Team:Berkeley/Attributions

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    <li><a href="https://2012.igem.org/Team:Berkeley">Home</a></li>
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        <a href="https://2012.igem.org/Team:Berkeley/Project">Project</a>
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        <a href="https://2012.igem.org/Team:Berkeley/Parts">Parts</a>
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    <li><a href="https://2012.igem.org/Team:Berkeley/Safety">Safety</a></li>
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    <li><a href="https://2012.igem.org/Team:Berkeley/Team">Team</a></li>
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    <li><a href="https://igem.org/2012_Judging_Form?id=900">Judging</a></li>
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    <li><a href="https://2012.igem.org/Team:Berkeley/Notebooks">Notebooks</a></li>
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    <li><a href="https://2012.igem.org/Team:Berkeley/Attributions">Attributions</a></li>
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<b>Wetlab</b>
<b>Wetlab</b>
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Many of our basic parts (promoters, terminators, and fluorescent proteins) are courtesy of the <a href="http://dueberlab.berkeley.edu/">Dueber Lab</a> at UC Berkeley, our host this year. The iGEM team chose the targeting proteins and sequences from the the <a href="http://yeastgfp.yeastgenome.org/"> Yeast GFP Database</a> created by the O'Shea and Weissman Labs at UCSF, and either PCRed them from genomic DNA or synthesized them via gene synthesis. The iGEM team then combined these parts with the basic parts provided by the Dueber Lab to build all the devices they utilized.
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Many of our basic parts (promoters, terminators, and fluorescent proteins) are courtesy of the <a href="http://dueberlab.berkeley.edu/">Dueber Lab</a> at UC Berkeley, our host this year. Our iGEM team chose the targeting proteins and sequences from the the <a href="http://yeastgfp.yeastgenome.org/"> Yeast GFP Database</a> created by the O'Shea and Weissman Labs at UCSF, and either PCRed them from genomic DNA or synthesized them via gene synthesis ourselves. We then combined these parts with the basic parts provided by the Dueber Lab to build all the devices we utilized.  
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All the device cloning was done by the iGEM team. This involved many Golden Gate Assembly reactions, minipreps, transformations, digestions, yeast integrations, etc. While some of the Golden Gate backbones were provided by the Dueber Lab, many of the parts specific to MiCode project, specifically the backbones for multigene and full MiCode assembly, were designed and cloned by the iGEM team.
 
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The leucine zipper sequences were courtesy of the <a href="http://web.mit.edu/biology/keating/KeatingLab/Home.html">
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All the higher-order (cassette, multigene, full MiCode) device cloning, which mainly involved Golden Gate Assembly, was done by our iGEM team. While some of the Golden Gate backbones were provided by the Dueber Lab, many of the parts specific to MiCode project, specifically the backbones for multigene and full MiCode assembly, were designed and cloned by us. Additionally, we produced all the yeast strains necessary throughout our entire iGEM project and did all the image acquisition and analysis.  
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Keating Lab</a> at MIT, in a collaborative effort to identify an orthogonal interaction set. With the sequences provided, the iGEM team constructed the leucine zippers via gene synthesis, combined them into their MiCode construction scheme, and assayed them in yeast.
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The leucine zipper sequences were provided courtesy of the <a href="http://web.mit.edu/biology/keating/KeatingLab/Home.html">Keating Lab</a> at MIT, in a collaborative effort to identify an orthogonal interaction set. With the sequences provided, we constructed the leucine zippers via gene synthesis, combined them into our MiCode construction scheme, and assayed them in yeast.
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On the software side, the iGEM team wrote the MATLAB code, constructed the Cell Profiler pipeline for automated image analysis, and tested it using images generated by the iGEM team.
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On the software side, we wrote the MATLAB code, constructed the Cell Profiler pipeline for automated image analysis, and tested it using images generated by our iGEM team. Matlab object identification functions from the <a href="http://www.mathworks.com/matlabcentral/">community forum</a> were used as templates for the basis of our own code. We developed CellProfiler pipelines with the aid of the <a href="http://www.cellprofiler.org/CPmanual/">CellProfiler manual</a> and sample pipelines from the <a href="http://cellprofiler.org/forum/"> online forum</a>.
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<b>Website</b>
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<b>Website, Presentation, and Poster</b>
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With their permission, we began with the template of the <a href="https://2011.igem.org/Team:Berkeley">Berkeley 2011 iGEM team</a>, and tweaked it to our needs this year.
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With their permission, we began with the website template of the <a href="https://2011.igem.org/Team:Berkeley">Berkeley 2011 iGEM team</a>, and tweaked it to our needs this year. All the content was created by us except for the blue banner and Berkeley logo (provided by the <a href="http://www.berkeley.edu/">University</a>), and the Javascript necessary for our slideshow on the front page (provided by <a href="http://nivo.dev7studios.com/">Dev7 Studios</a>).
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For the presentation and poster, any images not of our creation are cited where relevant.
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Latest revision as of 07:50, 17 October 2012

header
iGEM Berkeley iGEMBerkeley iGEMBerkeley


Wetlab

Many of our basic parts (promoters, terminators, and fluorescent proteins) are courtesy of the Dueber Lab at UC Berkeley, our host this year. Our iGEM team chose the targeting proteins and sequences from the the Yeast GFP Database created by the O'Shea and Weissman Labs at UCSF, and either PCRed them from genomic DNA or synthesized them via gene synthesis ourselves. We then combined these parts with the basic parts provided by the Dueber Lab to build all the devices we utilized.

All the higher-order (cassette, multigene, full MiCode) device cloning, which mainly involved Golden Gate Assembly, was done by our iGEM team. While some of the Golden Gate backbones were provided by the Dueber Lab, many of the parts specific to MiCode project, specifically the backbones for multigene and full MiCode assembly, were designed and cloned by us. Additionally, we produced all the yeast strains necessary throughout our entire iGEM project and did all the image acquisition and analysis.

The leucine zipper sequences were provided courtesy of the Keating Lab at MIT, in a collaborative effort to identify an orthogonal interaction set. With the sequences provided, we constructed the leucine zippers via gene synthesis, combined them into our MiCode construction scheme, and assayed them in yeast.


Computational

On the software side, we wrote the MATLAB code, constructed the Cell Profiler pipeline for automated image analysis, and tested it using images generated by our iGEM team. Matlab object identification functions from the community forum were used as templates for the basis of our own code. We developed CellProfiler pipelines with the aid of the CellProfiler manual and sample pipelines from the online forum.


Website, Presentation, and Poster

With their permission, we began with the website template of the Berkeley 2011 iGEM team, and tweaked it to our needs this year. All the content was created by us except for the blue banner and Berkeley logo (provided by the University), and the Javascript necessary for our slideshow on the front page (provided by Dev7 Studios).

For the presentation and poster, any images not of our creation are cited where relevant.

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