Difference between revisions of "User:Dennis9600"

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<p>The links below take you to analysis by my lab tool on the currently active labs as of 2013-Sep-13.&nbsp; In this edition I have added a field for the melt point of each design submitted and I have started to report the result of my forecasting tool.</p>
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<p>The links below take you to analysis by my lab tool on the currently active labs.&nbsp; In this edition I have added a field for the melt point of each design submitted and I have started to report the result of my forecasting tool.</p>
 
<p>The forecasting tool looks at factors that have correlated well with past synthesis score.&nbsp; The current version of the forecasting tool looks at the following factors:</p>
 
<p>The forecasting tool looks at factors that have correlated well with past synthesis score.&nbsp; The current version of the forecasting tool looks at the following factors:</p>
 
<p>1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</p>
 
<p>1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</p>
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<p>I have also looked at a) temperature and b) designer's EteRNA points.&nbsp; Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.&nbsp; Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.</p>
 
<p>I have also looked at a) temperature and b) designer's EteRNA points.&nbsp; Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.&nbsp; Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.</p>
 
<p>The current set of labs includes many that have locked bases forming non-canonical pairs.&nbsp; Past labs have rarely featured designs like that, so my forecasting tool probably shouldn't be very good at forecasting the outcome of these labs.</p>
 
<p>The current set of labs includes many that have locked bases forming non-canonical pairs.&nbsp; Past labs have rarely featured designs like that, so my forecasting tool probably shouldn't be very good at forecasting the outcome of these labs.</p>
<p><span style="font-size: medium;"><strong>New reports posted September 13 3:43PM MST</strong></span>:</p>
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<p>&nbsp;</p>
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<p><strong><span style="font-size: medium;">New Google Spreadsheet reports posted September 15 12:24PM MST</span></strong></p>
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<p>By popular demand (ok, one player asked), I am publishing a round of reports as Google Spreadsheets.&nbsp; The folder containing this new set of reports is <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2b1FFVmhEUVBPdDg">ReportsActiveLabs2013Sep15<br /></a></p>
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<p>If people prefer this format, or if I don't hear from anyone, I am going to continue using it.</p>
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<p>&nbsp;</p>
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<p><span style="font-size: medium;"><strong>Old text format reports posted September 13 3:43PM MST</strong></span>:</p>
 
<p><span style="font-size: small;"><a href="https://docs.google.com/file/d/0B-rDnoMjFSH2RmVGVDJnUk5RZjA/">Chicken Leg Reversed</a></span></p>
 
<p><span style="font-size: small;"><a href="https://docs.google.com/file/d/0B-rDnoMjFSH2RmVGVDJnUk5RZjA/">Chicken Leg Reversed</a></span></p>
 
<p><span style="font-size: small;"><a href="https://docs.google.com/file/d/0B-rDnoMjFSH2bXZjSWdsUGZvUE0/">Double 1-3 Loop</a></span></p>
 
<p><span style="font-size: small;"><a href="https://docs.google.com/file/d/0B-rDnoMjFSH2bXZjSWdsUGZvUE0/">Double 1-3 Loop</a></span></p>

Revision as of 19:27, 15 September 2013

The links below take you to analysis by my lab tool on the currently active labs.  In this edition I have added a field for the melt point of each design submitted and I have started to report the result of my forecasting tool.

The forecasting tool looks at factors that have correlated well with past synthesis score.  The current version of the forecasting tool looks at the following factors:

1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)

2) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model

3) The melt point of the design (as reported by the EteRNA server)

4) The percentages of C,U, and G in the design, and how far they differ from 13, 10, and 21% respectively (the Berex Strategy).

I have also looked at a) temperature and b) designer's EteRNA points.  Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.  Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.

The current set of labs includes many that have locked bases forming non-canonical pairs.  Past labs have rarely featured designs like that, so my forecasting tool probably shouldn't be very good at forecasting the outcome of these labs.

 

New Google Spreadsheet reports posted September 15 12:24PM MST

By popular demand (ok, one player asked), I am publishing a round of reports as Google Spreadsheets.  The folder containing this new set of reports is ReportsActiveLabs2013Sep15

If people prefer this format, or if I don't hear from anyone, I am going to continue using it.

 

Old text format reports posted September 13 3:43PM MST:

Chicken Leg Reversed

Double 1-3 Loop

ShapeTest 1st State

ShapeTest 2nd State

G-U_GAGA_Tetraloop_Boost

Hexaloop...

Large GU Stack

Neck Strength Analysis 3 of 3

Repetitious Sequences

Reversed motor Step 1

Robot Serial Killer 3

Shape Profile - A-C Mismatch

SHAPE Profile - A-G Mismatch

SHAPE Profile - C-A Mismatch

SHAPE Profile - C-C Mismatch

SHAPE Profile - C-U Mismatch

SHAPE Profile - G-A Mismatch

SHAPE Profile - U-C Mismatch

SHAPE Profile - U-U Mismatch

Unmodified tRNA Sequences

Wobble Quad Stability 1

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