SBIR Phase II: Fully Integrated Design and Automated Fabrication Services Software Platform for Engineering Living Systems

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase II project will be the development of a software platform for the engineering of living systems. Specifically, it will complete a software ecosystem that builds upon a core set of computational tools for the specification, design, build, test, analyze, and archive activities in synthetic biology and couple them with a rich set of interfaces to expert services (e.g., DNA synthesis, data analysis). The proposed work involves the completion of state-of-the-art design approaches and algorithms and couples it with the ability to create customized, modular workflows based on genetic circuit design, metabolic pathway modification, and genome engineering. The proposed work advances computational approaches in synthetic biology as well as innovating in the way that software services are monetized with biotechnology companies. The anticipated result of this work is a commercial software package and associated service agreements that can be deployed to both large and small biotechnology companies fundamentally changing the way that synthetic biology designs are conceived, designed, and physically created. This SBIR Phase II project will develop a software platform where the goal is to combine bio-design automation (BDA) software with explicitly integrated access to expert services in a workflow-driven software ecosystem. The creation of novel living systems using biotechnology to engineer new medicines, materials, and fuels is frequently an ad-hoc process involving long iteration cycles, wasted resources, and sub-optimal designs. The software will allow for the automated specification, design, fabrication, test, and archival of complete plans for the engineering of novel engineered biological systems. This software includes mechanisms for specifying biological "rules," DNA assembly strategies, and automated generation of robotic instructions. In particular, this effort will focus on the creation of genetic circuits, engineered metabolic pathways, and genome engineering. The approach provides tools representing state-of-the-art advances in BDA while introducing novel methods of interacting with a large, diverse set of expert service providers. Further, the approach will empower novice experimentalists while enabling expert computational engineers.