The long-term aims of this project are to improve the engineering practices of synthetic biologists, and thereby to hasten the pace of synthetic biology research. Synthetic biology is poised to make great contributions to health, medicine, energy, and the environment by building systems ranging from the production of anti-malarial drugs, to improved antibiotics, to tumor-tracking bacteria, to engineering new carbon-neutral energy sources, and to organisms that clean up environmental toxins and fight pollution. Our research approach is to combine well-established engineering principles with semantic web methods and technologies. More specifically, we will develop tools that support the engineering principles of modularity, reuse, and version control for the configuration of complete biological systems. The semantic web technologies that we apply to this domain include ontology development, the formal specification of semantics, and an OWL reasoning system to carry out validation, intelligent information retrieval, and configuration tasks. The specific goal of the proposed research is develop a prototype tool for the management of information throughout the synthetic biology research lifecycle. The capabilities of this tool will include version control, intelligent information retrieval about synthetic biology components, and configuration management to assist in assembling those components into working biological systems. We will design, develop, and test this tool in direct collaboration with working synthetic biologists from Dr. Sauro's laboratory. We divide our research work into three specific aims: (1) analyzing the work of synthetic biologists and extending our ontology to include configuration constraints and versioning knowledge for synthetic biology components;(2) developing version management capabilities for synthetic biologists;and (3) developing configuration and parts retrieval capabilities for synthetic biologists. To support both collaborative work and reuse of components, our tool and our research leverages the idea of an annotated library of synthetic biology components. Our work will use existing libraries, and our tool will add to these libraries through its use. To support the widest range of system reuse, our tool will be based on public, semantic web standards and will be developed as an open, modern web application. We envision an enterprise-wide use of our tool, which will allow for better communication, improved design, and better engineering of synthetic biological systems. In turn, these engineering improvements will help hasten the wide-scale industrial production, adoption, and use of synthetic biology constructs, leading to new advances in bioengineered therapeutic, energy, and food technologies.

Public Health Relevance

of the proposed research is that improved engineering for the synthetic biology enterprise will improve the quality and efficiency with which synthetic biological constructs can be designed and built. These improvements will enable new scientific advances that directly benefit the public-advances such as bioengineered therapies, improved antibiotics, and inexpensive production of pharmaceutical agents.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Small Business Technology Transfer (STTR) Grants - Phase II (R42)
Project #
5R42HG006737-03
Application #
8334022
Study Section
Special Emphasis Panel (ZRG1-IMST-K (14))
Program Officer
Bonazzi, Vivien
Project Start
2010-08-01
Project End
2013-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
3
Fiscal Year
2012
Total Cost
$379,537
Indirect Cost
Name
Clark and Parsia, LLC
Department
Type
DUNS #
171840031
City
Washington
State
DC
Country
United States
Zip Code
20001
Neal, Maxwell L; Cooling, Michael T; Smith, Lucian P et al. (2014) A reappraisal of how to build modular, reusable models of biological systems. PLoS Comput Biol 10:e1003849
Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst et al. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol 32:545-50