SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology (original) (raw)

Synthetic Biology Open Language (SBOL) Version 2.0.0

Journal of integrative bioinformatics, 2015

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 2.0 of SBOL, introducing a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well def...

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

2020

Many computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computations regardless of the particular platform that is being used.Here, we introduce the Galaxy-SynBioCADa portal, the first Galaxy toolshed for synthetic biology and metabolic engineering. It allows one to easily create workflows or use those already developed by the community. The portal is a growing commun...

Synthetic biology open language (SBOL) version 3.0.0

Journal of Integrative Bioinformatics, 2020

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. 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, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Compone...

Synthetic Biology Open Language (SBOL) Version 2.1.0

Journal of integrative bioinformatics, 2016

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 con...

A standard-enabled workflow for synthetic biology

Biochemical Society transactions, 2017

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 tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology...

Sharing Structure and Function in Biological Design with SBOL 2.0

ACS synthetic biology, 2016

To collaboratively design synthetic biology systems, it is important to communicate both the structural and functional aspects of a design in a standard manner. This paper presents the Synthetic Biology Open Language (SBOL) 2.0 and demonstrates how this standard enables effective collaborative design across different institutions and tools. SBOL 2.0 serves the diverse interests of the synthetic biology community. The standard includes the ability to describe both functional and structural aspects of a design, including DNA, RNA, small molecules, and proteins, as well as their interactions as part of functional modules. SBOL 2.0 has been developed via consensus, with careful consideration of recent design trends in synthetic biology and real use cases submitted by members of the commercial biotechnology community. The standard thus provides researchers with a standardized representation for describing, manipulating, and reproducing biological designs across the synthetic biology comm...

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

Nature Communications, 2022

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 portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows.

TASBE : A ToolChain to Accelerate Synthetic Biological Engineering

2011

Jacob Beal Ron Weiss Douglas Densmore Aaron Adler Jonathan Babb Swapnil Bhatia Noah Davidsohn Traci Haddock Fusun Yaman Richard Schantz Joseph Loyall BBN Technologies 10 Moulton Street Cambridge, MA, USA 02138 MIT 77 Massachusetts Ave Cambridge, MA, USA 02139 Boston University 8 Saint Mary’s St. Boston, MA, USA 02215 {jakebeal,fyaman, aadler, rschantz, jloyall}@bbn.com, {rweiss, ndavidso, jbabb}@mit.edu, {dougd,swapnilb,thaddock}@bu.edu