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 modelling 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. This talk describes one such workflow that we’ve been developing during my visit to Newcastle University, which utilizes the growing ecosystem of software tools that support the Synthetic Biology Open Language (SBOL) to describe genetic designs, and the mature ecosystem of tools that support the Systems Biology Markup Language (SBML) to model these designs. In particular, this presentation will demonstrate a workflow using tools including SynBioHub, SBOLDesigner, and iBioSim. SynBioHub (http://synbiohub.org) is a database designed for storing synthetic biology designs captured using the SBOL data model, and it provides both a RESTful API for computational access and a user-friendly Web-based frontend. SBOLDesigner is a sequence editor that allows the designer to fetch parts for a SynBioHub repository and compose them to construct larger designs. Finally, iBioSim is genetic modelling, analysis, and design tool that provides a means to construct SBML models for these designs that can be simulated and analysed using a variety of techniques. Both SBOLDesigner and iBioSim also support uploading these larger systems designs back to the SynBioHub repository.
Finally, this talk will demonstrate how this workflow can be utilized to produce SBOL for the ACS Synthetic Biology journal, which has recently recommended the use of SBOL in their publications.