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.Database URL: www.xenbase.org
Highlights
Xenbase is a model organism database (MOD) dedicated to supporting research on the South African clawed frog, Xenopus laevis, and its close relative Xenopus (Silurana) tropicalis, both of which are important systems for performing biomedical research [1, 2]
We describe how a new virtualized software architecture [6] helped us alleviate many of our problems
If the virtual machines (VMs) are running on separate physical systems, data transfer will be done over a dedicated connection between the servers, not the internet, so it will still be acceptably fast
Summary
Xenbase (www.xenbase.org) is a model organism database (MOD) dedicated to supporting research on the South African clawed frog, Xenopus laevis, and its close relative Xenopus (Silurana) tropicalis, both of which are important systems for performing biomedical research [1, 2]. 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. To do so we decoupled the different software services and components, such that each would run on a different virtual machine.
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