Synthetic Biology Open Language (SBOL) Version 2.3.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems is to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year's JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.

Engineering Genomes with Genotype Specification Language.

High quality DNA design tools are becoming increasingly important as synthetic biology continues to increase the rate and throughput of building and testing genetic constructs. To make effective use of expanded build and test capacity, genotype design tools must not only be efficient enough to allow for many designs to be easily created, but also expressive enough to support the complex design patterns required by scientists on the frontier of genome engineering. Genotype Specification Language (GSL) is a language-based design tool invented at Amyris that enables scientists to quickly create DNA designs using a familiar syntax. This syntax provides a layer of abstraction that moves users away from reading and writing raw DNA sequences toward composing designs in terms of functional parts . GSL increases the speed at which scientists can design DNA constructs, provides a precise and reproducible representation of parts, and achieves these goals while maintaining design flexibility. Finally, the GSL compiler can emit information such as the exact final DNA sequence of the design as well as the reagents (primers and template information) required to physically build the constructs. Since its open-source release in February 2016, the GSL compiler can be freely downloaded and used by genome engineers to efficiently specify genetic designs. This chapter briefly introduces GSL syntax and design principles before examining specific examples of genome engineering tasks with accompanying GSL code.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

In the eyes of Indigenous people in Canada: exposing the underlying colonial etiology of hepatitis C and the imperative for trauma-informed care.

Background: The distribution of hepatitis C (HCV) infection in Canada signals a widening gap between Indigenous and non-Indigenous people. Current evidence demonstrates that the rate of HCV infection among Indigenous people is at least five times higher than the rest of Canada. This analysis provides a reconciliatory response, which exposes the colonial etiology of the HCV gap in Canada and proposes potential anti-colonial approaches to HCV wellness and health care for Indigenous people. Methods: This analysis applies Two-Eyed Seeing as a reconciliatory methodology to advance the understanding of HCV burden and identify the key elements of responsive HCV care in the context of Indigenous nations in Canada. Results: The analysis underlines the colonial distribution of HCV burden in Canada, highlights Indigenous perspectives on HCV infection, hypothesizes a clinical pathway for the underlying colonial etiology of HCV infection, and identifies Indigenous healing as a promising anti-colonial conceptual approach to HCV wellness and health care among Indigenous people. Conclusions: In the eyes of Indigenous people, HCV infection is a colonial illness that entails healing as an anti-colonial approach to achieving wellness and gaining health. Future empirical research should elaborate on the colonial HCV pathway hypothesis and inform the development of a framework for HCV healing among Indigenous people in Canada.

Synthetic Biology Open Language (SBOL) Version 2.1.0.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

Resonant phase matching of Josephson junction traveling wave parametric amplifiers.

We propose a technique to overcome phase mismatch in Josephson-junction traveling wave parametric amplifiers in order to achieve high gain over a broad bandwidth. Using "resonant phase matching," we design a compact superconducting device consisting of a transmission line with subwavelength resonant inclusions that simultaneously achieves a gain of 20 dB, an instantaneous bandwidth of 3 GHz, and a saturation power of -98 dBm. Such an amplifier is well suited to cryogenic broadband microwave measurements such as the multiplexed readout of quantum coherent circuits based on superconducting, semiconducting, or nanomechanical elements, as well as traditional astronomical detectors.