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<p><span style="font-size: medium;"><strong>Analysis Reports and Spreadsheets produced by my Python script can be found in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2cDFibWt6T19nRzg&amp;usp=sharing">ReportsActiveLabs</a>.</strong></span></p>
<p><span style="font-size: medium;"><strong>Analysis Reports and Spreadsheets produced by my Python script can be found in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2cDFibWt6T19nRzg&amp;usp=sharing">ReportsActiveLabs</a>.&nbsp; You can bookmark this folder in your browser.&nbsp; I have decided to stick with one folder rather than change with each publication cycle.&nbsp; <br /></strong></span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><span style="font-size: medium;">11/4/2013: The results posted so far do not cover all of the active labs for this cycle.&nbsp; :-( </span></p>
<p><span style="font-size: medium;">I have been struggling with the current round of active labs.&nbsp; Two issues have been killing my analysis tools: </span></p>
<p><span style="font-size: medium;">1) There are non-canonical pairs in the target structures of many of the labs, e.g A-A pairs. </span></p>
<p><span style="font-size: medium;">I have modified my script so that it recognizes the presence of non-canonical pairs, and uses the --nsp option when calling the Vienna RNA tools.&nbsp; However, I don't believe the results that are produced.<br /></span></p>
<p><span style="font-size: medium;">2) The "tails" that are added to the hook aren't the same any more.&nbsp; They differ from lab to lab.&nbsp; I have a fix for this issue and you will start to see more and more lab results posted in the folder mentioned above.&nbsp; Thanks to ElNando for info that lead to the fix!<br /></span></p>
<p><span style="font-size: medium;"><br /></span></p>
<p><span style="font-size: medium;"><br /></span></p>
<p><span style="font-size: medium;">If you think you have an answer/suggestion for issue #1 above, please help me out by sending me a PM.&nbsp; Thanks in advance for any help!</span></p>
<p><span style="font-size: medium;">If you think you have an answer/suggestion for issue #1 above, please help me out by sending me a PM.&nbsp; Thanks in advance for any help!</span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><span style="font-size: small;"><strong>In this edition:</strong></span></p>
<p><span style="font-size: small;"><strong>In this edition:</strong></span></p>
<p><span style="font-size: small;"><strong>&nbsp;</strong>1)&nbsp; there is a field for the Vienna 2.1.1 melt point of each design submitted.&nbsp; This new field now appears in both the text reports and the spreadsheets.<br /></span></p>
<p><span style="font-size: small;"><strong>&nbsp; 1) If the target structure contains locked, non-Canonical pairs, the Vienna tools are called with a --nsp option that allows the pairing and assigns an energy of 0 to it.&nbsp; Zero may not</strong></span></p>
<p><span style="font-size: small;"><strong>be the best value to use, but it seems to be better than not doing anything.<br /></strong></span></p>
<p><span style="font-size: small;"><strong>&nbsp; 2) Some of the labs now have a starting sequence of 'GG' instead of 'GGAAA'.&nbsp; It looks like the devs have left things open for additional "tails" to be used in future labs.&nbsp; For now, my script</strong></span></p>
<p><span style="font-size: small;"><strong>recognizes both of the sequences that have appeared and uses the correct one for each lab.<br /></strong></span></p>
<p><span style="font-size: small;">&nbsp;3)&nbsp; There is a field for the Vienna 2.1.1 melt point of each design submitted.&nbsp; This new field now appears in both the text reports and the spreadsheets.<br /></span></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 scores.&nbsp; The current version of the forecasting tool looks at the following factors:</span></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 scores.&nbsp; The current version of the forecasting tool looks at the following factors:</span></p>
<p><span style="font-size: small;">a) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</span></p>
<p><span style="font-size: small;">&nbsp;&nbsp;&nbsp; a) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</span></p>
<p><span style="font-size: small;">b) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model</span></p>
<p><span style="font-size: small;">&nbsp;&nbsp;&nbsp; b) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model</span></p>
<p><span style="font-size: small;">c) The melt point of the design (as reported by the EteRNA server)</span></p>
<p><span style="font-size: small;">&nbsp;&nbsp;&nbsp; c) The melt point of the design (as reported by the EteRNA server)</span></p>
<p><span style="font-size: small;">d) 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><span style="font-size: small;">&nbsp;&nbsp;&nbsp; d) 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><span style="font-size: small;">e) log<sub>10</sub>(designer's EteRNA points).&nbsp; This factor is given a very low weight.<br /></span></p>
<p><span style="font-size: small;">&nbsp;&nbsp;&nbsp; e) log<sub>10</sub>(designer's EteRNA points).&nbsp; This factor is given a very low weight.<br /></span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><span style="font-size: small;"><strong>Things I have looked at:</strong><br /></span></p>
<p><span style="font-size: small;"><strong>Things I have looked at:</strong><br /></span></p>
<p><span style="font-size: small;">I have also looked at a) temperature and b) designer's EteRNA points as possible factors for my forecasting tool.&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.</span></p>
<p><span style="font-size: small;">I have also looked at the temperature setting of the energy model as a possible factors for my forecasting tool.&nbsp; I was suprised to find that the default setting of 37C is the best setting for my forecasting tool.</span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><strong><span style="font-size: medium;">Things to do:</span></strong></p>
<p><strong><span style="font-size: medium;">Things to do:</span></strong></p>
<p><strong><span style="font-size: medium;">I am currently working on a change to my scripts that will do a better job of analyzing labs that have non-canonical pairs locked into the target structure.&nbsp;&nbsp; The Vienna RNA folding tools have an option to allow non-standard pairs.&nbsp; This option gives them a pairing free energy of 0, which may not be correct, but may be better than nothing.<br /></span></strong></p>
<p><span style="font-size: large;">1. I am (still) thinking about how to add Vienna 2.1.1 and EteRNA melt curves and dot plots to these reports.&nbsp; I can modify my scripts to generate these, but they are in Postscript format.&nbsp; I am investigating Ghostscript and ImagMagick as possible tools to incorporate into my scripts to convert the graphics.&nbsp; I've been informed that EteRNA dot plots aren't strictly the same as Vienna 1.8.5 dot plots.&nbsp; I will need to incorporate the modifications that EteRNA made to Vienna 1.8.5 dot plots to get it right.</span></p>
<p><span style="font-size: large;">I am (still) thinking about how to add Vienna 2.1.1 melt curves and dot plots to these reports.&nbsp; I can modify my scripts to generate these, but they are in Postscript format.&nbsp; I haven't yet figured out how to incorporate them quickly in my reports and spreadsheets.&nbsp; If you think there is any easy way to do this, please let me know.<br /></span></p>
<p><span style="font-size: large;">2. As of 11/10/2013, a new round of synthesis results is available.&nbsp; I need to run the training portion of my forecasting tool on the new data.</span></p>
<p><span style="font-size: large;">3. Investigate Vienna's "ensemble diversity measure" as another possible factor for the forecasting tool to consider.</span></p>
<p><span style="font-size: large;">4. Look for published energy parameters for non-Canonical pairs in RNA sequences.&nbsp; There's got to be something better than 0 out there.</span></p>
<p><span style="font-size: large;">5. Look at "upgrading" to Vienna 2.1.3 (from Vienna 2.1.1) in my toolset.<br /></span></p>
<p>&nbsp;</p>
<p>&nbsp;</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><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>

Revision as of 12:24, 10 November 2013

Analysis Reports and Spreadsheets produced by my Python script can be found in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2cDFibWt6T19nRzg&usp=sharing">ReportsActiveLabs</a>.  You can bookmark this folder in your browser.  I have decided to stick with one folder rather than change with each publication cycle. 

 


If you think you have an answer/suggestion for issue #1 above, please help me out by sending me a PM.  Thanks in advance for any help!

 

In this edition:

  1) If the target structure contains locked, non-Canonical pairs, the Vienna tools are called with a --nsp option that allows the pairing and assigns an energy of 0 to it.  Zero may not

be the best value to use, but it seems to be better than not doing anything.

  2) Some of the labs now have a starting sequence of 'GG' instead of 'GGAAA'.  It looks like the devs have left things open for additional "tails" to be used in future labs.  For now, my script

recognizes both of the sequences that have appeared and uses the correct one for each lab.

 3)  There is a field for the Vienna 2.1.1 melt point of each design submitted.  This new field now appears in both the text reports and the spreadsheets.

My lab tool includes a forecasting tool that looks at factors that have correlated well with past synthesis scores.  The current version of the forecasting tool looks at the following factors:

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

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

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

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

    e) log10(designer's EteRNA points).  This factor is given a very low weight.

 

Things I have looked at:

I have also looked at the temperature setting of the energy model as a possible factors for my forecasting tool.  I was suprised to find that the default setting of 37C is the best setting for my forecasting tool.

 

 

Things to do:

1. I am (still) thinking about how to add Vienna 2.1.1 and EteRNA melt curves and dot plots to these reports.  I can modify my scripts to generate these, but they are in Postscript format.  I am investigating Ghostscript and ImagMagick as possible tools to incorporate into my scripts to convert the graphics.  I've been informed that EteRNA dot plots aren't strictly the same as Vienna 1.8.5 dot plots.  I will need to incorporate the modifications that EteRNA made to Vienna 1.8.5 dot plots to get it right.

2. As of 11/10/2013, a new round of synthesis results is available.  I need to run the training portion of my forecasting tool on the new data.

3. Investigate Vienna's "ensemble diversity measure" as another possible factor for the forecasting tool to consider.

4. Look for published energy parameters for non-Canonical pairs in RNA sequences.  There's got to be something better than 0 out there.

5. Look at "upgrading" to Vienna 2.1.3 (from Vienna 2.1.1) in my toolset.

 

Please let me know if you have any other things you would like to see in my lab reports.

 

Happy folding,

---Dennis9600

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