Thomas E. Gorochowski

Publications and posts

paraSBOLv: A Foundation for Standard-Compliant Genetic Design Visualization Tools

Diagrams constructed from standardized glyphs are central to communicating complex design information in many engineering fields. For example, circuit diagrams are commonplace in electronics and allow for a suitable abstraction of the physical system that helps support the design process. With the development of the…

DOI

SBOL Visual 2 Ontology

Standardizing the visual representation of genetic parts and circuits is essential for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts…

PDF DOI

SBOL Visual 2 Ontology

Standardizing the visual representation of genetic parts and circuits is essential for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts…

DOI

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of…

DOI

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of…

DOI

Communicating Structure and Function in Synthetic Biology Diagrams

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions…

PDF DOI

Communicating Structure and Function in Synthetic Biology Diagrams

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions…

DOI

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…

PDF DOI

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…

DOI