Accounting Facilities in the European Supercomputing Grid DEISA

Account management and resource usage monitoring are essential services for production Grids. The scope of a production Grid infrastructure, the heterogeneity of resources and services, the typical community usage profiles, and the depth of integration of the resource providers regarding operational procedures and policies imply specific requirements for accounting facilities. We present the accounting facilities currently used in production in the Distributed European Infra-structure for the Supercomputing Applications (DEISA). DEISA is a consortium of leading national supercomputing centres currently deploying and operating a persistent, production quality, distributed su-percomputing environment with continental scope. The DEISA accounting facilities gather information from the site-local batch systems and the distributed DEISA user administration system, and generate XML usage records conforming to the OGF usage record specification which are then stored locally in a XML data base at each DEISA site. The distributed accounting information can be fetched by clients such as users, project supervisors, site accounting managers and DEISA supervisors. The information is made available by site-local WSRF-compliant accounting information services that allow for a fine-grained setting of access rights. Each authorized client gets a specific view on the accounting information according to one of the following roles: a) a site accounting manager imports usage records of related home-site users from all DEISA sites for longterm archiving, b) a project supervisor retrieves information to assess the resource usage by his project partners, c) a DEISA supervisor (e.g. someone overlooking the usage on behalf of the DEISA executive committee) gets a report on the global usage of DEISA resources, and d) the user who can retrieve all the accounting information related to his own jobs. The privacy and integrity of the data provided and transferred from the accounting information service running at each site is guaranteed using X.509 certificates for mutual authentication and secure communication channels

CoPub update: CoPub 5.0 a text mining system to answer biological questions

In this article, we present CoPub 5.0, a publicly available text mining system, which uses Medline abstracts to calculate robust statistics for keyword co-occurrences. CoPub was initially developed for the analysis of microarray data, but we broadened the scope by implementing new technology and new thesauri. In CoPub 5.0, we integrated existing CoPub technology with new features, and provided a new advanced interface, which can be used to answer a variety of biological questions. CoPub 5.0 allows searching for keywords of interest and its relations to curated thesauri and provides highlighting and sorting mechanisms, using its statistics, to retrieve the most important abstracts in which the terms co-occur. It also provides a way to search for indirect relations between genes, drugs, pathways and diseases, following an ABC principle, in which A and C have no direct connection but are connected via shared B intermediates. With CoPub 5.0, it is possible to create, annotate and analyze networks using the layout and highlight options of Cytoscape web, allowing for literature based systems biology. Finally, operations of the CoPub 5.0 Web service enable to implement the CoPub technology in bioinformatics workflows. CoPub 5.0 can be accessed through the CoPub portal http://www.copub.org

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

Contains fulltext : 69241.pdf (publisher's version ) (Open Access)Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl