The vision of the Grid is to support the dynamic establishment and subsequent management of virtual organizations (VO

The BRIDGES project was funded by the UK Department of Trade and Industry (DTI) to address the needs of cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) Cardiovascular Functional Genomics (CFG) project. Security was at the heart of the BRIDGES project and an advanced data and compute Grid infrastructure incorporating latest Grid authorisation technologies was developed and delivered to the scientists. We outline these Grid infrastructures and describe the perceived security requirements at the project start including data classifications and how these evolved throughout the lifetime of the project. The uptake and adoption of the project results are also presented along with the challenges that must be overcome to support the secure exchange of life science data sets. We also present how we will use the BRIDGES experiences in future projects at the National e-Science Centre.

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.

Scientific gateways in the form of web portals are becoming the popular approach to share knowledge and resources around a topic in a community of researchers. Unfortunately, the development of web portals is expensive and requires specialists skills. Commercial and more generic web portals have a much larger user base and can afford this kind of development. Here we present two solutions that address this problem in the area of portals for scientific computing; both take the same approach. The whole process of designing, delivering and maintaining a portal can be made more cost-effective by generating a portal from a description rather than programming in the traditional sense. We show four successful use cases to show how this process works and the results it can deliver.