Targeted Development of Registries of Biological Parts
Blauvelt, Megan F.
Cooper, Kristal L.
DeLalla, Emily C.
Lyons, Blair M.
Mane, Shrinivasrao P.
Sweede, Matthew A.
Waldon, Sally A.
MetadataShow full item record
The 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 Findings: By 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/Significance: Organizational 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.
- Research Articles (VBI) 
Showing items related by title, author, creator and subject.
Sutphin, Michael D. (Virginia Tech. University Relations, 2009-10-08)The Potato Genome Sequencing Consortium (PGSC), an international team of scientists from industry and academia in 14 countries, has released a draft sequence of the potato genome with the help of a Virginia Tech researcher.
Whyte, Barry James (Virginia Tech. University Relations, 2006-08-31)An international team of researchers, which includes scientists from the Virginia Bioinformatics Institute at Virginia Tech, has published the draft genome sequences of two deadly plant pathogens, Phytophthora ramorum and ...
Steere, Edward; An, Lin; Zhang, Liqing (Department of Computer Science, Virginia Polytechnic Institute & State University, 2015-11-09), TR-15-05We present CANzip, a novel algorithm for compressing short read DNA sequencing data in FastQ format. CANzip is based on delta compression, a process in which only the differences of a specific data stream relative to a ...