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Title:
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A user-friendly web portal for T-Coffee on supercomputers
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Author:
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Rius Torrentó, Josep Maria; Cores Prado, Fernando; Solsona Tehàs, Francesc; Hemert, Jano van; Koetsier, Jos; Notredame, Cedric
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Notes:
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Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers.
Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments.
Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.
CN is funded by the Plan Nacional BFU2008-00419 and the European Comissison FP7 framework quantomics (KBBE-2A-222664) and Leishdrud (223414). J.R., F.C. and F.S. are funded by the Spanish ministry of education (TIN2008-05913) and the consolider Project (CSD 2007-00050) Super-computacion y e-Ciencia (SYEC). J.R. is also funded by the European Social Found and the HPC-EUROPA2 project (project number: 228398) and the CUR of DIUE of GENCAT. EPSRC, JISC, BBSRC and NERC for funding the development and application of Rapid (J.v.H. and J.K.). |
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Subject(s):
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-Algorismes computacionals
-Processament electrònic de dades -- Disseny de sistemes |
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Rights:
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cc-by, (c) Rius et al., 2011
http://creativecommons.org/licenses/by/2.0/es/deed.ca
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Document type:
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article
publishedVersion |
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Published by:
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BioMed Central
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