SBROME: a scalable optimization and module matching framework for automated biosystems design

L Huynh, A Tsoukalas, M Köppe… - ACS synthetic …, 2013 - ACS Publications
The development of a scalable framework for biodesign automation is a formidable
challenge given the expected increase in part availability and the ever-growing complexity …

Design automation for synthetic biological systems

D Densmore, S Hassoun - IEEE Design & Test of Computers, 2012 - ieeexplore.ieee.org
Through principled engineering methods, synthetic biology aims to build specialized
biological components that can be modularly composed to create complex systems. This …

Computational design of biological circuits: putting parts into context

E Karamasioti, C Lormeau, J Stelling - Molecular Systems Design & …, 2017 - pubs.rsc.org
The rational design of synthetic gene circuits has led to many successful applications over
the past decade. However, increasingly complex constructs also revealed that analogies to …

Toward scalable parts families for predictable design of biological circuits

JB Lucks, L Qi, WR Whitaker, AP Arkin - Current opinion in microbiology, 2008 - Elsevier
Our current ability to engineer biological circuits is hindered by design cycles that are costly
in terms of time and money, with constructs failing to operate as desired, or evolving away …

Optimal part and module selection for synthetic gene circuit design automation

L Huynh, I Tagkopoulos - ACS synthetic biology, 2014 - ACS Publications
An integral challenge in synthetic circuit design is the selection of optimal parts to populate a
given circuit topology, so that the resulting circuit behavior best approximates the desired …

Bio-design automation: software+ biology+ robots

DM Densmore, S Bhatia - Trends in biotechnology, 2014 - cell.com
Synthetic biology promises to usher in a new era of scientific innovation and discovery [1].
Applicationsof thistechnology are broad and diverse [2]. Although applications frequently …

[PDF][PDF] A software stack for specification and robotic execution of protocols for synthetic biological engineering

V Vasilev, C Liu, T Haddock, S Bhatia, A Adler… - … workshop on bio-design …, 2011 - Citeseer
Synthetic biology is an emerging field in which biologists modify or design the behavior of
organisms to engineer systems that perform computation in diverse biological applications …

Synthetic biology: from bacteria to stem cells

R Weiss - Proceedings of the 44th annual Design Automation …, 2007 - dl.acm.org
Synthetic biology is revolutionizing how we conceptualize and approach the engineering of
biological systems. Recent advances in the field are allowing us to expand beyond the …

Squaring a circle: to what extent are traditional circuit analogies impeding synthetic biology?

K Ilia, D Del Vecchio - GEN Biotechnology, 2022 - liebertpub.com
Synthetic biology has been significantly shaped by modular design principles through
analogies to electrical and computer engineering. Although convenient, these parallels often …

Automated design of robust genetic circuits: Structural variants and parameter uncertainty

T Schladt, N Engelmann, E Kubaczka… - ACS synthetic …, 2021 - ACS Publications
Genetic design automation methods for combinational circuits often rely on standard
algorithms from electronic design automation in their circuit synthesis and technology …