GridCertLib: a Single Sign-on Solution for Grid Web Applications and Portals

This paper describes the design and implementation of GridCertLib, a Java library leveraging a Shibboleth-based authentication infrastructure and the SLCS online certificate signing service, to provide short-lived X.509 certificates and Grid proxies. The main use case envisioned for GridCertLib, is to provide seamless and secure access to Grid/X.509 certificates and proxies in web applications and portals: when a user logs in to the portal using Shibboleth authentication, GridCertLib can automatically obtain a Grid/X.509 certificate from the SLCS service and generate a VOMS proxy from it. We give an overview of the architecture of GridCertLib and briefly describe its programming model. Its application to some deployment scenarios is outlined, as well as a report on practical experience integrating GridCertLib into portals for Bioinformatics and Computational Chemistry applications, based on the popular P-GRADE and Django softwares.Comment: 18 pages, 1 figure; final manuscript accepted for publication by the "Journal of Grid Computing

Grid Added Value to Address Malaria

Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria. The spirit is a non-proprietary peer-production of information-embedding goods. And we propose to use the grid technology to enable such a world wide "open source" like collaboration. The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for new drugs.Comment: 7 pages, 1 figure, 6th IEEE International Symposium on Cluster Computing and the Grid, Singapore, 16-19 may 2006, to appear in the proceeding

Multi-physics Extension of OpenFMO Framework

OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the subsequent development planning corresponding to MPS is presented. It is discussed which should be selected as a scientific software, lightweight and reconfigurable form or large and self-contained form.Comment: 4 pages with 11 figure files, to appear in the Proceedings of ICCMSE 200

Development of Grid e-Infrastructure in South-Eastern Europe

Over the period of 6 years and three phases, the SEE-GRID programme has established a strong regional human network in the area of distributed scientific computing and has set up a powerful regional Grid infrastructure. It attracted a number of user communities and applications from diverse fields from countries throughout the South-Eastern Europe. From the infrastructure point view, the first project phase has established a pilot Grid infrastructure with more than 20 resource centers in 11 countries. During the subsequent two phases of the project, the infrastructure has grown to currently 55 resource centers with more than 6600 CPUs and 750 TBs of disk storage, distributed in 16 participating countries. Inclusion of new resource centers to the existing infrastructure, as well as a support to new user communities, has demanded setup of regionally distributed core services, development of new monitoring and operational tools, and close collaboration of all partner institution in managing such a complex infrastructure. In this paper we give an overview of the development and current status of SEE-GRID regional infrastructure and describe its transition to the NGI-based Grid model in EGI, with the strong SEE regional collaboration.Comment: 22 pages, 12 figures, 4 table

Open-architecture Implementation of Fragment Molecular Orbital Method for Peta-scale Computing

We present our perspective and goals on highperformance computing for nanoscience in accordance with the global trend toward "peta-scale computing." After reviewing our results obtained through the grid-enabled version of the fragment molecular orbital method (FMO) on the grid testbed by the Japanese Grid Project, National Research Grid Initiative (NAREGI), we show that FMO is one of the best candidates for peta-scale applications by predicting its effective performance in peta-scale computers. Finally, we introduce our new project constructing a peta-scale application in an open-architecture implementation of FMO in order to realize both goals of highperformance in peta-scale computers and extendibility to multiphysics simulations.Comment: 6 pages, 9 figures, proceedings of the 2nd IEEE/ACM international workshop on high performance computing for nano-science and technology (HPCNano06

Large Scale In Silico Screening on Grid Infrastructures

Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large-scale deployment.Comment: 14 pages, 2 figures, 2 tables, The Third International Life Science Grid Workshop, LSGrid 2006, Yokohama, Japan, 13-14 october 2006, to appear in the proceeding