A Synthetic Biology Workflow Using Sbol

A synthetic biology workflow requires genetic design repositories to organize collections of parts, sequence-level design and visualization tools to compose genetic parts into complete constructs, and genetic circuit design tools to construct, model, and simulate complete systems enabling the evaluation of alternative design choices. Data standards, such as the Synthetic Biology Open Language (SBOL), are critical to enabling the exchange of information within such a workflow, allowing a diversity of repositories and software tools to be seamlessly connected. This talk describes one such workflow that leverages the growing ecosystem of software tools that support 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 from a SynBioHub repository and compose them to construct larger designs that can be submitted back into the repository. Finally, iBioSim is a genetic modeling, analysis, and design tool that provides a means to construct complete circuit designs in SBOL and pair them with SBML models for these designs that can be simulated and analyzed using a variety of techniques. Both SBOLDesigner and iBioSim also support uploading these larger system 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.