The Virtual Xenbase: Transitioning an online bioinformatics resource to a private cloud

Abstract

As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization.