libSBOLj 2.0: A Java Library to Support SBOL 2.0

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic desig

BBF RFC 108: Synthetic Biology Open Language (SBOL) Version 2.0.0

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

Synthetic Biology Open Language (SBOL) Version 2.0.0

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 deve

BBF RFC 112: Synthetic Biology Open Language (SBOL) Version 2.1.0

BBF RFC 112 (the SBOL 2.1.0 standard) replaces BBF RFC 108 (the SBOL 2.0 standard), as well as the minor update SBOL 2.0.1.The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information

A standard-enabled workflow for synthetic biology

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 journal has recommended the use of SBOL in their publications

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

Doctor of Philosophy

dissertationSynthetic biology is applying engineering concepts to biological processes to enable genetic circuit designs, among other applications. As more biological parts are being discovered, it is vital to have an automated procedure to allow complex circuit designs to be built. Technology mapping is a set of procedures that maps biological components to a design specification. Current technology mapping frameworks for genetic circuits are used to design combinational circuits. This dissertation illustrates the process of building an automated workflow for a technology mapping framework to design asynchronous sequential genetic circuits. An automated process to create a library of gates for logic and memory circuits is described to construct gates from DNA parts retrieved from a standardize data repository. Genetic constraints address what parts can be mapped to the design specification when the gates and designs are constructed. The proposed automaton workflow begins with a specification provided in a formal design language, such as Verilog. The input design specification is converted into a genetic regulatory network represented using the Synthetic Biology Open Language (SBOL). The network is decomposed into base functions (NOR gates, inverters, and genetic toggle switches) and matching and covering algorithms are performed to produce the output design. The output design is converted to the Systems Biology Markup Language (SBML) data format for testing and simulation. The outcome of this work provides the synthetic biology community insights on how asynchronous sequential circuit designs can be built through an automated procedure to perform technology mapping from libraries composed of logic gates and memory circuits

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and intr