Team:Berkeley Software/Eugene Results

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Revision as of 00:53, 19 October 2009 by Lbilitchenko (Talk | contribs)



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)
    [http://partsregistry.org/Part:BBa_K112809 BBa_K112809] iGEM08_UC_Berkeley (2008-11-03) T4 Lysis Device with Pbad 21 7 0 19 3 84 158:1 94
    [http://partsregistry.org/Part:BBa_K112133 BBa_K112133] iGEM08_UC_Berkeley (2008-10-30) Xis Int temperature sensitive expression cassette 31 11 1 17 3 82 128:1 94
    [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] Endy Lab
    (2005-07-04)    		 T7 Consensus Promoter Sequence 10 4 0 16 3 81 68:1 94
    [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] iGEM08_Edinburgh (2008-10-07) T7 Consensus Promoter Sequence 6 2 0 15 3 80 72:1 93
    [http://partsregistry.org/Part:BBa_I8510 BBa_I8510] Knight Lab
    (2008-01-09)    		 3OC6HSL->Inverter-> lacZalpha with orthogonal GFP protein generator 60 20 0 27 6 78 151:1 109
    [http://partsregistry.org/Part:BBa_F2620 BBa_F2620] Haseloff Lab, MIT
    (2004-08-09)    		 3OC6HSL -> PoPS Receiver 18 6 0 19 3 84 56:1 94
    [http://partsregistry.org/Part:BBa_J23040 BBa_J23040] iGEM2006_Berkeley (2006-08-01) AHL-dependent inverter 30 10 0 19 2 89 125:1 94
    [http://partsregistry.org/Part:BBa_J5519 BBa_J5519] iGEM2006_Toronto (2006-10-29) Arabinose -> LacI ts -| cI 434 30 10 0 19 2 89 180:1 93
    [http://partsregistry.org/Part:BBa_J5522 BBa_J5522] iGEM2006_Toronto
    (2006-10-29)    		 Arabinose -> LacI ts -| pLac -> tetR -| pTet 32 11 0 22 2 91 159:1 93
    [http://partsregistry.org/Part:BBa_K106695 BBa_K106695] iGEM08_UCSF (2008-10-28) Sir3 under a strong constitutive promoter 8 4 0 16 2 88 291:1 94


    Conclusions
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