Bio-Algorithmic Workflows for Standardized Synthetic Biology Constructs.

A synthetic biology workflow covers the roadmap from conceptualization of a genetic device to its construction and measurement. It is composed of databases that provide DNA parts/plasmids, wet-lab methods , software tools to design circuits, simulation packages , and tools to analyze circuit performance. The interdisciplinary nature of such a workflow requires that experimental results and their in-silico counterparts proceed alongside, with constant feedback between them. We present an end-to-end use case for engineering a simple synthetic device, where information standards maintain coherence throughout the workflow. These are the Standard European Vector Architecture (SEVA), the Synthetic Biology Open Language (SBOL), and the Systems Biology Markup Language (SBML).