Jos Koetsier

Supporting Decentralized, Security Focused Dynamic Virtual Organizations across the Grid

The ability to dynamically create and subsequently manage secure virtual organisations (VO) is one of the key challenges facing the Grid community. Existing approaches for establishing and managing VOs typically suffer from lack of fine grained security since they largely focus on public key infrastructures with statically defined access control lists, or they are based upon a centralised site for storage of VO specific security information. What is really needed is a federated model of security where sites are able to manage their own security information for their own institutional members, delegating where necessary to trusted local or remote entities, as well as defining and enforcing authorisation policies for their own resources. In this paper we present tools that support such capabilities and highlight how they have been applied to dynamically create and manage security focused VOs in the education domain. We believe that this federated VO security model for fine grained access to Grid services and resources should be the future model upon which security focused Grids are based.

Grid infrastructures for secure access to and use of bioinformatics data: experiences from the BRIDGES project

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.

Single sign-on and authorization for dynamic virtual organizations

This is a pre-print of an article whose final and definitive form has been published in International Federation for Information Processing

Generating web-based user interfaces for computational science

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. Copyright

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

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.

Rapid Chemistry Portals through Engaging Researchers

In this study, we apply a methodology for rapid development of portlets for scientific computing to the domain of computational chemistry. We report results in terms of the portals delivered, the changes made to our methodology and the experience gained in terms of interaction with domain-specialists. Our major contributions are: several web portals for teaching and research in computational chemistry; a successful transition to having our development tool used by the domain specialist as opposed by us, the developers; and an updated version of our methodology and technology for rapid development of portlets for computational science, which is free for anyone to pick up and use.

TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal

Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis, however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized port lets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface.