Team:Berkeley Software/Eugene Results

From 2009.igem.org

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<tr>
<tr>
<th> Total </th>
<th> Total </th>
 +
<td></td>
 +
<td></td>
 +
<th align="center">276</th>
 +
<th align="center">85</th>
 +
<th align="center">1</th>
 +
<th align="center">189</th>
 +
<th align="center">29</th>
 +
<th align="center"></th>
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<th align="center">26436:189</th>
 +
<th align="center">952</th>
 +
</tr>
 +
<tr>
 +
<th> Averages</th>
 +
<td></td>
 +
<td></td>
 +
<th>24.60</th>
 +
<th>8.50</th>
 +
<th>0.10</th>
 +
<th>18.90</th>
 +
<th>2.90</th>
 +
<th>84.72</th>
 +
<th>139:1</th>
 +
<th>95.20</th>
</tr>
</tr>
</table>
</table>

Revision as of 02:17, 19 October 2009



Content:
  •  Intro
  •  Language Definition
  •  Examples
  • Implementation
  •  Results
  •  Conclusions
    		•            
    Eugene.png

    Results

    Table 1 is an examination of actual experimentally created devices from a variety of sources. The first two devices were created in the summer of 2008 in J.C Anderson’s lab at UC Berkeley for the International Genetically Engineering Machine Competition. These can be found in MIT’s registry of standard biological parts. The third device is from Drew Endy’s lab at Stanford. The fourth part is from Edinburgh’s 2008 iGEM team. The fifth part is from Tom Knight’s lab at MIT. The description of these devices as well as their registry id is provided. In addition we detail the number of properties, parts, and devices used by Eugene to specify them. For running the examples a MacBook Pro was used with a 2.4 GHz processor speed and 2 GB of memory.

    Table 1: Examination of Experimental Designs Specified Using Eugene

    Device Group Description Number of Lines of Code in program Percentage change Lines Ratio Compilation
    Property Values Parts Devices Total Main File Total to Main File Sequence bp:Lines Time(ms)
    BBa_K112809 iGEM08_UC_Berkeley (2008-11-03) T4 Lysis Device with Pbad 21 7 0 19 3 84 158:1 94
    BBa_K112133 iGEM08_UC_Berkeley (2008-10-30) Xis Int temperature sensitive expression cassette 31 11 1 17 3 82 128:1 94
    BBa_E7104 Endy Lab
    (2005-07-04)    		 T7 Consensus Promoter Sequence 10 4 0 16 3 81 68:1 94
    BBa_K118021 iGEM08_Edinburgh (2008-10-07) T7 Consensus Promoter Sequence 6 2 0 15 3 80 72:1 93
    BBa_I8510 Knight Lab
    (2008-01-09)    		 3OC6HSL->Inverter-> lacZalpha with orthogonal GFP protein generator 60 20 0 27 6 78 151:1 109
    BBa_F2620 Haseloff Lab, MIT
    (2004-08-09)    		 3OC6HSL -> PoPS Receiver 18 6 0 19 3 84 56:1 94
    BBa_J23040 iGEM2006_Berkeley (2006-08-01) AHL-dependent inverter 30 10 0 19 2 89 125:1 94
    BBa_J5519 iGEM2006_Toronto (2006-10-29) Arabinose -> LacI ts -| cI 434 30 10 0 19 2 89 180:1 93
    BBa_J5522 iGEM2006_Toronto
    (2006-10-29)    		 Arabinose -> LacI ts -| pLac -> tetR -| pTet 32 11 0 22 2 91 159:1 93
    BBa_K106695 iGEM08_UCSF
    (2008-10-28)    		 Sir3 under a strong constitutive promoter 8 4 0 16 2 88 291:1 94
    Total 276 85 1 189 29 26436:189 952
    Averages 24.60 8.50 0.10 18.90 2.90 84.72 139:1 95.20


    Conclusions
    Retrieved from "http://2009.igem.org/Team:Berkeley_Software/Eugene_Results"