The Synthetic Biology Open Language a data exchange standard for biological engineering

Thesis (Ph.D.)--University of Washington, 2012Synthetic biology is the emerging research and engineering field concerned with the design and construction of new biological functions and systems. Synthetic biologists are engineering organisms to solve outstanding problems in medicine, bio-energy, environmental health, and nutrition. Their goal is to improve the biological engineering process by applying standardization, decoupling, and abstraction. To more efficiently engineer gene circuits synthetic biologists need software tools that support standardized data exchange. For my dissertation research I led the development and deployment of the Synthetic Biology Open Language (SBOL). In this dissertation, I present the SBOL community, the specification, and demonstrations of its use. The SBOL community is supported by stakeholders from the synthetic biology software community. The SBOL Core specifies the vocabulary, data model, and format to define the standard. I describe SBOL Core as a common representation for synthetic biology designs capable of describing theoretical DNA component designs; annotated DNA sequence; and collections of components. To aid the exchange synthetic biological designs among software tools I explain the software libraries which support the implementation of SBOL. Then, I illustrate the recognition of its value and acceptance by the stakeholders through the deployment of the technology at collaborating sites. Finally, I show how the choice of Semantic Web technology to facilitate the information exchange between software can also be used for information retrieval to improve the selection of DNA components in new designs. Through this work I contribute to the development of informatics standards a computational infrastructure to enable a rapid biological engineering process for biotechnology