| dc.contributor.author |
Rius Torrentó, Josep Maria |
| dc.contributor.author |
Cores Prado, Fernando |
| dc.contributor.author |
Solsona Tehàs, Francesc |
| dc.contributor.author |
Hemert, Jano van |
| dc.contributor.author |
Koetsier, Jos |
| dc.contributor.author |
Notredame, Cedric |
| dc.date |
2011-07-08T08:18:16Z |
| dc.date |
2011-07-08T08:18:16Z |
| dc.date |
2011 |
| dc.identifier |
1471-2105 |
| dc.identifier |
http://hdl.handle.net/10459.1/41533 |
| dc.identifier |
https://doi.org/10.1186/1471-2105-12-150 |
| dc.identifier.uri |
http://hdl.handle.net/10459.1/41533 |
| dc.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. |
| dc.description |
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.). |
| dc.language |
eng |
| dc.publisher |
BioMed Central |
| dc.relation |
MICINN/PN2008-2011/BFU2008-00419 |
| dc.relation |
MICINN/PN2008-2011/TIN2008-05913 |
| dc.relation |
MIECI/PN2004-2007/CSD 2007-00050 |
| dc.relation |
Reproducció del document publicat a https://doi.org/10.1186/1471-2105-12-150 |
| dc.relation |
BMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5 |
| dc.relation |
info:eu-repo/grantAgreement/EC/FP7/222664 |
| dc.relation |
info:eu-repo/grantAgreement/EC/FP7/223414 |
| dc.relation |
info:eu-repo/grantAgreement/EC/FP7/228398 |
| dc.rights |
cc-by, (c) Rius et al., 2011 |
| dc.rights |
http://creativecommons.org/licenses/by/2.0/es/deed.ca |
| dc.rights |
info:eu-repo/semantics/openAccess |
| dc.subject |
Algorismes computacionals |
| dc.subject |
Processament electrònic de dades -- Disseny de sistemes |
| dc.title |
A user-friendly web portal for T-Coffee on supercomputers |
| dc.type |
article |
| dc.type |
publishedVersion |
