Clotho 3.0: An improved common framework for synthetic biology computing

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Stephanie Paige, Ernst Oberortner, Maxwell Bates, J. Christopher Anderson, Douglas Densmore

Cross-disciplinary Integration of Design Automation Research (CIDAR) group at Boston University, United States

The design and construction of synthetic biological systems demands managing a network of interrelated information (eg, parts data, assembly techniques). and, increasingly, software tools that use this information. These tools often perform steps along a workflow (eg, from design to physical assembly of a device). A proliferation of software tools that each solve one problem without awareness of other tools hinders users. Ways to move data between related formats, aggregate data relevant to a task, or move fluidly between tools in a workflow will be sporadically implemented without guarantee of interoperability. Our solution is Clotho 3.0, a new version of our platform for high-quality, interoperable applications. In version 3.0, data models are newly extensible, allowing developers to extend Clotho’s default model and add entirely new ones. 3.0 manages conversions between data formats to aggregate data from different sources. The new version also improves app management, enabling fluid workflows that span multiple apps and automating updates of installed applications and their dependencies. Alongside Clotho 3.0, we also present the Nona Foundation, a community incubator of open source synthetic biology software. These features enable biologists to incorporate agilely cutting-edge developments in techniques and information into their research. They help collaborators share apps and data without compatibility hassles. They allow bioinformaticists to instantiate their own database within Clotho and operate on it with new or existing apps. They prevent users expending excessive effort on maintaining their installations of software tools. By making it easier to write high-quality applications, Clotho means synthetic biologists will have more efficient, flexible tools available for their work.