Peter W. Arzberger

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Access to and sharing of data are essential for the conduct and advancement of science. This article argues that publicly funded research data should be openly available to the maximum extent possible. To seize upon advancements of cyberinfrastructure and the explosion of data in a range of scientific disciplines, this access to and sharing of publicly(More)
Avian influenza virus subtype H5N1 is a potential pandemic threat with human-adapted strains resistant to antiviral drugs. Although virtual screening (VS) against a crystal or relaxed receptor structure is an established method to identify potential inhibitors, the more dynamic changes within binding sites are neglected. To accommodate full receptor(More)
The ongoing global effort of genome sequencing is making large scale comparative proteomic analysis an intriguing task. The Encyclopedia of Life (EOL; http://eol.sdsc.edu) project aims to provide current functional and structural annotations for all available proteomes, a computational challenge never seen before in biology. Using an integrative genome(More)
M. Riedel∗,†, E. Laure, Th. Soddemann, L. Field, J. P. Navarro, J. Casey,M. Litmaath, J. Ph. Baud, B. Koblitz, C. Catlett, D. Skow,C. Zheng, P. M. Papadopoulos,M. Katz, N. Sharma, O. Smirnova, B. Kónya, P. Arzberger, F. Würthwein, A. S. Rana, T. Martin,M. Wan,V. Welch, T. Rimovsky, S. Newhouse, A. Vanni, Y. Tanaka, Y. Tanimura, T. Ikegami, D. Abramson, C.(More)
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(More)
Hemagglutinin (HA) binds to sialylated glycans exposed on the host cell surface in the initial stage of avian influenza virus infection. It has been previously hypothesized that glycan topology plays a critical role in the human adaptation of avian flu viruses, such as the potentially pandemic H5N1. Comparative molecular dynamics studies are complementary(More)
Recent national and multinational investments (1) in networking and continued gains in information technological capability (2) have given rise to a complex cyberinfrastructure that is rapidly increasing our ability to produce, manage, and use data (3). As research becomes increasingly global (4), data-intensive, and multifaceted (5, 6), it is imperative to(More)
E communities comprise complex networks of individuals interacting with each other and with their environment. Two major challenges for scientists, managers, and policymakers are (1) understanding the forces that organize these heterogeneous systems across space and time (Levin 1992, Levin et al. 1997, Brown et al. 2002) and (2) using this understanding to(More)
The grid-based infrastructure enables large-scale scientific applications to be run on distributed resources and coupled in innovative ways. However, in practice, grid resources are not very easy to use for the end-users who have to learn how to generate security credentials, stage inputs and outputs, access grid-based schedulers, and install complex client(More)
Begun in 1994, the mission of the National Biomedical Computation Resource (NBCR) is to conduct, catalyze and enable multiscale biomedical research by harnessing advanced computation and data cyberinfrastructure through multidiscipline and multi-institutional integrative research and development activities. Here we report the more recent research and(More)