Peter W. Arzberger

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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)
SUMMARY Many production Grid and e-Science infrastructures have begun to offer services to end-users during the past several years with an increasing number of scientific applications that require access to a wide variety of resources and services in multiple Grids. Therefore, the Grid Interoperation Now—Community Group of the Open Grid Forum—organizes and(More)
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)
The ongoing global effort of genome sequencing is making large scale comparative proteomic analysis an intriguing task. The Encyclopedia of Life (EOL; 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)
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)
— The Grid-based computational infrastructure enables large-scale scientific applications to be run on distributed resources and coupled in innovative ways. However, in practice, Grid-based resources are not very easy to use for the end-user. The end-user has to learn how to generate security credentials, stage inputs and outputs, access Grid-based(More)
The goal of the Encyclopedia of Life (EOL) Project is to predict structural information for all proteins, in all organisms. This calculation presents challenges both in terms of the scale of the computational resources required (approximately 1.8 million CPU hours), as well as in data and workflow management. While tools are available that solve some(More)
The inevitable move from a single large scale server to a distributed Grid environment is beginning to be realized across international Grid test-bed like Pacific Rim Applications and Grid Middleware Assembly (PRAGMA). Although jobs submitted to a single large server have been widely analyzed, job characteristics in a Grid environment are different as we(More)
:In order to deliver cyberinfrastructure to the general scientific and biomedical research community, transparent access and ease of use is of critical importance. Applications in systematic modeling of biological processes across scales of time and length demand more and more sophisticated algorithms and larger and longer simulations. The increased level(More)