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

这一小型企业创新研究(SBIR)第二阶段项目的更广泛影响/商业潜力将是为生命系统工程开发一个软件平台。具体地说，它将完成一个软件生态系统，该软件生态系统建立在一套核心计算工具的基础上，用于规范、设计、构建、测试、分析和归档合成生物学中的活动，并将它们与一套丰富的专家服务(例如DNA合成、数据分析)接口结合在一起。拟议的工作包括完成最先进的设计方法和算法，并将其与基于遗传电路设计、代谢途径修改和基因组工程创建定制、模块化工作流程的能力结合起来。这项拟议的工作推进了合成生物学中的计算方法，并在软件服务与生物技术公司的货币化方面进行了创新。这项工作的预期结果是一个商业软件包和相关的服务协议，可以部署到大小生物技术公司，从根本上改变合成生物学设计的构思、设计和物理创建的方式。这个SBIR第二阶段项目将开发一个软件平台，目标是在一个工作流驱动的软件生态系统中将生物设计自动化(BDA)软件与明确集成的专家服务访问相结合。使用生物技术创造新的生命系统来设计新的药物、材料和燃料通常是一个特别的过程，涉及长迭代周期、浪费资源和次优设计。该软件将允许对新型工程生物系统工程的完整计划进行自动化规范、设计、制造、测试和存档。该软件包括指定生物“规则”、DNA组装策略和自动生成机器人指令的机制。特别是，这项努力将集中在创建遗传电路、工程新陈代谢途径和基因组工程。该方法提供了代表BDA最先进进展的工具，同时引入了与大量不同的专家服务提供商互动的新方法。此外，这种方法将增强新手实验者的能力，同时支持专业计算工程师。

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.