High throughput protein similarity searches in the LIBI grid problem solving environment

Authors:
Maria Mirto;Ivan Rossi;Italo Epicoco;Sandro Fiore;Piero Fariselli;Rita Casadio;Giovanni Aloisio
Affiliations:
SPACI Consortium & ISUFI University of Salento, Lecce & CACT of NNL/CNR-INFM;Biocomputing Group, University of Bologna, Italy and BioDec Srl, Casalecchio di Reno, Bologna, Italy;SPACI Consortium & ISUFI University of Salento, Lecce & CACT of NNL/CNR-INFM;SPACI Consortium & ISUFI University of Salento, Lecce & CACT of NNL/CNR-INFM;Biocomputing Group, University of Bologna, Italy;Biocomputing Group, University of Bologna, Italy;SPACI Consortium & ISUFI University of Salento, Lecce & CACT of NNL/CNR-INFM
Venue:
ISPA'07 Proceedings of the 2007 international conference on Frontiers of High Performance Computing and Networking
Year:
2007

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Abstract

Bioinformatics applications are naturally distributed, due to distribution of involved data sets, experimental data and biological databases. They require high computing power, owing to the large size of data sets and the complexity of basic computations, may access heterogeneous data, where heterogeneity is in data format, access policy, distribution, etc., and require a secure infrastructure, because they could access private data owned by different organizations. The Problem Solving Environment (PSE) is an approach and a technology that can fulfil such bioinformatics requirements. The PSE can be used for the definition and composition of complex applications, hiding programming and configuration details to the user that can concentrate only on the specific problem. Moreover, Grids can be used for building geographically distributed collaborative problem solving environments and Grid aware PSEs can search and use dispersed high performance computing, networking, and data resources. In this work, the PSE solution has been chosen as the integration platform of bioinformatics tools and data sources. In particular an experiment of multiple sequence alignment on large scale, supported by the LIBI PSE, is presented.