Targeted Development of Registries of Biological Parts

Abstract

BackgroundThe design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea.Methods/Principal FindingsBy analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified.Conclusions/SignificanceOrganizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.

Synthetic Biology and Microdevices

“…This power arises from the Registry of Standard Biological Parts which can be further maintained and improved when a quality control of the BioBricks is included in order to maximize the benefits for its users [Peccoud et al 2008]. In addition, the reusability of biological parts will also be slightly improved by systematically disclosing annotated sequence information when reporting synthetic gene networks in research articles, as recently addressed by Peccoud et al [2011].…”

Mining Environmental Plasmids for Synthetic Biology Parts and Devices

“…Although the collection is mostly used and produced by undergraduate students, and quality control is not optimal, the large number of items and their inclusion as standardized parts has made the registry a very valuable resource for many synthetic biology endeavors (125)(126)(127)(128).…”

Making big promises come true? Articulating and realizing value in synthetic biology

“…Several researchers have commented that they have started using BioBrick-style approaches to help restructure their laboratory practices, but this stage a majority of the synthetic biologists I have spoken with have not made their personal collections of biological parts available to a public repository like the Registry of Standard Biological Parts, providing justifications ranging from laziness to concerns over ownership. Nor do many of them use others' parts from the MIT Registry, citing problems with reliability and a lack of part characterization data as key issues (see also Peccoud et al, 2008).…”