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 …

Genetic circuit design automation

AAK Nielsen, BS Der, J Shin, P Vaidyanathan… - Science, 2016 - science.org
INTRODUCTION Cells respond to their environment, make decisions, build structures, and
coordinate tasks. Underlying these processes are computational operations performed by …

Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron

M Taketani, J Zhang, S Zhang, AJ Triassi… - Nature …, 2020 - nature.com
Bacteroides thetaiotaomicron is a human-associated bacterium that holds promise for
delivery of therapies in the gut microbiome. Therapeutic bacteria would benefit from the …

Programming Escherichia coli to function as a digital display

J Shin, S Zhang, BS Der, AAK Nielsen… - Molecular systems …, 2020 - embopress.org
Synthetic genetic circuits offer the potential to wield computational control over biology, but
their complexity is limited by the accuracy of mathematical models. Here, we present …

Precision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads

Y Park, A Espah Borujeni, TE Gorochowski… - Molecular systems …, 2020 - embopress.org
Genetic circuits have many applications, from guiding living therapeutics to ordering process
in a bioreactor, but to be useful they have to be genetically stable and not hinder the host …

The Synthetic Biology Open Language (SBOL) version 3: simplified data exchange for bioengineering

JA McLaughlin, J Beal, G Mısırlı, R Grünberg… - … in Bioengineering and …, 2020 - frontiersin.org
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that
allows knowledge about biological designs to be captured using a machine-tractable …

Sharing structure and function in biological design with SBOL 2.0

N Roehner, J Beal, K Clancy, B Bartley… - ACS synthetic …, 2016 - ACS Publications
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative
engineering of biological systems across different institutions and tools. SBOL is developed …

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

J Hérisson, T Duigou, M Du Lac, K Bazi-Kabbaj… - Nature …, 2022 - nature.com
Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic
engineering, and industrial biotechnology. The tools and workflows currently shared on the …

Discovering design principles for biological functionalities: Perspectives from systems biology

P Bhattacharya, K Raman, AK Tangirala - Journal of Biosciences, 2022 - Springer
Network architecture plays a crucial role in governing the dynamics of any biological
network. Further, network structures have been shown to remain conserved across …

Galaxy-SynBioCAD: Automated Pipeline for Synthetic Biology Design and Engineering

J Hérisson, T Duigou, M Du Lac, K Bazi-Kabbaj… - bioRxiv, 2022 - biorxiv.org
Abstract We introduce the Galaxy-SynBioCAD portal, the first toolshed for synthetic biology,
metabolic engineering, and industrial biotechnology. The tools and workflows currently …