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.

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.

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.

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.

Which results in the downloadable table partially shown here:

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

¹ https://2011.igem.org/Jamborees
² https://2012.igem.org/Jamborees
³ http://www.ncbi.nlm.nih.gov/genbank
⁴ http://www.pdb.org/pdb/home/home.do
⁵ http://openwetware.org/wiki/Parts_characterization#Discussion_Topics
⁶ http://www.jbioleng.org/content/3/1/4