Reproducibility Test Lab: Difference between revisions

From Eterna Wiki

No edit summary
No edit summary
Line 50: Line 50:
<td><span style="font-family: courier new,courier;">GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC&nbsp;</span></td>
<td><span style="font-family: courier new,courier;">GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC&nbsp;</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&amp;filter1=Id&amp;filter1_arg2=2339041 2339041].<br />Score = 92.&nbsp; 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&amp;filter1=Id&amp;filter1_arg2=2339041 2339041].<br />Score = 92.&nbsp; Big loop of all A.<br /></td>
<td>&nbsp;</td>
</tr>
<tr>
<td>
<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&amp;filter1=Id&amp;filter1_arg2=2335964 2335964].<br />Score = 91. Lab has lots of 1-1 loops.&nbsp; Sequence is Christmas tree that scored well.<br /></td>
<td>&nbsp;</td>
</tr>
<tr>
<td>
<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&amp;filter1=Id&amp;filter1_arg2=2433439 2433439]. From switch lab, with a similar estimated MFE between the two states (without aptamer.)</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&amp;filter1=Id&amp;filter1_arg2=SOLNNNN SOLNNNN].<br />Score = NN.</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&amp;filter1=Id&amp;filter1_arg2=SOLNNNN SOLNNNN].<br />Score = NN.</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&amp;filter1=Id&amp;filter1_arg2=SOLNNNN SOLNNNN].<br />Score = NN.</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>[http://eterna.cmu.edu/web/lab/LABNNNN LabName] representative. Round N. ID=[http://eterna.cmu.edu/game/browse/LABNNNN/?filter1_arg1=SOLNNNN&amp;filter1=Id&amp;filter1_arg2=SOLNNNN SOLNNNN].<br />Score = NN.</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tr>

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.
Score = 94.

SHAPE 2366937.png
GCAAGGACGA AUAAGCCAUA ACCGCAGGGA AACACUGAAC GGAGCCGAAA GAGCAAGCAA UAA

Cloud Lab 4 representative. Round 2. ID=2655773.
Score = 88.

SHAPE 2655773.png
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.
 
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.
 
  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.
 

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
 
 

 

 
     
     
     
     
     
     
     

 

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!