Collaborative Research: ABI Development: A Modular, Community Based Design Platform for Synthetic Biology (Clotho)

University Of California-Berkeley, Berkeley CA

Investigators

Abstract

Synthetic biology attempts to design novel biological systems to address a number of challenges in bioenergy, biotherapeutics, and bioremediation. However, synthetic biology is facing two very fundamental challenges: data management and standardization. This project will complete the development of the Clotho software platform for synthetic biology. Clotho is an environment which links repositories of biological data (databases) to modular, user created 'Apps' through a common interface which reflects a data model specifically tailed to synthetic biology. Apps then can be used together to create specific design flows ranging from high level specification of biological functionality all the way down to basic sample tracking and laboratory management. The project will strive to (1) create the first standardized data model for synthetic biology captured as a software platform. (2) To create a complete application programming interface to access this data model via software 'Apps'. (3) To create a global community of users via a website designed from the ground up to create, share, and collaborate around software development. (4) To create a polished initial software distribution including appropriate user interfaces and applications to address the immediate needs of synthetic biology labs. The broader significance of this project is to establish a design framework for the automation and standardization of software in synthetic biology. Educational opportunities include Clotho development in the International Genetically Engineered Machine (iGEM) competition. Design automation coursework will use Clotho at UC Berkeley and Boston University. The App store (clothoapps.org) will serve as a portal not only for Clotho development but also as a community resource. Discussions regarding software tool development and use, documentation of ongoing research projects, and storage and retrieval of code and software libraries will be enabled by this effort. Finally, the International Workshop on Bio-Design Automation (IWBDA) will host Clotho developer and user meetings.