Editorial pubs.acs.org/synthbio
IWBDA 2016
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output of a given circuit, either in isolation or in combination with other similarly stochastic circuits. This should improve the ability to use genetic circuits as parts by characterizing the bounds that can be assumed on their behavior rather than relying on models without error measures. Otero-Muras et al. (DOI: 10.1021/acssynbio.6b00306) apply a state-of-the-art result in multiobjective mixed-integer nonlinear programming to the optimal design of synthetic genetic circuits and show its application to decoding naturally occurring phenomena into circuit designs that could produce them. Two papers focus on programmable matter at the micro and meso scales. Kozyra et al. (DOI: 10.1021/acssynbio.6b00271) use fully artificial sequences rather than the usual phage (thus bio-orthogonal) to construct DNA and RNA origami with all locations fully addressable via a guarantee that each 6-mer sequence will be unique. Lehner et al. (DOI: 10.1021/ acssynbio.6b00395) use a modified low-cost 3D printer along with a bacteria/alginate mixture that gels as it is printed onto a calcium chloride-coated substrate to pattern 3D assemblies of bacteria. These kinds of spatial control have the potential to enhance development and experimentation in spatial genetic programming, signaling, and pattern formation. The final paper is oriented toward improving the ability of experimentalists to automate their processes. Gupta et al. (DOI: 10.1021/acssynbio.6b00304) offer an intuitive and visual approach to programming automation for biology, with the hope that doing so will enable nonprogrammers to more easily take advantage of the automation systems that are emerging.
he International Workshop on Bio-Design Automation (IWBDA) brings together researchers working in the areas of systems biology, synthetic biology, and design automation. Effective pursuit of engineering goals in biology requires the coordination of all three disciplines: systems biology to understand and model, synthetic biology to architect, and design automation to execute efficiently. Accordingly, IWBDA is a venue where researchers in each of these disciplines are encouraged to cross-pollinate, discover one another’s work, and form collaborations. The eighth IWBDA, organized by the nonprofit Bio-Design Automation Consortium, took place from August 16th to 18th, 2016, at Newcastle University in Newcastle upon Tyne, United Kingdom. This special issue of ACS Synthetic Biology includes ten papers based on work presented at IWBDA that contribute to the key needs for achieving goals in the bioengineering space: articulating, formalizing and communicating the goal, modeling the processes involved with sufficient accuracy to perform design, and architecting matter according to that design. Four of these papers are directed toward solidifying and advancing standards and visualization in design and communication for synthetic biology. Der et al. (DOI: 10.1021/ acssynbio.6b00252) have released a visualization toolkit to ease and standardize communication of designs and results within the field of synthetic biology; the toolkit is customizable and designed to be integrated into other software packages. ScottBrown et al. (DOI: 10.1021/acssynbio.6b00273) supports visualization of a Systems Biology Markup Language model and allows easy highlighting of changes made between two similar model versionshelping bring the virtues of version control to synthetic biology. Zundel et al. (DOI: 10.1021/ acssynbio.6b00277) present a tool for ensuring standards adherence and language-correctness of description written in Synthetic Biology Open Language (SBOL), enabling automatic conversion of existing data to the most current version of SBOL and lowering the burden of SBOL adoption for synthetic biology software tools. Finally, Cox et al. (DOI: 10.1021/ acssynbio.6b00286) have developed a glyph-based visual language for protein description and design that enables unambiguous communication between researchers, standardized representation across tools from different sources, and a clear taxonomy of the relevant functional units of proteins. Three papers focus on quantitative modeling for the design of synthetic devices. du Lac et al. (DOI: 10.1021/ acssynbio.5b00217) work to improve in silico design by accounting for the effect of different bacterial growth phases and media conditions on how many copies of a gene are present. This method takes an important step in modeling sophistication by refining the initial assumptions of constant gene copy number and improving prediction where the simple models are substantially inaccurate. Baig et al. (DOI: 10.1021/ acssynbio.6b00296) deal with the issues of stochasticity that make genetic logic circuits only poorly resemble electronic ones via a simulation approach that characterizes the variations in © 2017 American Chemical Society
Avi Robinson-Mosher*
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Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Present Address
D. E. Shaw Research 120 W. 45th St., 39th Fl. New York, NY 10036. Notes
Views expressed in this editorial are those of the author and not necessarily the views of the ACS.
Special Issue: IWBDA 2016 Received: June 30, 2017 Published: July 21, 2017 1114
DOI: 10.1021/acssynbio.7b00239 ACS Synth. Biol. 2017, 6, 1114−1114
