Computational Tools: Difference between revisions
Eli Fisker (talk | contribs) m (Adding subpage for scripts) |
Eli Fisker (talk | contribs) m (Adding description and link to JandersonLee's tool - I have trouble making the link work correct. Feel free to correct it.) |
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<h3>Cloud Lab Data Mining Tool</h3> | <h3>Cloud Lab Data Mining Tool</h3> | ||
<p>Lab data analysis tool made by [[User:Omei|Omei]]. You can use this tool to group similar designs together, find good loops for designing and for general design comparison. You can see the SHAPE numbers while hovering over the SHAPE colors. For more about the tool, see Omei's [http://eternawiki.org/wiki/index.php5/User:Omei/Cloud_Lab_Data_Mining_Tool WIKI introduction].</p> | <p>Lab data analysis tool made by [[User:Omei|Omei]]. You can use this tool to group similar designs together, find good loops for designing and for general design comparison. You can see the SHAPE numbers while hovering over the SHAPE colors. For more about the tool, see Omei's [http://eternawiki.org/wiki/index.php5/User:Omei/Cloud_Lab_Data_Mining_Tool WIKI introduction].</p> | ||
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<h2>LabDataMiner</h2> | |||
<p>Lab data search and analysis tool made by JandersonLee. This tool can be used to search for sequences and structures in our labs. This is a strong tool for digging out data across labs. For more about how to use the tool, it see the manual [<a href="/wiki/index.php5/LabDataMiner">http://eternawiki.org/wiki/index.php5/LabDataMiner</a> here]. </p> | |||
<p> </p> | <p> </p> | ||
<h3>CSE tool - Computationally Selected Elements</h3> | <h3>CSE tool - Computationally Selected Elements</h3> | ||
Revision as of 01:19, 15 November 2013
== Folding (Structure prediction) ==
<tbody> </tbody>| Name | Online server | Sources and/or binaries |
| ViennaRNA | http://rna.tbi.univie.ac.at/ | http://www.tbi.univie.ac.at/~ronny/RNA/index.html |
=== See also ===
== Design (Inverse Folding) ==
<tbody> </tbody>| Name | Server | Sources and/or binaries |
| NUPACK | http://nupack.org/ | http://nupack.org/downloads |
== Viewers ==
=== 2D viewers ===
<tbody> </tbody>| Name | Server | Sources and/or binaries |
| VARNA | http://varna.lri.fr/ |
=== 3D viewers ===
<tbody> </tbody>| Name | Server | Sources and/or binaries |
| UCSF Chimera | http://www.cgl.ucsf.edu/chimera/ | http://www.cgl.ucsf.edu/chimera/download.html |
== Lab results analysis ==
=== Data mining ===
Here are two data mining tools that are open source and have lots of built in functionality: FAKE with GAME, or its replacement Rapid-I (it's huge). All types of modeling supported. GUI drag & drop model building.
http://sourceforge.net/projects/fakegame/
Player created tools
Cloud Lab Data Mining Tool
Lab data analysis tool made by Omei. You can use this tool to group similar designs together, find good loops for designing and for general design comparison. You can see the SHAPE numbers while hovering over the SHAPE colors. For more about the tool, see Omei's WIKI introduction.
LabDataMiner
Lab data search and analysis tool made by JandersonLee. This tool can be used to search for sequences and structures in our labs. This is a strong tool for digging out data across labs. For more about how to use the tool, it see the manual [<a href="/wiki/index.php5/LabDataMiner">http://eternawiki.org/wiki/index.php5/LabDataMiner</a> here].
CSE tool - Computationally Selected Elements
Lab data analysis tool programmed by Jnicol. He based it on Mat's idea for a lab data analysis tool. This tool will give you the average of the SHAPE score of whatever stretch of bases you put in and sort the data after the SHAPE score. This tool contains the early labs, but not the latests. Here is a link to the tool and a manual.
