Team:UC Davis/Database

From 2013.igem.org

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[1] M Galdzicki, D Chandran, JH Gennari, HM Sauro, "Design and Analysis of Bio-molecular Circuits", pp. 281, 2011
[1] M Galdzicki, D Chandran, JH Gennari, HM Sauro, "Design and Analysis of Bio-molecular Circuits", pp. 281, 2011
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<a id="external_links"><h3>External Links</h3></a>
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<sup>1 </sup><a href="https://2011.igem.org/Jamborees">https://2011.igem.org/Jamborees</a><br>
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<sup>2 </sup><a href="https://2012.igem.org/Jamborees">https://2012.igem.org/Jamborees</a><br>
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<sup>3 </sup><a href="http://www.ncbi.nlm.nih.gov/genbank">http://www.ncbi.nlm.nih.gov/genbank</a><br>
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<sup>4 </sup><a href="http://www.pdb.org/pdb/home/home.do">http://www.pdb.org/pdb/home/home.do</a><br>
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<sup>5 </sup><a href="http://openwetware.org/wiki/Parts_characterization#Discussion_Topics">http://openwetware.org/wiki/Parts_characterization#Discussion_Topics</a><br>
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<sup>6 </sup><a href="http://www.jbioleng.org/content/3/1/4">http://www.jbioleng.org/content/3/1/4</a>
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Revision as of 04:47, 26 September 2013

The BioBrick Characterization Data Depot (BBCDD) is a semi-standardized database designed for iGEM teams to upload their characterization to. Originally intended to share the multivariate characterization data of riboTALs, the BBCDD was repurposed for sharing characterization data of all part types.

Motivation: Empowerment and Openness

The from the iGEM DNA distribution kit and registry, to the eagerness of faculty and universities across the globe, the iGEM competition empowers students to make a raw idea into a tangible, presentable project. This fact is made clear depth by the number and depth of projects in past years.[1]

In addition to empowering iGEM-ers, a uploading data to a standardized characterization database promotes openness. In other biological applications, such as genomic sequencing4, open data is the norm for strong reasons; open data allows communities to validate successes and understand failures, while supporting future researchers downstream. For these reasons, iGEM is founded upon an open community. Open data through the BBCDD is another way for iGEM-ers to contribute to an open community.

Approaches: Past, and the BBCDD

Past approaches to designing a BioBrick characterization database dealt with difficult questions6 of data standardization; for the other part types, we created a flexible data format to accommodate different methods of characterization and data types that teams could possibly use.

totally unpolished: For our new part part RiboTal, we wanted to see how it functions before making data standards for it. Go see how we went about answering some data standards issues here: link.

Visit the BBCDD

Data Standards

See the BBCDD's standards, and how examples of creating more.

Initial Population

See how we initially populated the BBCDD.

References

[1] M Galdzicki, D Chandran, JH Gennari, HM Sauro, "Design and Analysis of Bio-molecular Circuits", pp. 281, 2011