    Exclusion 3
    Exclusion 4
    Exclusion 5
    Exclusion 6
    Sensor, turn-off variant 1
     
     

    R98 NG Fusion Table

       
           
    R100 R100 google spreadsheet    
    R101 R101 FMN MS2 Riboswitch Structure, with Switch Graphs    
    R102 [3]    
    R103 R103 Google spreadsheet    

     

    Lab Data Resources

    Players and developers have made valuable collections of lab data.

    Signal to noise averages per lab by Meechl

    Signal to noise averages per round by Meechl

    Cloud Lab Data by Meechl

    All Rounds by Meechl

    List of past labs by Omei

    All Rounds - All the data - Fusion table by Omei

    Lab Summary - Round data by developers

    Synthesized Labs - Lab data by developers

    Das Lab Files by developers and Omei 

    Comments on MS2 round 1 lab results by Salish99

    MS2 Spreadsheet by Meechl

    Fusion Table for MS2 Riboswitches on Chip (Round 1) by Omei

    Fusion Table Resources

    Intro To Fusion Tables by Eli Fisker

    Variations On Maslow Design, Round 2 by Omei

    Creating A Nearby Solutions Fusion Table by JandersonLee

    See also