Team:UC Davis/Database

From 2013.igem.org

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Revision as of 18:46, 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. Originally intended to share the multivariate characterization data of riboTALs, the Depot 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.1,2

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.[1]

In addition to empowering iGEM-ers, a uploading data to a standardized characterization database promotes openness. In other biological applications, such as genomic sequencing3 and protein structuring4, 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.

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 data and protocol standards for the promoters, a simple part that also have a history6 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.

Example Upload

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.

Example Search

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