PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts

Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. While repositories of such parts exist to promote their reuse, there is still a need to design novel parts from scratch. PartsGenie, freely available at http://parts.synbiochem.co.uk, is introduced to facilitate the computational design of such synthetic biology parts. PartsGenie has been designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language (SBOL), and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimisation algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie can therefore be used as a single, stand-alone tool, or integrated into larger synthetic biology pipelines that are being developed in the SYNBIOCHEM centre and elsewhere.