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

合成生物学试图设计新的生物系统来解决生物能源、生物治疗和生物修复方面的许多挑战。然而，合成生物学正面临着两个非常基本的挑战：数据管理和标准化。本项目将完成Clotho合成生物学软件平台的开发。Clotho是一个将生物数据存储库（数据库）链接到模块化的环境，用户通过一个公共接口创建“应用程序”，该接口反映了专门针对合成生物学的数据模型。然后，应用程序可以一起使用来创建特定的设计流程，范围从生物功能的高级规范一直到基本的样品跟踪和实验室管理。该项目致力于(1)为合成生物学创建第一个作为软件平台捕获的标准化数据模型。(2)创建一个完整的应用程序编程接口，通过软件“Apps”访问该数据模型。(3)通过一个从头开始设计的网站创建一个全球用户社区，以围绕软件开发进行创建、共享和协作。(4)创建一个完善的初始软件发行版，包括适当的用户界面和应用程序，以满足合成生物学实验室的即时需求。本项目更广泛的意义在于为合成生物学软件的自动化和标准化建立一个设计框架。教育机会包括国际基因工程机器（iGEM）竞赛中的Clotho发展。加州大学伯克利分校和波士顿大学的设计自动化课程将使用Clotho。应用商店（clothoapps.org）不仅是Clotho开发的门户，也是一个社区资源。关于软件工具开发和使用的讨论，正在进行的研究项目的文档，以及代码和软件库的存储和检索将通过这项工作得以实现。最后，生物设计自动化国际研讨会（IWBDA）将主办Clotho开发者和用户会议。

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 strives 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.