Virtualizing Lifemapper Software Infrastructure for Biodiversity Expedition

One of the activities of the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) is fostering Virtual Biodiversity Expeditions (VBEs) by bringing domain scientists and cyber infrastructure specialists together as a team. Over the past few years PRAGMA members have been collaborating on virtualizing the Lifemapper software. Virtualization and cloud computing have introduced great flexibility and efficiency into IT projects. Virtualization provides application scalability, maximizes resources utilization, and creates a more efficient, agile, and automated infrastructure. However, there are downsides to the complexity inherent in these environments, including the need for special techniques to deploy cluster hosts, dependence on virtual environments, and challenging application installation, management, and configuration. In this paper, we report on progress of the Lifemapper virtualization framework focused on a reproducible and highly configurable infrastructure capable of fast deployment. Lifemapper is a complex biological software infrastructure developed by the Biodiversity Institute at The University of Kansas that creates and maintains an archive of species distribution maps calculated from public specimen data and a suite of data and tools for biodiversity researchers that calculate single and multi-species distribution predictions and macroecological analyses. Our goal is to create a viable virtualization solution that can be easily adopted and reused by scientists at multiple institutions and projects. This solution 1) allows fast deployment of ready-made cluster images; 2) reproduces the complete Lifemapper processing pipeline on demand at multiple sites and in different hosting environments; and 3) enables scientists to perform Lifemapper-facilitated data processing on restricted-use data, very large datasets, or other unique data. A key contribution of this work is describing the practical experience in taking a complex, clustered, domain-specific, data analysis and simulation system and making it available to operate on a variety of system configurations. Uses of this portability range from whole cluster replication to teaching and experimentation on a single laptop. System virtualization is used to practically define and make portable the full application stack, including all of its complex set of supporting software.