Automatic design is based on computational modeling and optimization methods to provide prototype designs to targeted problems in an unsupervised manner. For biological circuits, we need to produce quantitative predictions of cell behavior for a given genotype as consequence of the different molecular interactions. Automatic design techniques aim at solving the inverse problem of finding the sequences of nucleotides that better fit a targeted behavior. In the post‐genomic era, our molecular knowledge and modeling capabilities have allowed to start using such methodologies with success. Herein, we describe how the emergence of this new type of tools could enable novel synthetic biology applications. We highlight the essential elements to develop automatic design procedures for synthetic biology pointing out their advantages and bottlenecks. We discuss in detail the experimental difficulties to overcome in the in vivo implementation of designed networks. The use of automatic design to engineer biological networks is starting to emerge as a new technique to perform synthetic biology, which should not be neglected in the future.
Perspectives on the automatic design of regulatory systems for synthetic biology
G. Rodrigo,J. Carrera,Thomas E. Landrain,A. Jaramillo
Published 2012 in FEBS Letters
ABSTRACT
PUBLICATION RECORD
- Publication year
2012
- Venue
FEBS Letters
- Publication date
2012-07-16
- Fields of study
Biology, Medicine, Computer Science
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- automatic design
A computational approach that searches for biological designs or nucleotide sequences that realize a target behavior.
Aliases: automatic design techniques, design automation
- computational modeling
Mathematical or algorithmic representation of molecular interactions used to predict circuit behavior.
Aliases: modeling, computational models
- designed networks
Regulatory networks produced by an automatic design workflow for a chosen target behavior.
Aliases: designed regulatory networks, engineered networks
- inverse problem
The design task of inferring sequences or genotypes from a desired biological behavior.
Aliases: design inverse problem
- in vivo implementation
The experimental realization of designed circuits inside living cells or organisms.
Aliases: in vivo deployment, live-cell implementation
- optimization methods
Algorithms used to search design space for sequences or parameters that best satisfy a target objective.
Aliases: optimization, optimization algorithms
- regulatory systems
Biological circuits whose molecular interactions control gene expression or cell behavior.
Aliases: regulatory circuits, biological regulatory systems
- synthetic biology applications
Engineered uses of designed genetic or regulatory systems in synthetic biology settings.
Aliases: synthetic biology uses, applications in synthetic biology
REFERENCES
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