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. 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.

We describe early experiments in the adoption of the OptIPuter architecture to provide data-intensive capabilities to several remote users of a large-scale, multi-year effort to organize and make publicly available data describing a wide variety of marine microbial ecologies, their genomic content, and the local environments in which they live-marine microbial metagenomics. Microbial genomes are millions of base pairs in length, requiring both a global view of the genome and the ability to zoom into detail interactively, enabled by the OptIPortal. We describe the design of a scientific data and compute server, enhanced by OptIPuter technologies, and early examples of its use in support of high performance science applications in this emerging scientific field.

This practices and experience paper describes the coordination, design, implementation, availability, and performance of the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) Grid Testbed. Applications in high-energy physics, genome annotation, quantum computational chemistry, wildfire simulation, and protein sequence alignment have driven the middleware requirements, and the testbed provides a mechanism for international users to share software beyond the essential, de facto standard Globus core. In this paper, we describe how human factors, resource availability and performance issues have affected the middleware, applications and the testbed design. We also describe how middleware components in grid monitoring, grid accounting, grid Remote Procedure Calls, grid-aware file systems, and grid-based optimization have dealt with some of the major characteristics of our testbed. We also briefly describe a number of mechanisms that we have employed to make software more easily available to testbed administrators.

To facilitate the interactive visualization, analysis, and correlation of massive amounts of data from multiple sites, the NSF-funded OptIPuter project is designing a powerful distributed cyberinfrastructure to support data-intensive scientific research and collaboration. This research exploits a new world in which the central architectural element is optical networking, not computers. This transition is caused by the use of parallelism, as in supercomputing a decade ago. However, this time the parallelism is in multiple wavelengths of light, or lambdas, on single optical fibers, creating supernetworks. Dedicated 1- to 10- Gigabit deterministic network connections are being deployed internationally by the Global Lambda Integrated Facility (GLIF), nationally by the National LambdaRail (NLR), regionally by academic consortia, and locally on campuses, connecting scientists' laboratories to collaborators and/or data sources all over the world, providing researchers with guaranteed bandwidth for data movement, guaranteed latency for visualization/collaboration and data analysis, and guaranteed scheduling for remote instrument control. Bandwidth alone isn't the solution; the OptIPuter is working on new grid-computing paradigms − that is, new middleware, transport protocols and optical signaling, control and management software − to enable applications to dynamically manage lambda resources just as they do any grid resource, creating a Lambda- Grid of interconnected high-performance computers, data storage devices, and instrumentation. This paper summarizes some of the OptIPuter's developments over dedicated end-to-end lightpaths among partner sites in San Diego, Chicago and Amsterdam.