Biomaterial Database

A standard-enabled workflow for synthetic biology. 2017

Chris J Myers, and Jacob Beal, and Thomas E Gorochowski, and Hiroyuki Kuwahara, and Curtis Madsen, and James Alastair McLaughlin, and Göksel Mısırlı, and Tramy Nguyen, and Ernst Oberortner, and Meher Samineni, and Anil Wipat, and Michael Zhang, and Zach Zundel

Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, Rm. 2110, Salt Lake City, UT 84112, U.S.A. myers@ece.utah.edu.

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.

UI	MeSH Term	Description	Entries
D008954	Models, Biological	Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.	Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D012984	Software	Sequential operating programs and data which instruct the functioning of a digital computer.	Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software
D057188	Workflow	Description of pattern of recurrent functions or procedures frequently found in organizational processes, such as notification, decision, and action.	Work Flow,Work Flows,Workflows
D058615	Synthetic Biology	A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems.	Biologies, Synthetic,Biology, Synthetic,Synthetic Biologies