TY - JOUR T1 - Generating web-based user interfaces for computational science JF - Concurrency and Computation: Practice and Experience Y1 - 2011 A1 - van Hemert, J. A1 - Koetsier, J. A1 - Torterolo, L. A1 - Porro, I. A1 - Melato, M. A1 - Barbera, R. AB - 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. PB - Wiley VL - 23 ER - TY - JOUR T1 - A user-friendly web portal for T-Coffee on supercomputers JF - BMC Bioinformatics Y1 - 2011 A1 - J. Rius A1 - F. Cores A1 - F. Solsona A1 - van Hemert, J. I. A1 - Koetsier, J. A1 - C. Notredame KW - e-Science KW - portal KW - rapid AB - 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. VL - 12 UR - http://www.biomedcentral.com/1471-2105/12/150 ER - TY - CHAP T1 - Molecular Orbital Calculations of Inorganic Compounds T2 - Inorganic Experiments Y1 - 2010 A1 - C. A. Morrison A1 - N. Robertson A1 - Turner, A. A1 - van Hemert, J. A1 - Koetsier, J. ED - J. Derek Woollins JF - Inorganic Experiments PB - Wiley-VCH SN - 978-3527292530 ER - TY - JOUR T1 - Giving Computational Science a Friendly Face JF - Zero-In Y1 - 2009 A1 - van Hemert, J. I. A1 - Koetsier, J. AB - Today, most researchers from any discipline will successfully use web-based e-commerce systems to book flights to attend their conferences. But when these same researchers are confronted with compute-intensive problems, they cannot expect elaborate web-based systems to enable their domain-specific tasks. VL - 1 UR - http://www.beliefproject.org/zero-in/zero-in-third-edition/zero-in-issue-3 IS - 3 ER - TY - CONF T1 - Rapid chemistry portals through engaging researchers T2 - Fifth IEEE International Conference on e-Science Y1 - 2009 A1 - Koetsier, J. A1 - Turner, A. A1 - Richardson, P. A1 - van Hemert, J. I. ED - Trefethen, A ED - De Roure, D AB - 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. JF - Fifth IEEE International Conference on e-Science CY - Oxford, UK ER - TY - CONF T1 - Rapid development of computational science portals T2 - Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences Y1 - 2009 A1 - Koetsier, J. A1 - van Hemert, J. I. ED - Gesing, S. ED - van Hemert, J. I. KW - portal JF - Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences T3 - CEUR Workshop Proceedings PB - e-Science Institute CY - Edinburgh UR - http://ceur-ws.org/Vol-513/paper05.pdf ER -