Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology

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Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Robert Sidney Cox, Michal Galdzicki, Nathan Hillson, Akshay Maheshwari, Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Herbert Sauro, Larisa Soldatova, Guy-Bart Stan, Mandy Wilson, Drew Endy

Autodesk Research, United States

The Synthetic Biology Open Language Visual (SBOL Visual) project is an effort toward developing a community-driven open standard for visual representation of genetic designs. Standardized visual notation for communicating designs has proven to be useful in many engineering disciplines. A de facto visual notation does exist in synthetic biology; however, it is incomplete, is often extended ad hoc, and exists as a poorly defined, voluntary, communal convention rather than an explicit standard. Because synthetic biology endeavors often require a multidisciplinary team, a common visual system of communication with well-defined semantics is vital. It is also important that the emerging ecosystem of biological design tools converge upon a common visual language to maximize adoption and minimize ambiguity in results. Given the central role and rich history of visual representation in the life sciences, a well-defined visual notation will also prompt the construction of the formal infrastructure needed to support effective ontologies, meaningful models, and tools tailored to community needs. SBOL Visual comprises a set of symbols used to visually depict functional information encoded by nucleic acid sequences. SBOL Visual is presently being used by synthetic biologists to depict genetic designs in peer-reviewed publications and presentations. Software developers in academia and industry are using SBOL Visual in their computer-aided design tools for synthetic biology. In addition to specifying a symbol set, we initialize a framework for supporting the synthetic biology community’s involvement in growing and maturing SBOL Visual. While the symbols specified in the current version of SBOL Visual are drawn from the de facto visual notation of the synthetic biology community, SBOL Visual must ultimately be community driven if it is to meet the needs of synthetic biologists. Through active input from the synthetic biology community, SBOL Visual will mature into a foundational tool for the communication of genetic design.