Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems

To design the complex systems that synthetic biologists propose to create, software tools must be developed. Critical to success is the enablement of collaboration across our community such that individual tools that perform specific tasks combine with other tools to provide multiplicative benefits. This will require standardization of the form of the data that exists within the field (Parts, Strains, measurements, etc.), a software environment that enables communication between tools, and a sharing mechanism for distributing the tools. Additionally, this data model must describe the data in a sufficiently rigorous and validated form such that meaningful layers of abstraction can be built upon the base. Herein, we describe a software platform called "Clotho" which provides such a data model, and the plugin and sharing mechanisms needed for a rich tool environment. This document provides a tutorial for users of Clotho and information for software developers who wish to contribute new tools (known as "Apps") to it.