Reproducibility Test Lab: Difference between revisions
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<td>[http://eterna.cmu.edu/web/lab/ | <p><span style="font-family: courier new,courier;">AAAAAGCUCC AUGAGGAUAU AGAGCAGAAA AUAUGCCUAG AAGGCAUGGU AAAAUAGCAA AAA</span></p> | ||
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<td>[http://eterna.cmu.edu/web/lab/2426167 LS2] representative. ID=[http://eterna.cmu.edu/game/browse/2426167/?filter1_arg1=2435428&filter1=Id&filter1_arg2=2435428 2435428]. Switch lab. Good scores in both states. State 1 not predicted to be MFE by Eterna energy model.<br /></td> | |||
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<td>[http://eterna.cmu.edu/web/lab/ | <p><span style="font-family: courier new,courier;">UAAGCACCAG GAGCAGGACC AGCGAAACAA AACAAACAAA GCAGGACCAG CACCAGGAGC AAA</span></p> | ||
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<td>[http://eterna.cmu.edu/web/lab/2712495 Ball and Chain] representative. ID=[http://eterna.cmu.edu/game/browse/2712495/?filter1_arg1=2763519&filter1=Id&filter1_arg2=2763519 2763519]. Score = 96. Systematic testing of CG bases anchoring 1-1 loops with both As.<br /></td> | |||
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<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. | <td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. Score = NN.</td> | ||
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<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. | <td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. Score = NN.</td> | ||
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<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. | <td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. Score = NN.</td> | ||
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<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. | <td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&filter1=Id&filter1_arg2=SOLNNNN SOLNNNN]. Score = NN.</td> | ||
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<p><span style="font-family: courier new,courier;">GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC </span></p> | <p><span style="font-family: courier new,courier;">GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC </span></p> | ||
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<td>[http://eterna.cmu.edu/web/lab/2712696 Huffman]. ID=[http://eterna.cmu.edu/game/browse/2712696/?filter1_arg1=2736789&filter1=Id&filter1_arg2=2736789 2736789]. | <td>[http://eterna.cmu.edu/web/lab/2712696 Huffman]. ID=[http://eterna.cmu.edu/game/browse/2712696/?filter1_arg1=2736789&filter1=Id&filter1_arg2=2736789 2736789]. Score = 96. Sequence apperared to have stable stack including non-canconical pairs.<br /></td> | ||
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<p><span style="font-family: courier new,courier;">AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA</span></p> | <p><span style="font-family: courier new,courier;">AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA</span></p> | ||
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<td>[http://eterna.cmu.edu/web/lab/2333413 Triloop Buffet]. Round 2. ID=[http://eterna.cmu.edu/game/browse/2333413/?filter1_arg1=2676335&filter1=Id&filter1_arg2=2676335 2676335]. | <td>[http://eterna.cmu.edu/web/lab/2333413 Triloop Buffet]. Round 2. ID=[http://eterna.cmu.edu/game/browse/2333413/?filter1_arg1=2676335&filter1=Id&filter1_arg2=2676335 2676335]. Score = 91. Sequence apperared to show tertiary bonding.</td> | ||
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Revision as of 00:31, 1 September 2013
[http: LabName] representative.
Round N. ID=[http: DesignID].
Score = NN.
The Reproducibilty Test Lab is a special lab that is (will be) synthesized in each synthesis round. The objectives for this lab are:
- Provide a consistent measure of the reproducibilty of the cloud lab synthesis results, for long term quality control,
- Determine how much of the variation in synthesis results is captured by the error estimates reported for each synthesized base,
- Provide some guidance as to where the synthesis process might be improved, in order to increase reproducibility, and
- Give those analysing the synthesis data a better understanding of the variation to expect when comparing data from different synthesis rounds.
Initial Sequences
<tbody> </tbody>Sequence | Description or rationale for inclusion |
Original SHAPE data, or expected folding |
AGUCAUCUAC UACGAAAAAC ACAUUCUAUU CGAAAACGAA UAGAAUGUGU CGUAGUAGAU GAC |
Cloud Lab 1 representative. Round 1. ID=2366937. |
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GCAAGGACGA AUAAGCCAUA ACCGCAGGGA AACACUGAAC GGAGCCGAAA GAGCAAGCAA UAA |
Cloud Lab 4 representative. Round 2. ID=2655773. |
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GAGAUGGGUA ACGAAAGUUG CGCUGCCGAA UGAAAGUUCU GGAUGAAAGU CUGGUGGCCU AUC | Cloud Lab 9 representative. Round 2. ID=2588792. Score = 78. High GU content. |
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AGAGUGAAGG ACGGAGAAUC UCCGUCGUCG CGAAGCGGCC CUGGGCUUCC CAGGCUUCAC UCA | Cloud Lab 15 representative. Round 1. ID=2337872. Score = 96. |
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GAGAUAUUAU AAUAUUAUAA UAUGCAAAGA AAUAAGAAGC AUAUUAUAAU AUUAUAAUAU CAA | Cloud Lab 18 representative. Round 2. ID=2596919. Score = 98. High AU count. |
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GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC | Clouud Lab 19 representative. Round 1. ID=2339041. Score = 92. Big loop of all A. |
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GCGGCGGCAA AGGCGGCGCA ACGCGGCGGA AAAUCGGCGG CGACGCGGCG GAAAUCGGCG GCG |
Cloud Lab 20 representative. Round 1. ID=2335964. Score = 91. Lab has lots of 1-1 loops. Sequence is Christmas tree that scored well. |
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GUACAAAUCC UCGAAAACUC GAGGAUAUAU CAAAAGAUAG AAGGCGAGAA AAAAAGGAGG UAC |
Hair Trigger representative. ID=2433439. From switch lab, with a similar estimated MFE between the two states (without aptamer.) | |
AAAAAGCUCC AUGAGGAUAU AGAGCAGAAA AUAUGCCUAG AAGGCAUGGU AAAAUAGCAA AAA |
LS2 representative. ID=2435428. Switch lab. Good scores in both states. State 1 not predicted to be MFE by Eterna energy model. |
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UAAGCACCAG GAGCAGGACC AGCGAAACAA AACAAACAAA GCAGGACCAG CACCAGGAGC AAA |
Ball and Chain representative. ID=2763519. Score = 96. Systematic testing of CG bases anchoring 1-1 loops with both As. |
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LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC |
Huffman. ID=2736789. Score = 96. Sequence apperared to have stable stack including non-canconical pairs. |
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AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA |
Triloop Buffet. Round 2. ID=2676335. Score = 91. Sequence apperared to show tertiary bonding. | |
AUCGAAAGAU | Very short sequence |
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Omei → rhiju: Will do. Am I correct in thinking that can refine the set over time, if we decide we would benefit from different sequences?
rhiju → Omei: yes of course. I think we're granting you (and the players you represent) a 'standing order' of 40 sequences over each cycle to characterize errors and to make suggestions to us devs for viewing & experimental improvements. I'm excited to see what you find!