Team:UC Davis/Database


Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type.

Motivation: Sharing

Our team wanted to share our work in the clearest and most useful way possible, given the multivariance of RiboTals. We did so in the prescribed way of sharing part characterizations through the iGEM registry's experience pages, but excel charts and text summaries left us feeling like we could do more to communicate our work. An imminent solution was to upload our raw, RiboTal data in an intuitive, easy-to-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types.

In addition to being a useful way for iGEM-ers to share their data, The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology. In participating in The Depot, iGEM-ers would encounter issues of sharing raw data such as,
-How would others want to use my work?
-Who is my work relevant to, and how should I account for that?
-What can be standardized to make shared data comparable, and therefore more useful for everyone?

We are very excited to present The Depot as an intuitive way to share data, as well as a platform to iGEM-ers to think about the human elements of sharing their work.

Approaches to Data Standardization:

An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability1. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.

Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data format standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.

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.

Searching The Depot

Search functionality current offers searching for part types across all experiments, or for all data for a particular experiment. The results of your searches are immediately downloadable. Search functionality is to be expanded upon.

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.

About the Depot

Check out the motivations behind the Depot.