The design of synthetic biological devices is most commonly performed by hand, involving a large investment of time and effort and requiring extensive knowledge of available biological components. Software tools have the potential to make this process both easier and more effective by assisting users in the storage, selection, and arrangement of biological components, as well as the visualization and verification of finalized designs.
Clotho, which is developed by CIDAR in collaboration with the Anderson Lab at the University of California, Berkeley, provides a way for synthetic biologists to store and interact with biological data, preserving detailed information on biological parts for use in device design. It also provides a framework for applications that act upon this data, which are then able to automate many design tasks.
One example of this is Pigeon, a web-based software tool that renders textual descriptions of genetic circuit designs into graphical images using standardized visual elements. The combination of Eugene, Clotho, and Pigeon allows the rapid design and assessment of genetic circuit libraries, producing results that can be easily recognized and understood by other members of the synthetic biology community.