A user-friendly web portal for T-Coffee on supercomputers

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...

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Detalles Bibliográficos
Autores: Rius Torrentó, Josep Maria, Cores Prado, Fernando, Solsona Tehàs, Francesc, Hemert, Jano van, Koetsier, Jos, Notredame, Cedric
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2011
País:España
Institución:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/41533
Acceso en línea:https://doi.org/10.1186/1471-2105-12-150
http://hdl.handle.net/10459.1/41533
Access Level:acceso abierto
Palabra clave:Algorismes computacionals
Processament electrònic de dades -- Disseny de sistemes
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spelling A user-friendly web portal for T-Coffee on supercomputersRius Torrentó, Josep MariaCores Prado, FernandoSolsona Tehàs, FrancescHemert, Jano vanKoetsier, JosNotredame, CedricAlgorismes computacionalsProcessament electrònic de dades -- Disseny de sistemesBackground: 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.).BioMed Central2011info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1186/1471-2105-12-150http://hdl.handle.net/10459.1/41533reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)Inglésinfo:eu-repo/grantAgreement/MICINN//BFU2008-00419info:eu-repo/grantAgreement/MICINN//TIN2008-05913info:eu-repo/grantAgreement/MEC//CSD2007-00050Reproducció del document publicat a https://doi.org/10.1186/1471-2105-12-150BMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5info:eu-repo/grantAgreement/EC/FP7/222664info:eu-repo/grantAgreement/EC/FP7/223414info:eu-repo/grantAgreement/EC/FP7/228398cc-by, (c) Rius et al., 2011info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.0/es/deed.caoai:repositori.udl.cat:10459.1/415332026-06-24T12:42:17Z
dc.title.none.fl_str_mv A user-friendly web portal for T-Coffee on supercomputers
title A user-friendly web portal for T-Coffee on supercomputers
spellingShingle A user-friendly web portal for T-Coffee on supercomputers
Rius Torrentó, Josep Maria
Algorismes computacionals
Processament electrònic de dades -- Disseny de sistemes
title_short A user-friendly web portal for T-Coffee on supercomputers
title_full A user-friendly web portal for T-Coffee on supercomputers
title_fullStr A user-friendly web portal for T-Coffee on supercomputers
title_full_unstemmed A user-friendly web portal for T-Coffee on supercomputers
title_sort A user-friendly web portal for T-Coffee on supercomputers
dc.creator.none.fl_str_mv Rius Torrentó, Josep Maria
Cores Prado, Fernando
Solsona Tehàs, Francesc
Hemert, Jano van
Koetsier, Jos
Notredame, Cedric
author Rius Torrentó, Josep Maria
author_facet Rius Torrentó, Josep Maria
Cores Prado, Fernando
Solsona Tehàs, Francesc
Hemert, Jano van
Koetsier, Jos
Notredame, Cedric
author_role author
author2 Cores Prado, Fernando
Solsona Tehàs, Francesc
Hemert, Jano van
Koetsier, Jos
Notredame, Cedric
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Algorismes computacionals
Processament electrònic de dades -- Disseny de sistemes
topic Algorismes computacionals
Processament electrònic de dades -- Disseny de sistemes
description 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.
publishDate 2011
dc.date.none.fl_str_mv 2011
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1186/1471-2105-12-150
http://hdl.handle.net/10459.1/41533
url https://doi.org/10.1186/1471-2105-12-150
http://hdl.handle.net/10459.1/41533
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/MICINN//BFU2008-00419
info:eu-repo/grantAgreement/MICINN//TIN2008-05913
info:eu-repo/grantAgreement/MEC//CSD2007-00050
Reproducció del document publicat a https://doi.org/10.1186/1471-2105-12-150
BMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5
info:eu-repo/grantAgreement/EC/FP7/222664
info:eu-repo/grantAgreement/EC/FP7/223414
info:eu-repo/grantAgreement/EC/FP7/228398
dc.rights.none.fl_str_mv cc-by, (c) Rius et al., 2011
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/2.0/es/deed.ca
rights_invalid_str_mv cc-by, (c) Rius et al., 2011
http://creativecommons.org/licenses/by/2.0/es/deed.ca
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
repository.name.fl_str_mv
repository.mail.fl_str_mv
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