From the registry, to the wikis, iGEM is founded upon the idea of sharing. Having an open culture allows scientific communities to validate successes and understand failures, while supporting future researchers downstream. To participate in this open culture, our team wanted to share our RiboTALs' multivariate characterization data in the most useful way possible. While the current use of registry pages serve many part types and iGEM teams well, the complexity and volume of data we collected made this method of sharing feel less appropriate, and less accessible. 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 for any part type in a way that is useful to everyone is an extremely difficult objective, but we wanted to take a step towards making it easier. Now we are pleased to introduce our step towards that solution, The Depot, an open BioBrick characterization database to further promote sharing in iGEM.

Past approaches to designing a BioBrick characterization database dealt with difficult questions⁵, which entailed 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 the list goes on and on for each part type. Additionally, these decisions are posed for a global scale, where accessibility and timetables are major concerns. Moreover, since synthetic biology is a relatively young field, many facets of part characterizations are likely to change over time. 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 not the 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 sections of the protocol to promoters, a part type with a history⁶ of data standardization, more comparable across experiments.

Uploading to the Depot^back to top

The process is straightforward. Users register, then upload their four files that adhere to Depot standards, as well as other information relevant 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 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