TY - CONF T1 - Generic User Management for Science Gateways via Virtual Organizations T2 - EGI Technical Forum 2012 Y1 - 2012 A1 - Schlemmer, Tobias A1 - Grunzke, Richard A1 - Gesing, Sandra A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver JF - EGI Technical Forum 2012 ER - 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 Generic Parallel Processing Model for Facilitating Data Mining and Integration JF - Parallel Computing Y1 - 2011 A1 - Liangxiu Han A1 - Chee Sun Liew A1 - van Hemert, Jano A1 - Malcolm Atkinson KW - Data Mining and Data Integration (DMI) KW - Life Sciences KW - OGSA-DAI KW - Parallelism KW - Pipeline Streaming KW - workflow AB - To facilitate Data Mining and Integration (DMI) processes in a generic way, we investigate a parallel pipeline streaming model. We model a DMI task as a streaming data-flow graph: a directed acyclic graph (DAG) of Processing Elements PEs. The composition mechanism links PEs via data streams, which may be in memory, buffered via disks or inter-computer data-flows. This makes it possible to build arbitrary DAGs with pipelining and both data and task parallelisms, which provides room for performance enhancement. We have applied this approach to a real DMI case in the Life Sciences and implemented a prototype. To demonstrate feasibility of the modelled DMI task and assess the efficiency of the prototype, we have also built a performance evaluation model. The experimental evaluation results show that a linear speedup has been achieved with the increase of the number of distributed computing nodes in this case study. PB - Elsevier VL - 37 IS - 3 ER - TY - CONF T1 - Granular Security for a Science Gateway in Structural Bioinformatics T2 - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011) Y1 - 2011 A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Balaskó, Ákos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Herres-Pawlis, Sonja A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver JF - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011) PB - CEUR Workshop Proceedings ER - TY - CONF T1 - Grid-Workflows in Molecular Science T2 - Software Engineering 2010, Grid Workflow Workshop Y1 - 2010 A1 - Birkenheuer, Georg A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Blunk, Dirk A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Packschies, Lars JF - Software Engineering 2010, Grid Workflow Workshop PB - GI-Edition - Lecture Notes in Informatics (LNI) 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 - JOUR T1 - Guest Editorial: Research Data: It’s What You Do With Them JF - International Journal of Digital Curation Y1 - 2009 A1 - Malcolm Atkinson AB - These days it may be stating the obvious that the number of data resources, their complexity and diversity is growing rapidly due to the compound effects of increasing speed and resolution of digital instruments, due to pervasive data-collection automation and due to the growing power of computers. Just because we are becoming used to the accelerating growth of data resources, it does not mean we can be complacent; they represent an enormous wealth of opportunity to extract information, to make discoveries and to inform policy. But all too often it still takes a heroic effort to discover and exploit those opportunities, hence the research and progress, charted by the Fourth International Digital Curation Conference1 and recorded in this issue of the International Journal of Digital Curation, are an invaluable step on a long and demanding journey. VL - 4 UR - http://www.ijdc.net/index.php/ijdc/article/view/96 IS - 1 ER - TY - CONF T1 - Graph Colouring Heuristics Guided by Higher Order Graph Properties T2 - Lecture Notes in Computer Science Y1 - 2008 A1 - Juhos, Istv\'{a}n A1 - van Hemert, Jano ED - van Hemert, Jano ED - Cotta, Carlos KW - evolutionary computation KW - graph colouring AB - Graph vertex colouring can be defined in such a way where colour assignments are substituted by vertex contractions. We present various hyper-graph representations for the graph colouring problem all based on the approach where vertices are merged into groups. In this paper, we show this provides a uniform and compact way to define algorithms, both of a complete or a heuristic nature. Moreover, the representation provides information useful to guide algorithms during their search. In this paper we focus on the quality of solutions obtained by graph colouring heuristics that make use of higher order properties derived during the search. An evolutionary algorithm is used to search permutations of possible merge orderings. JF - Lecture Notes in Computer Science PB - Springer VL - 4972 ER - TY - JOUR T1 - A Grid infrastructure for parallel and interactive applications JF - Computing and Informatics Y1 - 2008 A1 - Gomes, J. A1 - Borges, B. A1 - Montecelo, M. A1 - David, M. A1 - Silva, B. A1 - Dias, N. A1 - Martins, JP A1 - Fernandez, C. A1 - Garcia-Tarres, L. , A1 - Veiga, C. A1 - Cordero, D. A1 - Lopez, J. A1 - J Marco A1 - Campos, I. A1 - Rodríguez, David A1 - Marco, R. A1 - Lopez, A. A1 - Orviz, P. A1 - Hammad, A. VL - 27 IS - 2 ER - TY - CONF T1 - Grid Enabling Your Data Resources with OGSA-DAI T2 - Applied Parallel Computing. State of the Art in Scientific Computing Y1 - 2007 A1 - Antonioletti, M. A1 - Atkinson, M. A1 - Chue Hong, N. P. A1 - Dobrzelecki, B. A1 - Hume, A. C. A1 - Jackson, M. A1 - Karasavvas, K. A1 - Krause, A. A1 - Schopf, J. M. A1 - Sugden. T. A1 - Theocharopoulos, E. JF - Applied Parallel Computing. State of the Art in Scientific Computing T3 - Lecture Notes in Computer Science VL - 4699 ER - TY - CONF T1 - Grid Enabling your Data Resources with OGSA-DAI T2 - Workshop on State-of-the-Art in Scientific and Parallel Computing Y1 - 2006 A1 - Antonioletti, M. A1 - Atkinson, M. A1 - Hong, N. Chue A1 - Dobrzelecki, B. A1 - Hume, A. A1 - Jackson, M. A1 - Karasavvas, K. A1 - Krause, A. A1 - Sugden, T. A1 - Theocharopoulos, E. JF - Workshop on State-of-the-Art in Scientific and Parallel Computing ER - TY - CONF T1 - Grid Infrastructures for Secure Access to and Use of Bioinformatics Data: Experiences from the BRIDGES Project T2 - Proceedings of the First International Conference on Availability, Reliability and Security, ARES Y1 - 2006 A1 - Richard O. Sinnott A1 - Micha Bayer A1 - A. J. Stell A1 - Jos Koetsier JF - Proceedings of the First International Conference on Availability, Reliability and Security, ARES T3 - Proceedings of the The First International Conference on Availability, Reliability and Security CY - Vienna, Austria ER - TY - Generic T1 - Genetic Programming, Proceedings of the 8th European Conference T2 - Lecture Notes in Computer Science Y1 - 2005 A1 - Keijzer, M. A1 - Tettamanzi, A. A1 - Collet, P. A1 - van Hemert, J. A1 - Tomassini, M. ED - M. Keijzer ED - A. Tettamanzi ED - P. Collet ED - van Hemert, J. ED - M. Tomassini KW - evolutionary computation JF - Lecture Notes in Computer Science PB - Springer VL - 3447 SN - 3-540-25436-6 UR - http://www.springeronline.com/sgw/cda/frontpage/0,11855,3-40100-22-45347265-0,00.html?changeHeader=true ER - TY - Generic T1 - Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data T2 - All Hands Meeting 2004 Y1 - 2004 A1 - Richard Sinnott A1 - Malcolm Atkinson A1 - Micha Bayer A1 - Dave Berry A1 - Anna Dominiczak A1 - Magnus Ferrier A1 - David Gilbert A1 - Neil Hanlon A1 - Derek Houghton A1 - Hunt, Ela A1 - David White AB - The BRIDGES project is a UK e-Science project that provides grid based support for biomedical research into the genetics of hypertension – the Cardiovascular Functional Genomics Project (CFG). Its main goal is to provide an effective environment for CFG, and biomedical research in general, including access to integrated data, analysis and visualization, with appropriate authorisation and privacy, as well as grid based computational tools and resources. It also aims to provide an improved understanding of the requirements of academic biomedical research virtual organizations and to evaluate the utility of existing data federation tools. JF - All Hands Meeting 2004 CY - Nottingham, UK UR - http://www.allhands.org.uk/2004/proceedings/papers/87.pdf ER - TY - CONF T1 - Grid-Based Metadata Services T2 - SSDBM Y1 - 2004 A1 - Deelman, Ewa A1 - Singh, Gurmeet Singh A1 - Atkinson, Malcolm P. A1 - Chervenak, Ann L. A1 - Hong, Neil P. Chue A1 - Kesselman, Carl A1 - Patil, Sonal A1 - Pearlman, Laura A1 - Su, Mei-Hui JF - SSDBM ER - TY - RPRT T1 - Grid Database Access and Integration: Requirements and Functionalities Y1 - 2003 A1 - Atkinson, M. P. A1 - Dialani, V. A1 - Guy, L. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Storey, T. A1 - Watson, P. AB - This document is intended to provide the context for developing Grid data service standard recommendations within the Global Grid Forum. It defines the generic requirements for accessing and integrating persistent structured and semi-structured data. In addition, it defines the generic functionalities which a Grid data service needs to provide in supporting discovery of and controlled access to data, in performing data manipulation operations, and in virtualising data resources. The document also defines the scope of Grid data service standard recommendations which are presented in a separate document. JF - Global Grid Forum ER - TY - CONF T1 - The GRUMPS Architecture: Run-time Evolution in a Large Scale Distributed System T2 - Proceedings of the Workshop on Engineering Complex Object-Oriented Solutions for Evolution (ECOOSE), held as part of OOPSLA 2001. Y1 - 2001 A1 - Evans, Huw A1 - Peter Dickman A1 - Malcolm Atkinson AB - This paper describes the first version of the distributed programming architecture for the Grumps1 project. The architecture consists of objects that communicate in terms of both asynchronous and synchronous events. A novel three-level extensible naming scheme is discussed that allows Grumps developers to deploy systems that can refer to entities not identified at the time when the Grumps system and application-level code were implemented. Examples detailing how the topology of a Grumps system may be changed at run-time and how new object implementations may be distributed during system execution are given. The separation of policy from mechanism is shown to be a major part of how system evolution is supported and this is made even more flexible when expressed through the use of Java interfaces for crucial core concepts. JF - Proceedings of the Workshop on Engineering Complex Object-Oriented Solutions for Evolution (ECOOSE), held as part of OOPSLA 2001. ER - TY - BOOK T1 - GRUMPS Summer Anthology, 2001 Y1 - 2001 A1 - Atkinson, M. A1 - Brown, M. A1 - Cargill, J. A1 - Crease, M. A1 - Draper, S. A1 - Evans, H. A1 - Gray, P. A1 - Mitchell, C. A1 - Ritchie, M. A1 - Thomas, R. AB - This is the first collection of papers from GRUMPS [http://grumps.dcs.gla.ac.uk]. The project only started up in February 2001, and this collection (frozen at 1 Sept 2001) shows that it got off to a productive start. Versions of some of these papers have been submitted to conferences and workshops: the website will have more information on publication status and history. GRUMPS decided to begin with a first study, partly to help the team coalesce. This involved installing two pieces of software in a first year computing science lab: one (the "UAR") to record a large volume of student actions at a low level with a view to mining them later, another (the "LSS") directly designed to assist tutor-student interaction. Some of the papers derive from that, although more are planned. Results from this first study can be found on the website. The project also has a link to UWA in Perth, Western Australia, where related software has already been developed and used as described in one of the papers. Another project strand concerns using handsets in lecture theatres to support interactivity there, as two other papers describe. As yet unrepresented in this collection, GRUMPS will also be entering the bioinformatics application area. The GRUMPS project operates on several levels. It is based in the field of Distributed Information Management (DIM), expecting to cover both mobile and static nodes, synchronous and detached clients, high and low volume data sources. The specific focus of the project (see the original proposal on the web site) is to address records of computational activity (where any such pre-existing usage might have extra record collection installed) and data experimentation, where the questions to be asked of the data emerge concurrently with data collection which will therefore be dynamically modifiable: a requirement that further pushes on the space of DIM. The level above concerns building and making usable tools for asking questions of the data, or rather of the activities that generate the data. Above that again is the application domain level: what the original computational activities serve, education and bioinformatics being two identified cases. The GRUMPS team is therefore multidisciplinary, from DIM architecture researchers to educational evaluators. The mix of papers reflects this. PB - Academic Press ER - TY - JOUR T1 - Guest editorial JF - VLDB J. Y1 - 2000 A1 - Atkinson, Malcolm P. VL - 9 ER - TY - JOUR T1 - Graph Coloring with Adaptive Evolutionary Algorithms JF - Journal of Heuristics Y1 - 1998 A1 - Eiben, A. E. A1 - van der Hauw, J. K. A1 - van Hemert, J. I. KW - constraint satisfaction KW - graph colouring AB - This paper presents the results of an experimental investigation on solving graph coloring problems with Evolutionary Algorithms (EA). After testing different algorithm variants we conclude that the best option is an asexual EA using order-based representation and an adaptation mechanism that periodically changes the fitness function during the evolution. This adaptive EA is general, using no domain specific knowledge, except, of course, from the decoder (fitness function). We compare this adaptive EA to a powerful traditional graph coloring technique DSatur and the Grouping GA on a wide range of problem instances with different size, topology and edge density. The results show that the adaptive EA is superior to the Grouping GA and outperforms DSatur on the hardest problem instances. Furthermore, it scales up better with the problem size than the other two algorithms and indicates a linear computational complexity. PB - Kluwer Academic Publishers VL - 4 ER -