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<p>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 | <p><span style="font-size: small;">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 Vienna 2.1.1 melt point of each design submitted. This new field made it into the text reports, but not the spreadsheets. (Something to do for the next publication.)<br /></span></p> | ||
<p> | <p><span style="font-size: small;">My lab tool includes a forecasting tool that looks at factors that have correlated well with past synthesis score. The current version of the forecasting tool looks at the following factors:</span></p> | ||
<p>1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</p> | <p><span style="font-size: small;">1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</span></p> | ||
<p>2) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model</p> | <p><span style="font-size: small;">2) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model</span></p> | ||
<p>3) The melt point of the design (as reported by the EteRNA server)</p> | <p><span style="font-size: small;">3) The melt point of the design (as reported by the EteRNA server)</span></p> | ||
<p>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).</p> | <p><span style="font-size: small;">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).</span></p> | ||
<p>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.</p> | <p><span style="font-size: small;">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.</span></p> | ||
<p>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.</p> | <p><span style="font-size: small;">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.</span></p> | ||
<p> </p> | <p> </p> | ||
<p | <p><span style="font-size: large;"><strong>N</strong>ew set of reports and spreadsheets posted September 20 1:34PM MST</span></p> | ||
<p> | <p><span style="font-size: medium;">The folder containing both reports and spreadsheets is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2RGJTaGZFSkVkS1U&usp=sharing">ReportsActive2013Sep20</a></span>. </p> | ||
<p> </p> | <p> </p> | ||
<p><span style="font-size: | <p><span style="font-size: large;">I am thinking about how to add Vienna 2.1.1 melt curves and dot plots to these reports. I can modify my scripts to generate these, but they are in Postscript format. I haven't yet figured out how to incorporate them quickly in my reports and spreadsheets. If you think there is any easy way to do this, please let me know.<br /></span></p> | ||
<p> </p> | |||
<p><span style="font-size: large;">Please let me know if you have any other things you would like to see in my lab reports.</span></p> | |||
<p> | |||
<p><span style="font-size: | |||
Revision as of 20:48, 20 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 Vienna 2.1.1 melt point of each design submitted. This new field made it into the text reports, but not the spreadsheets. (Something to do for the next publication.)
My lab tool includes a forecasting tool that 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 set of reports and spreadsheets posted September 20 1:34PM MST
The folder containing both reports and spreadsheets is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2RGJTaGZFSkVkS1U&usp=sharing">ReportsActive2013Sep20</a>.
I am thinking about how to add Vienna 2.1.1 melt curves and dot plots to these reports. I can modify my scripts to generate these, but they are in Postscript format. I haven't yet figured out how to incorporate them quickly in my reports and spreadsheets. If you think there is any easy way to do this, please let me know.
Please let me know if you have any other things you would like to see in my lab reports.
