Targeted development of registries of biological parts.
BACKGROUND
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.


RESULTS
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
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.
Peccoud
Jean
J
Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America. peccoud@vt.edu
Blauvelt
Megan F
MF
Cai
Yizhi
Y
Cooper
Kristal L
KL
Crasta
Oswald
O
DeLalla
Emily C
EC
Evans
Clive
C
Folkerts
Otto
O
Lyons
Blair M
BM
Mane
Shrinivasrao P
SP
Shelton
Rebecca
R
Sweede
Matthew A
MA
Waldon
Sally A
SA
D001695:Biology; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D015723:Gene Library; D005821:Genetic Techniques; D005822:Genetic Vectors; D007256:Information Systems; D008954:Models, Biological; D010957:Plasmids / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D049490:Systems Biology; D013696:Temperature
D004247:DNA