Team:UC Davis/Database

From 2013.igem.org

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<h1 class="title">Motivation: Empowerment and Openness</h1>
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<h1 class="title">Motivation: Openness</h1>
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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.<a href="#external_links"><sup>1,2</sup></a>
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The from the the registry, to the wikis, iGEM is founded upon the idea of sharing. Having a open culture allows scientific communities to validate successes, understand failures, while supporting future researchers downstream.To participate in this open culture, our team wanted to share RiboTals multivate characterization data in the most useful way possible. While the current use of experiences pages serve many part types and iGEM teams well, the complexity and volume of data we collected made this method sharing feel less appropriate, and less accessable. We also noticed in our research of sharing data that teams focused on sharing conclusions and calculations of their data, but rarely found the time to share their raw numbers.
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With continued research, it was clear that our dilemma with RiboTals was not unique. Sharing data in a way that is useful to everyone is an extremely difficult objective. But we wanted to step towards making it easier; introduce our solution, The Depot, an open BioBrick characterization database to further promoter sharing in iGEM.
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However, as BioBrick circuits become more complex, their design process can be dramatically slowed by the large number of relationships and dependencies between their individual parts. Empowering iGEM-ers with an standardized, accessible database for the characterization of BioBrick parts is the clear solution to address problems in high complexity circuits.<a href="#ref">[1]</a>
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In addition to empowering iGEM-ers, a uploading data to a standardized characterization database promotes openness. In other biological applications, such as genomic sequencing<a href="#external_links"><sup>3</sup></a> and protein structuring<a href="#external_links"><sup>4</sup></a>, 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 Depot is another way for iGEM-ers to contribute to an open community.
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Revision as of 23:32, 27 September 2013

The BioBrick Characterization Data Depot (the Depot) is a way for teams to share their characterization data with the world. It uses a semi-standardized database designed to be both flexible and structured for the differing ways teams characterize their parts. Originally intended to share the multivariate characterization data of riboTALs, the Depot was repurposed for sharing characterization data of all part types.

Motivation: Openness

The from the the registry, to the wikis, iGEM is founded upon the idea of sharing. Having a open culture allows scientific communities to validate successes, understand failures, while supporting future researchers downstream.To participate in this open culture, our team wanted to share RiboTals multivate characterization data in the most useful way possible. While the current use of experiences pages serve many part types and iGEM teams well, the complexity and volume of data we collected made this method sharing feel less appropriate, and less accessable. We also noticed in our research of sharing data that teams focused on sharing conclusions and calculations of their data, but rarely found the time to share their raw numbers.

With continued research, it was clear that our dilemma with RiboTals was not unique. Sharing data in a way that is useful to everyone is an extremely difficult objective. But we wanted to step towards making it easier; introduce our solution, The Depot, an open BioBrick characterization database to further promoter sharing in iGEM.

Approaches: Past, and the Depot

Past approaches to designing a BioBrick characterization database dealt with difficult questions5 dealing with two main topics: what are reasonable standards that a database can enforce, and how to make characterizations across labs or experiments comparable. To answer these questions, one would have to make many, many decisions. Decisions like choosing between the use of different characterization protocols, lab equipment, machine settings, data format, and on and on for each part type. Additionally, these decisions are posed in a global scale, where accessibility and timetables are major concerns. More so, because synthetic biology is a relatively young field, many facets of part characterizations are likely to change. The complexity of decisions and synthetic biology's youth make shelving the idea of a completely standardized database very appealing.

We agreed, at least in some senses. An enforced, strictly standardized database for all part types is unlike our approach we took for the Depot. In our approach, we instead created a flexible data format standard that many different characterizations could easily conform to. Additionally, we standardized parts of the protocol to promoters, a part type with a history6 of data standardization, more comparable across experiments.

totally unpolished: For our new transcription factors known as RiboTALs, 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.

Uploading to the Depot

The process is straightforward. Users register, then upload their four files that adhere to Depot standards, as well as other relevant information to their experiment. A prototype page that shows the basic functional elements is shown here.

Searching The Depot

Search functionality is currently geared towards location of user-specified data values for BioBrick parts. This demonstrates a very simple, yet illustrative example of leveraging a database. The results of your searches are downloadable.

A prototype page that shows the basic functional elements of search is shown here: A prototype example search is shown here:

Which results in the downloadable table partially shown here:

Visit the Depot

Data Standards

See the Depot's standards and data requirements so you can share your data as well.

Initial Population

See how we initially populated the Depot.

References

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