TY - CONF T1 - User-friendly workflows in quantum chemistry T2 - IWSG 2013 Y1 - 2013 A1 - Herres-Pawlis, Sonja A1 - Balaskó, Ákos A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Hoffmann, Alexander A1 - Kacsuk, Peter A1 - Krüger, Jens A1 - Packschies, Lars A1 - Terstyansky, Gabor A1 - Weingarten, Noam JF - IWSG 2013 PB - CEUR Workshop Proceedings CY - Zurich, Switzerland UR - http://ceur-ws.org/Vol-993/paper14.pdf ER - TY - CONF T1 - The Use of Reputation as Noise-resistant Selection Bias in a Co-evolutionary Multi-agent System T2 - Genetic and Evolutionary Computation Conference Y1 - 2012 A1 - Nikolaos Chatzinikolaou A1 - Dave Robertson JF - Genetic and Evolutionary Computation Conference CY - Philadelphia 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 - CONF T1 - Understanding TSP Difficulty by Learning from Evolved Instances T2 - Lecture Notes in Computer Science Y1 - 2010 A1 - Smith-Miles, Kate A1 - van Hemert, Jano A1 - Lim, Xin ED - Blum, Christian ED - Battiti, Roberto AB - Whether the goal is performance prediction, or insights into the relationships between algorithm performance and instance characteristics, a comprehensive set of meta-data from which relationships can be learned is needed. This paper provides a methodology to determine if the meta-data is sufficient, and demonstrates the critical role played by instance generation methods. Instances of the Travelling Salesman Problem (TSP) are evolved using an evolutionary algorithm to produce distinct classes of instances that are intentionally easy or hard for certain algorithms. A comprehensive set of features is used to characterise instances of the TSP, and the impact of these features on difficulty for each algorithm is analysed. Finally, performance predictions are achieved with high accuracy on unseen instances for predicting search effort as well as identifying the algorithm likely to perform best. JF - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 6073 UR - http://dx.doi.org/10.1007/978-3-642-13800-3_29 N1 - 10.1007/978-3-642-13800-3_29 ER - TY - CONF T1 - Using architectural simulation models to aid the design of data intensive application T2 - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) Y1 - 2009 A1 - Javier Fernández A1 - Liangxiu Han A1 - Alberto Nuñez A1 - Jesus Carretero A1 - van Hemert, Jano JF - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) PB - IEEE Computer Society CY - Sliema, Malta ER - TY - CONF T1 - Using Simulation for Decision Support: Lessons Learned from FireGrid T2 - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) Y1 - 2009 A1 - Gerhard Wickler A1 - George Beckett A1 - Liangxiu Han A1 - Sung Han Koo A1 - Stephen Potter A1 - Gavin Pringle A1 - Austin Tate ED - J. Landgren, U. Nulden ED - B. Van de Walle JF - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) CY - Gothenburg, Sweden ER - TY - JOUR T1 - Using the DCC Lifecycle Model to Curate a Gene Expression Database: A Case Study JF - International Journal of Digital Curation Y1 - 2009 A1 - O’Donoghue, J. A1 - van Hemert, J. I. AB - Developmental Gene Expression Map (DGEMap) is an EU-funded Design Study, which will accelerate an integrated European approach to gene expression in early human development. As part of this design study, we have had to address the challenges and issues raised by the long-term curation of such a resource. As this project is primarily one of data creators, learning about curation, we have been looking at some of the models and tools that are already available in the digital curation field in order to inform our thinking on how we should proceed with curating DGEMap. This has led us to uncover a wide range of resources for data creators and curators alike. Here we will discuss the future curation of DGEMap as a case study. We believe our experience could be instructive to other projects looking to improve the curation and management of their data. PB - UKOLN VL - 4 UR - http://www.ijdc.net/index.php/ijdc/article/view/134 IS - 3 ER - TY - CONF T1 - Use of Evolutionary Algorithms for Telescope Scheduling T2 - Integrated Modeling of Telescopes Y1 - 2002 A1 - Grim, R. A1 - Jansen, M. L. M. A1 - Baan, A. A1 - van Hemert, J. I. A1 - de Wolf, H. ED - Torben Anderson KW - constraint satisfaction KW - scheduling AB - LOFAR, a new radio telescope, will be designed to observe with up to 8 independent beams, thus allowing several simultaneous observations. Scheduling of multiple observations parallel in time, each having their own constraints, requires a more intelligent and flexible scheduling function then operated before. In support of the LOFAR radio telescope project, and in co-operation with Leiden University, Fokker Space has started a study to investigate the suitability of the use of evolutionary algorithms applied to complex scheduling problems. After a positive familiarisation phase, we now examine the potential use of evolutionary algorithms via a demonstration project. Results of the familiarisation phase, and the first results of the demonstration project are presented in this paper. JF - Integrated Modeling of Telescopes PB - The International Society for Optical Engineering ({SPIE}) VL - 4757 ER -