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The comparison of protein tertiary structures is a key milestone in many structural bioinformatics activities that rely in comparing very large structure datasets. As the number of proteins in the dataset increases, the corresponding computational time taken by the protein structure comparison algorithms also increases, squarely for an all-against-all comparison and linearly for an all-against-target...
In this paper, we describe an extension to the ACGT GridR environment which allows the parallelization of loops in R scripts in view of their distributed execution on a computational grid. The ACGT GridR service is extended by a component that uses a set of preprocessor-like directives to organize and distribute calculations. The use of parallelization directives as special R comments provides users...
In a growing number of scientific disciplines, large data collections are emerging as important community resources. Data and metadata management exploiting the data grid paradigm is becoming more and more important as the number of involved data sources is continuously increasing and decentralizing. Efficient grid data access services are perceived as mandatory components for data management. In...
This works presents the porting on the grid of a parallel application of phylogenetic inference, MrBayes, in the LIBI (International Laboratory of Bioinformatics) platform. Moreover a bioinformatic case study about the analysis of 11 phylogenies, including a series of large sequences data sets that represent the nascent barcode reference database for Lepidoptera is also presented. The case study has...
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