Web of Registries: A distributed cyberinfrastructure for synthetic biology

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Hector Plahar, Timothy S. Ham, Zinovii Dmytriv, Joanna Chen, Nathan J. Hillson and Jay D. Keasling

Joint BioEnergy Institute (Lawrence Berkeley National Lab), United States

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICE) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access and interaction with the platform via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. Starting with version 3.3, ICE also includes a distributed software platform to enable the efficient sharing of composable biological elements across labs in the synthetic biology research community, thus expanding the search space of biological constructs. It offers community collaboration capabilities and opportunities which enable scientists to publish and share their data sets. Advanced security mechanisms are also in place to restrict access to particular data sets that researchers are not yet ready to share with the wider community or will prefer to keep private or restricted to a smaller group. The software also enables defining and managing members of these groups. This Web of Registries infrastructure is constructed to be compatible with existing and emerging computer-aided design tools for synthetic biological systems. JBEI-ICE has been adopted as the registry platform in multiple research labs and institutions including Synberc, PlantFab (Cambridge) and JBEI. A public instance is also available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects.