Reproducibility Test Lab: Difference between revisions
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<td><span style="font-family: courier new,courier;">GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC </span></td> | <td><span style="font-family: courier new,courier;">GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC </span></td> | ||
<td>[http://eterna.cmu.edu/web/lab/2333436 Clouud Lab 19] representative. Round 1. ID=[http://eterna.cmu.edu/game/browse/2333436/?filter1_arg1=2339041&filter1=Id&filter1_arg2=2339041 2339041].<br />Score = 92. Big loop of all A.<br /></td> | <td>[http://eterna.cmu.edu/web/lab/2333436 Clouud Lab 19] representative. Round 1. ID=[http://eterna.cmu.edu/game/browse/2333436/?filter1_arg1=2339041&filter1=Id&filter1_arg2=2339041 2339041].<br />Score = 92. Big loop of all A.<br /></td> | ||
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<p><span style="font-family: courier new,courier;">GCGGCGGCAA AGGCGGCGCA ACGCGGCGGA AAAUCGGCGG CGACGCGGCG GAAAUCGGCG GCG</span></p> | |||
</td> | |||
<td>[http://eterna.cmu.edu/web/lab/2333440 Cloud Lab 20] representative. Round 1. ID=[http://eterna.cmu.edu/game/browse/2333440/?filter1_arg1=2335964&filter1=Id&filter1_arg2=2335964 2335964].<br />Score = 91. Lab has lots of 1-1 loops. Sequence is Christmas tree that scored well.<br /></td> | |||
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<p><span style="font-family: courier new,courier;">GUACAAAUCC UCGAAAACUC GAGGAUAUAU CAAAAGAUAG AAGGCGAGAA AAAAAGGAGG UAC</span></p> | |||
</td> | |||
<td>[http://eterna.cmu.edu/web/lab/2426157 Hair Trigger] representative. ID=[http://eterna.cmu.edu/game/browse/2426157/?filter1_arg1=2433439&filter1=Id&filter1_arg2=2433439 2433439]. From switch lab, with a similar estimated MFE between the two states (without aptamer.)</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].<br />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].<br />Score = NN.</td> | |||
<td> </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].<br />Score = NN.</td> | |||
<td> </td> | |||
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<td> </td> | |||
<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].<br />Score = NN.</td> | |||
<td> </td> | <td> </td> | ||
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Revision as of 22:59, 31 August 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. |
|
GCAAGGACGA AUAAGCCAUA ACCGCAGGGA AACACUGAAC GGAGCCGAAA GAGCAAGCAA UAA |
Cloud Lab 4 representative. Round 2. ID=2655773. |
|
GAGAUGGGUA ACGAAAGUUG CGCUGCCGAA UGAAAGUUCU GGAUGAAAGU CUGGUGGCCU AUC | Cloud Lab 9 representative. Round 2. ID=2588792. Score = 78. High GU content. |
|
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. |
|
GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC | Clouud Lab 19 representative. Round 1. ID=2339041. Score = 92. Big loop of all A. |
|
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. |
|
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.) | |
LabName representative. Round N. ID=SOLNNNN. Score = NN. |
||
LabName representative. Round N. ID=SOLNNNN. Score = NN. |
||
LabName representative. Round N. ID=SOLNNNN. Score = NN. |
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LabName representative. Round N. ID=SOLNNNN. Score = NN. |
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LabName representative. Round N. ID=SOLNNNN. Score = NN. |
||
LabName representative. Round N. ID=SOLNNNN. Score = NN. |
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GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC |
Huffman. ID=2736789. Score = 96. Sequence apperared to have stable stack including non-canconical pairs. |
|
AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA |
Triloop Buffet. Round 2. ID=2676335. Score = 91. Sequence apperared to show tertiary bonding. |
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AUCGAAAGAU | Very short sequence |
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rhiju → Omei: please submit up to 40 sequences, this weekend if possible!
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!
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!