SynBioHub 3 - An Improved Synthetic Biology Repository
Abstract
SynBioHub is a repository for storing, sharing, and finding modular genetic designs in synthetic biology. While valuable to the community, the original SynBioHub faces architectural limitations including coupled frontend-backend code, performance issues, and limited support for newer standards. This thesis presents SynBioHub3, a complete redesign using Java and Spring Boot that addresses these challenges through a strict separation of concerns based on the Model-View-Controller pattern. The new architecture creates a dedicated REST API interface, eliminates server-side rendering, and improves performance - notably in the download algorithm, which shows significant speed gains. SynBioHub3 implements core functionality including search, downloads, and authentication while maintaining backward compatibility with existing applications. This reimplementation provides a more maintainable, scalable foundation for synthetic biology data sharing that better supports FAIR principles and the community’s growing needs.
