[HTML][HTML] Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

N Gurdo, DC Volke, D McCloskey, PI Nikel - New Biotechnology, 2023‏ - Elsevier
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking
technologies, developed over the past 20 years, have enormously accelerated the …

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

M Galdzicki, KP Clancy, E Oberortner, M Pocock… - Nature …, 2014‏ - nature.com
The re-use of previously validated designs is critical to the evolution of synthetic biology from
a research discipline to an engineering practice. Here we describe the Synthetic Biology …

Design automation in synthetic biology

E Appleton, C Madsen, N Roehner… - Cold Spring Harbor …, 2017‏ - cshperspectives.cshlp.org
Design automation refers to a category of software tools for designing systems that work
together in a workflow for designing, building, testing, and analyzing systems with a target …

An end-to-end workflow for engineering of biological networks from high-level specifications

J Beal, R Weiss, D Densmore, A Adler… - ACS synthetic …, 2012‏ - ACS Publications
We present a workflow for the design and production of biological networks from high-level
program specifications. The workflow is based on a sequence of intermediate models that …

A standard-enabled workflow for synthetic biology

CJ Myers, J Beal, TE Gorochowski… - Biochemical Society …, 2017‏ - portlandpress.com
A synthetic biology workflow is composed of data repositories that provide information about
genetic parts, sequence-level design tools to compose these parts into circuits, visualization …

Automated selection of synthetic biology parts for genetic regulatory networks

F Yaman, S Bhatia, A Adler, D Densmore… - ACS synthetic …, 2012‏ - ACS Publications
Raising the level of abstraction for synthetic biology design requires solving several
challenging problems, including map** abstract designs to DNA sequences. In this paper …

Needs and opportunities in bio-design automation: four areas for focus

E Appleton, D Densmore, C Madsen… - Current Opinion in …, 2017‏ - Elsevier
Bio-design automation (BDA) is an emerging field focused on computer-aided design,
engineering principles, and automated manufacturing of biological systems. Here we …

Data integration and mining for synthetic biology design

G Mısırlı, J Hallinan, M Pocock, P Lord… - ACS synthetic …, 2016‏ - ACS Publications
One aim of synthetic biologists is to create novel and predictable biological systems from
simpler modular parts. This approach is currently hampered by a lack of well-defined and …

Toward the first data acquisition standard in synthetic biology

I Sainz de Murieta, M Bultelle, RI Kitney - ACS synthetic biology, 2016‏ - ACS Publications
This paper describes the development of a new data acquisition standard for synthetic
biology. This comprises the creation of a methodology that is designed to capture all the …

The SBOL stack: a platform for storing, publishing, and sharing synthetic biology designs

C Madsen, JA McLaughlin, G Mısırlı… - ACS synthetic …, 2016‏ - ACS Publications
Recently, synthetic biologists have developed the Synthetic Biology Open Language
(SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and …