Meta Analysis of Biobricks

        The Registry of Standard Biological Parts has been a longstanding partner of iGEM. The promotion of synthetic biology communication and cooperation have become tenants of every iGEM team. The database was an incredible step forward in biological research and standardization. And for this reason, we must now reevaluate the registry.

Moore's Law and Biology

        Moore’s Law is a principle developed in 1975 claiming the maximum number of transistors per microchip doubles every two years. Analogous to the technological limits in computer engineering, biology has seen a similar trend in the cost of sequencing and synthesizing DNA. The high cost of synthetic biology is what initially drove the movement to physical databases of biological parts. For example, a gene segment costing $800 when the Registry of Biological Parts was conceived, while only costing around $30 by modern standards. In the last decade and a half, synthesis prices have halved approximately every 2.5 years.

       This registry, if it serves as a replacement and utility to the physical construction of biological parts, is a rapidly depreciating database due simply to the trend in technological costs. This direction has prevented the registry from gaining momentum in research groups. Only 11% of the 70 iGEM team we contacted said to have used the registry to order parts. At the time of this study (August 28th, 2015), only 69% of requests made to the registry were processed. Of the requests that were completed, it took on average 7.5 days to process the request internally. Additionally, only 2.5 requests were made per day in 2015 with each part averaging $130 from IDT (each part was pulled from the request form and processed through IDT in our study). Furthermore, studies have suggested 5’ cut sites can have significant impacts on gene expression and function (Lou 2012).


Today's Registry

        Maybe there still is value in the registry, and maybe it does save groups synthesis costs and time. After all, current saves researchers $325 on average a day. But when we return to this conversation in 5 years and the savings is only about $80 a day? The National Science Foundation (NSF, $37 million over 10 years), and Defense Advanced Research Projects Agency (DARPA, undisclosed grant), and National Institutes of Health (NIH, undisclosed grant) funnel hefty grants as well as the International Genetically Engineered Machines (iGEM) competition to develop and contribute to the physical stock of parts. Should we be investing in this type of technology?

        In addition to the physical database, we were interested in the meta-analysis of biobricks. Are parts highly used in other projects? What do the usage statistics look like? We contacted the iGEM staff to determine whether they would release the complete list of Biobricks with usage data and our request was denied.

       But we had computers and we had website scraping tools, so we scraped all parts web pages for every iGEM team part from 2005 to 2014 for their usage information. Processing this information, we can get a snapshot of what is happening with the all the information this organization has accumulated. Biobricks are unconnected to any other Biobrick 72% the time, and 92% are used less than once a year. 61% of part usage is within the same team in the same year. Despite these trends, the superb parts had an entirely different story to tell.



The Best of the Registry

       Below, the top 1.3% of Biobricks by usage were mapped to all Biobricks they were used in and processed in Gephi as a network of information. The resulting image is the marvel of what the Registry of Standard Biological Parts has achieved. With each point representing a Biobrick, each color representing a year of competition, you can see the interconnectivity of iGEM at its best. Teams across the world and years building from others work and linking their work into this network of information.

       And this is what we believe the best direction is for the registry and iGEM as a whole. There has been this emphasis on forcing projects into this physical standard of biobricks and punished teams for omitting submission of a registry part. These leaves massive portions of the registry dark, untouched. The registry was a revolutionary idea initially, but the registry must evolve to coexist with the modern scientific environment. Drop the physical system and commit the registry to be a haven of synthetic biology research focusing on the scientific network, not the part number.