Research Resources

A collection of research resources for the engineering biology community.

Web of Registries

The Synthetic Biology Engineering Research Center (Synberc) pioneered the idea of a web of registries. The Joint BioEnergy Institute‘s Inventory of Composable Elements (ICE) is an open source registry software and 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. ICE is built upon the idea of a Web of Registries (funded in part by Synberc), and thus provides strong support for distributed, interconnected use. It includes several useful graphical applications for sequence annotation, manipulation and analysis.

Rosetta Backrub

Rosetta Backrub is the flexible backbone protein structure modeling and design server of the Kortemme Lab. The server utilizes the “backrub” method, first described by Davis et al. for flexible protein backbone modeling implemented in Rosetta.

Ribosome Binding Site (RBS) Calculator

The RBS Calculator is a tool developed by Howard Salis, then a postdoctoral researcher in the Voigt Lab, that can be used to control several devices within a synthetic biological system. The RBS calculator has been licensed by multiple Synberc and non-Synberc companies, and has been incorporated into Vector NTI, a molecular biology software package commercialized by Thermo Fisher.

Clotho

Clotho was developed by Synberc researchers and affiliates for engineering synthetic biological systems and managing the data which is used to create them. It also provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology.