Implementation of the Vectorized Position-Specific Iterated Smith-Waterman Algorithm with Heuristic Filtering Algorithm on Cray Architecture

ABSTRACT: Smith-Waterman is the algorithm for finding local optimal alignments of two amino acid sequences, but is too slow for use in regular large database scanning. We have implemented SW algorithm on Cray X1 architecture, exploiting vectorization and parallelization. In addition we have proposed heuristic database filtering algorithm, which is particularly well suited for the Cray architecture, exploiting possibilities given by the BMM unit

Migration of the Mathematical Collection of Polish Virtual Library of Science to the YADDA Platform

summary:YADDA framework facilitates information exchange between digital document repositories. YaddaWeb, its web-based interface, provides browse and search functionalities. Content providers use DeskLight application to add or modify metadata and content. Internally, YADDA contains flexible repository aggregation mechanisms, multiple hierarchy support and full-text indexing capabilities. YADDA framework is an excellent solution for Open Access paradigm of content exchange. Migration of the Mathematical Collection of Polish Virtual Library of Science to YADDA is currently being prepared

Report on the First Workshop on Linking and Contextualizing Publications and Datasets

Manghi P, Bolikowski L, Houssos N, Schirrwagen J. Report on the First Workshop on Linking and Contextualizing Publications and Datasets. SIGMOD Record. 2014;43(2):57-60

Data Curation in the OpenAIRE Scholarly Communication Infrastructure

Schirrwagen J, Manghi P, Manola N, Bolikowski L, Rettberg N, Schmidt B. Data Curation in the OpenAIRE Scholarly Communication Infrastructure. Information Standards Quarterly. 2013;25(3):13-19.OpenAIRE is the European Union initiative for an Open Access Infrastructure for Research in support of open scholarly communication and access to the research output of European funded projects and open access content from a network of institutional and disciplinary repositories. This article outlines the curation activities conducted in the OpenAIRE infrastructure, which employs a multi-level, multi-targeted approach: the publication and implementation of interoperability guidelines to assist in the local data curation processes, the data curation due to the integration of heterogeneous sources supporting different types of data, the inference of links to accomplish the publication research contextualization and data enrichment, and the end-user metadata curation that allows users to edit the attributes and provide links among the entities