Nicholas Roehner
Former SBOL Editor · BBN Technologies
Publications and posts
Synthetic Biology Curation Tools (SYNBICT)
Much progress has been made in developing tools to generate component-based design representations of biological systems from standard libraries of parts. Most biological designs, however, are still specified at the sequence level. Consequently, there exists a need for a tool that can be used to automatically infer…
Curation Principles Derived from the Analysis of the SBOL iGEM Data Set
As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in…
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3
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…
Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)
Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by…
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.2
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…
Synthetic biology open language visual (SBOL visual) version 2.2
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…
Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted…
Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted…
Synthetic Biology Open Language (SBOL) Version 2.3
textlesssection class=\"abstract\"textgreatertextlessh2 class=\"abstractTitle text-title my-1\" id=\"d230e2\"textgreaterAbstracttextless/h2textgreatertextlessptextgreaterSynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering…
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
Abstract 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…
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.…
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…
Synthetic Biology Open Language (SBOL) Version 2.1.0
textlesssection class=\"abstract\"textgreatertextlessh2 class=\"abstractTitle text-title my-1\" id=\"d807e2\"textgreaterSummarytextless/h2textgreatertextlessptextgreaterSynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles…
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.…
A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of…
Sharing Structure and Function in Biological Design with SBOL 2.0
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and…
A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of…
Sharing Structure and Function in Biological Design with SBOL 2.0
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and…
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 design automation tools. The latest version of the standard, SBOL 2.0,…
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.
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.
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 introduces the foundational concepts of standards and model annotation…
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 introduces the foundational concepts of standards and model annotation…
The Synthetic Biology Open Language
The design and construction of engineered organisms is an emerging new discipline called synthetic biology and holds considerable promise as a new technological platform. The design of biologically engineered systems is however nontrivial, requiring contributions from a wide array of disciplines. One particular issue…
The Synthetic Biology Open Language
The design and construction of engineered organisms is an emerging new discipline called synthetic biology and holds considerable promise as a new technological platform. The design of biologically engineered systems is however nontrivial, requiring contributions from a wide array of disciplines. One particular issue…
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models
As engineering foundations such as standards and abstraction begin to mature within synthetic biology, it is vital that genetic design automation (GDA) tools be developed to enable synthetic biologists to automatically select standardized DNA components from a library to meet the behavioral specification for a genetic…
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models
As engineering foundations such as standards and abstraction begin to mature within synthetic biology, it is vital that genetic design automation (GDA) tools be developed to enable synthetic biologists to automatically select standardized DNA components from a library to meet the behavioral specification for a genetic…
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
The synthetic biology research community describes a standard language for exchanging designs of biological 'parts'.
The Synthetic Biology Open Language (SBOL) Provides a Community Standard for Communicating Designs in Synthetic Biology
The synthetic biology research community describes a standard language for exchanging designs of biological 'parts'.
A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language
Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application…
A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language
Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application…
Synthetic Biology Open Language (SBOL) Version 1.1.0
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a…
Synthetic Biology Open Language (SBOL) Version 1.1.0
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a…
Design and Test of Genetic Circuits Using $ tt iBioSim$iBioSim
The simulation of biological systems prior to their physical implementation can save time, money, and potentially provide insights into alternate designs. This paper presents a simulation environment which allows for a visual design process ultimately leading to a formal model which can be efficiently simulated.
Design and Test of Genetic Circuits Using $tt iBioSim$iBioSim
The simulation of biological systems prior to their physical implementation can save time, money, and potentially provide insights into alternate designs. This paper presents a simulation environment which allows for a visual design process ultimately leading to a formal model which can be efficiently simulated.
Title: Synthetic Biology Open Language (SBOL) Version 1.0.0
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.0.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data…
Title: Synthetic Biology Open Language (SBOL) Version 1.0.0
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.0.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data…