Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems.
ACS Synth Biol
; 5(6): 507-17, 2016 06 17.
Article
en En
| MEDLINE
| ID: mdl-27110633
ABSTRACT
Recently, semirational approaches that rely on combinatorial assembly of characterized DNA components have been used to engineer biosynthetic pathways. In practice, however, it is not practical to assemble and test millions of pathway variants in order to elucidate how different DNA components affect the behavior of a pathway. To address this challenge, we apply a rigorous mathematical approach known as design of experiments (DOE) that can be used to construct empirical models of system behavior without testing all variants. To support this approach, we have developed a tool named Double Dutch, which uses a formal grammar and heuristic algorithms to automate the process of DOE library design. Compared to designing by hand, Double Dutch enables users to more efficiently and scalably design libraries of pathway variants that can be used in a DOE framework and uniquely provides a means to flexibly balance design considerations of statistical analysis, construction cost, and risk of homologous recombination, thereby demonstrating the utility of automating decision making when faced with complex design trade-offs.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Programas Informáticos
/
Biología Sintética
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
ACS Synth Biol
Año:
2016
Tipo del documento:
Article
País de afiliación:
Estados Unidos