The Synthetic Biology Open Language Standard: Sharing Design Information in Synthetic Biology

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Michal Galdzicki, Matthew Pocock, Mandy Wilson, Ernst Oberortner, Jackie Quinn, Aaron Adler, Bryan Bartley, Jacob Beal, Swapnil Bhatia, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, John H. Gennari, Raik Gruenberg, Jennifer Hallinan, Nathan Hillson, Cassie Huang, Jeffrey Johnson, Goksel Misirli, Chris J. Myers, Jean Peccoud, Hector Plahar, Cesar A. Rodriguez, Nicholas Roehner, Evren Sirin, Guy-Bart Stan, Anil Wipat, Fusun Yaman, Herbert M. Sauro

University of Washington, United States

The Synthetic Biology Open Language (SBOL) is a community-driven standard to exchange information pertinent to DNA designs among software tools, research groups, and commercial service providers. Compared to existing flat annotation formats, such as GenBank or FASTA, SBOL provides expressive and extensible data exchange capabilities, to share rich information about synthetic biological designs. The SBOL community, consisting of academic and industry members, defined a core data model that enables the exchange of DNA sequences and their components. The core data model provides extension capabilities to annotate the DNA components with additional information. In working groups, SBOL developers act jointly to provide minimal but expressive extensions to annotate DNA components with regulatory interactions, host context information, performance characteristics, or simulation results. The structured, hierarchical nature of the core data model and its extensions makes it possible to share all the required information to fully re-engineer synthetic biological designs. To integrate the SBOL standard into a software tool, we have developed software libraries and specification documents. To reassure a growing SBOL community and to receive input from the Synthetic Biology academic and industrial community, we demonstrate SBOL’s current data exchange capabilities on two case studies. The first case study exemplifies the exchange of DNA components between three sites using four different software tools. The second case study illustrates the data exchange between a graphical design tool and a textual design language. Both case studies demonstrate SBOL’s applicability and utilization in the exchange of DNA components while designing novel synthetic biological systems using biological CAD tools. The SBOL community aims to reach a wider range of software to make SBOL more accessible to non-developers. Furthermore, we continue to enrich SBOL’s data exchange capabilities, making it ultimately possible to fully re-engineer synthetic biological designs using biological CAD tools.