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

Josep Rius,Francesc Solsona,Jos Koetsier,Fernando Cores,Cedric Notredame,Jano I Van Hemert

doi:10.1186/1471-2105-12-150

Josep Rius, Francesc Solsona + Show 4 more

Open Access

https://doi.org/10.1186/1471-2105-12-150

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Journal: BMC bioinformatics	Publication Date: May 12, 2011
Citations: 13	License type: CC BY 2.0

Affiliation: University of Lleida, University of Edinburgh

Abstract

BackgroundParallel 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.ResultsIn 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.ConclusionsThe 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.

Highlights

Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool
The computational requirements of these problems consists of months of computer time and terabytes of memory, which in turn requires High-Performance Computing (HPC) systems with thousands of processors, known as supercomputers
* Correspondence: jrius@diei.udl.cat 1Department of Computer Science and Industrial Engineering, University of Lleida, C/Jaume II 69, E-25001 Lleida, Spain Full list of author information is available at the end of the article based on terminals used over several decades. We address this issue by introducing a user-friendly portal that provides controlled access in a versatile way to an accurate multiple sequence alignment tool–Parallel T-Coffee [1]–that runs efficiently on the required computing resources

Summary

Results

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

Background

Results and Discussion

Conclusions