Synthetic Biology Merges with Computer Science to Create New Utility Software for Bio Data
Researchers from the Synthetic Biology Engineering Research Center (SynBERC), an NSF-funded center headquartered at the University of California (UC) at Berkeley, collaborated with computer science colleagues from Boston University to develop smartphone-like software for standardizing and managing biological data from one lab to the next. NSF has now awarded a three-year $1.1M Office of Cyberinfrastructure grant to the team to take it to the next level.
Five years ago, a computer scientist and a bioengineer asked each other if they could create a computational toolkit that used synthetic biology principles to better design and build biological components for use in human health, energy, and the environment. Their efforts to date have resulted in Clotho, a program that aims to provide a much-needed data management tool for synthetic biologists.
Clotho is a software environment that links large databases of biological data to user- created “apps” through a common interface. Underpinning Clotho is a data model specifically designed to describe how biological parts will behave when combined in new ways, a key goal of synthetic biology. Apps can be used together to create customized design processes, ranging from high-level specification of biological functionality all the way down to basic sample tracking and laboratory management.
The grant will provide the research team with funding to develop and distribute the software for research and commercial uses. Just as important, it will allow the Clotho researchers to refine their standardized data, algorithms, and methodologies for synthetic biology. Developing these basic models of how biology works in different contexts has been a major challenge for the synthetic biology community. If successful, the project will create not only a software-based standard data model for synthetic biology, but also develop a global community of users to create, share, and collaborate around a Clotho "App store."
The project includes collaborations with researchers at the University of Washington and BIOFAB, a design-build facility for synthetic biology parts founded by SynBERC researchers.