TY - CHAP T1 - Evolutionary Computation and Constraint Satisfaction Y1 - 2015 A1 - van Hemert, J. ED - Kacpryk, J. ED - Pedrycz, W. KW - constraint satisfaction KW - evolutionary computation AB - In this chapter we will focus on the combination of evolutionary computation techniques and constraint satisfaction problems. Constraint Programming (CP) is another approach to deal with constraint satisfaction problems. In fact, it is an important prelude to the work covered here as it advocates itself as an alternative approach to programming (Apt). The first step is to formulate a problem as a CSP such that techniques from CP, EC, combinations of the two (c.f., Hybrid) or other approaches can be deployed to solve the problem. The formulation of a problem has an impact on its complexity in terms of effort required to either find a solution or proof no solution exists. It is therefore vital to spend time on getting this right. Main differences between CP and EC. CP defines search as iterative steps over a search tree where nodes are partial solutions to the problem where not all variables are assigned values. The search then maintain a partial solution that satisfies all variables assigned values. Instead, in EC most often solver sample a space of candidate solutions where variables are all assigned values. None of these candidate solutions will satisfy all constraints in the problem until a solution is found. Another major difference is that many constraint solvers from CP are sound whereas EC solvers are not. A solver is sound if it always finds a solution if it exists. PB - Springer ER - TY - CONF T1 - Applying selectively parallel IO compression to parallel storage systems T2 - Euro-Par Y1 - 2014 A1 - Rosa Filgueira A1 - Malcolm Atkinson A1 - Yusuke Tanimura A1 - Isao Kojima JF - Euro-Par ER - TY - CONF T1 - FAST: Flexible Automated Syncrhonization Transfer tool T2 - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date Y1 - 2014 A1 - Rosa Filgueira A1 - Iraklis Klampanos A1 - Yusuke Tanimura A1 - Malcolm Atkinson. JF - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date PB - ACM CY - New York, NY, USA ER - TY - CONF T1 - Automatic Extraction of the Optic Disc Boundary for Detecting Retinal Diseases T2 - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) Y1 - 2013 A1 - M.S. Haleem A1 - L. Han A1 - B. Li A1 - A. Nisbet A1 - van Hemert, J. A1 - M. Verhoek ED - L. Linsen ED - M. Kampel KW - retinal imaging AB - In this paper, we propose an algorithm based on active shape model for the extraction of Optic Disc boundary. The determination of Optic Disc boundary is fundamental to the automation of retinal eye disease diagnosis because the Optic Disc Center is typically used as a reference point to locate other retinal structures, and any structural change in Optic Disc, whether textural or geometrical, can be used to determine the occurrence of retinal diseases such as Glaucoma. The algorithm is based on determining a model for the Optic Disc boundary by learning patterns of variability from a training set of annotated Optic Discs. The model can be deformed so as to reflect the boundary of Optic Disc in any feasible shape. The algorithm provides some initial steps towards automation of the diagnostic process for retinal eye disease in order that more patients can be screened with consistent diagnoses. The overall accuracy of the algorithm was 92% on a set of 110 images. JF - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) PB - {ACTA} Press ER - TY - CONF T1 - The demand for consistent web-based workflow editors T2 - Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science Y1 - 2013 A1 - Gesing, Sandra A1 - Atkinson, Malcolm A1 - Klampanos, Iraklis A1 - Galea, Michelle A1 - Berthold, Michael R. A1 - Barbera, Roberto A1 - Scardaci, Diego A1 - Terstyanszky, Gabor A1 - Kiss, Tamas A1 - Kacsuk, Peter KW - web-based workflow editors KW - workflow composition KW - workflow interoperability KW - workflow languages and concepts JF - Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science PB - ACM CY - New York, NY, USA SN - 978-1-4503-2502-8 UR - http://doi.acm.org/10.1145/2534248.2534260 ER - TY - CHAP T1 - DISPEL Enactment T2 - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business Y1 - 2013 A1 - Chee Sun Liew A1 - Krause, Amrey A1 - Snelling, David ED - Malcolm Atkinson ED - Rob Baxter ED - Peter Brezany ED - Oscar Corcho ED - Michelle Galea ED - Parsons, Mark ED - Snelling, David ED - van Hemert, Jano KW - Data Streaming KW - Data-Intensive Engineering KW - Dispel KW - Workflow Enactment AB - Chapter 12: "DISPEL enactment", describes the four stages of DISPEL enactment. It is targeted at the data-intensive engineers who implement enactment services. JF - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business PB - John Wiley & Sons Inc. ER - TY - CONF T1 - MPI collective I/O based on advanced reservations to obtain performance guarantees from shared storage systems T2 - CLUSTER Y1 - 2013 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - CLUSTER ER - TY - CONF T1 - Towards Addressing CPU-Intensive Seismological Applications in Europe T2 - International Supercomputing Conference Y1 - 2013 A1 - Michele Carpené A1 - I.A. Klampanos A1 - Siew Hoon Leong A1 - Emanuele Casarotti A1 - Peter Danecek A1 - Graziella Ferini A1 - Andre Gemünd A1 - Amrey Krause A1 - Lion Krischer A1 - Federica Magnoni A1 - Marek Simon A1 - Alessandro Spinuso A1 - Luca Trani A1 - Malcolm Atkinson A1 - Giovanni Erbacci A1 - Anton Frank A1 - Heiner Igel A1 - Andreas Rietbrock A1 - Horst Schwichtenberg A1 - Jean-Pierre Vilotte AB - Advanced application environments for seismic analysis help geoscientists to execute complex simulations to predict the behaviour of a geophysical system and potential surface observations. At the same time data collected from seismic stations must be processed comparing recorded signals with predictions. The EU-funded project VERCE (http://verce.eu/) aims to enable specific seismological use-cases and, on the basis of requirements elicited from the seismology community, provide a service-oriented infrastructure to deal with such challenges. In this paper we present VERCE’s architecture, in particular relating to forward and inverse modelling of Earth models and how the, largely file-based, HPC model can be combined with data streaming operations to enhance the scalability of experiments.We posit that the integration of services and HPC resources in an open, collaborative environment is an essential medium for the advancement of sciences of critical importance, such as seismology. JF - International Supercomputing Conference CY - Leipzig, Germany ER - 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 - Abstract: Reservation-Based I/O Performance Guarantee for MPI-IO Applications Using Shared Storage Systems T2 - SC Companion Y1 - 2012 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - SC Companion ER - TY - CONF T1 - A Data Driven Science Gateway for Computational Workflows T2 - UNICORE Summit 2012 Y1 - 2012 A1 - Grunzke, Richard A1 - Birkenheuer, G. A1 - Blunk, D. A1 - Breuers, S. A1 - Brinkmann, A. A1 - Gesing, Sandra A1 - Herres-Pawlis, S A1 - Kohlbacher, O. A1 - Krüger, J. A1 - Kruse, M. A1 - Müller-Pfefferkorn, R. A1 - Schäfer, P. A1 - Schuller, B. A1 - Steinke, T. A1 - Zink, A. JF - UNICORE Summit 2012 ER - TY - JOUR T1 - Data-Intensive Architecture for Scientific Knowledge Discovery JF - Distributed and Parallel Databases Y1 - 2012 A1 - Atkinson, Malcolm P. A1 - Chee Sun Liew A1 - Michelle Galea A1 - Paul Martin A1 - Krause, Amrey A1 - Adrian Mouat A1 - Oscar Corcho A1 - Snelling, David KW - Knowledge discovery, workflow management system AB - This paper presents a data-intensive architecture that demonstrates the ability to support applications from a wide range of application domains, and support the different types of users involved in defining, designing and executing data-intensive processing tasks. The prototype architecture is introduced, and the pivotal role of DISPEL as a canonical language is explained. The architecture promotes the exploration and exploitation of distributed and heterogeneous data and spans the complete knowledge discovery process, from data preparation, to analysis, to evaluation and reiteration. The architecture evaluation included large-scale applications from astronomy, cosmology, hydrology, functional genetics, imaging processing and seismology. VL - 30 UR - http://dx.doi.org/10.1007/s10619-012-7105-3 IS - 5 ER - 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 - Generic T1 - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences Y1 - 2012 ED - Gesing, Sandra ED - Glatard, Tristan ED - Krüger, Jens ED - Delgado Olabarriaga, Silvia ED - Solomonides, Tony ED - Silverstein, J. ED - Montagnat, J. ED - Gaignard, A. ED - Krefting, Dagmar PB - IOS Press VL - 175 ER - TY - CONF T1 - The MoSGrid Community - From National to International Scale T2 - EGI Community Forum 2012 Y1 - 2012 A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas JF - EGI Community Forum 2012 ER - TY - CONF T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Grid Workflow Workshop 2011 Y1 - 2012 A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, B. A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver JF - Grid Workflow Workshop 2011 PB - CEUR Workshop Proceedings ER - TY - CHAP T1 - Multi-agent Negotiation of Virtual Machine Migration Using the Lightweight Coordination Calculus T2 - Agent and Multi-Agent Systems. Technologies and Applications Y1 - 2012 A1 - Anderson, Paul A1 - Shahriar Bijani A1 - Vichos, Alexandros ED - Jezic, Gordan ED - Kusek, Mario ED - Nguyen, Ngoc-Thanh ED - Howlett, Robert ED - Jain, Lakhmi JF - Agent and Multi-Agent Systems. Technologies and Applications T3 - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 7327 SN - 978-3-642-30946-5 UR - http://dx.doi.org/10.1007/978-3-642-30947-2_16 ER - TY - CONF T1 - A Science Gateway Getting Ready for Serving the International Molecular Simulation Community T2 - Proceedings of Science Y1 - 2012 A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas JF - Proceedings of Science ER - TY - JOUR T1 - Searching in peer-to-peer networks JF - Computer Science Review (Elsevier) Y1 - 2012 A1 - I.A. Klampanos A1 - J.M. Jose UR - http://www.sciencedirect.com/science/article/pii/S1574013712000238 ER - TY - JOUR T1 - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics JF - Journal of Grid Computing Y1 - 2012 A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Wewior, Martin A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Herres-Pawlis, Sonja A1 - Breuers, Sebastian A1 - Balaskó, Ákos A1 - Kozlovszky, Miklos A1 - Fabri, AnnaSzikszay A1 - Packschies, Lars A1 - Kacsuk, Peter A1 - Blunk, Dirk A1 - Steinke, Thomas A1 - Brinkmann, André A1 - Fels, Gregor A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Kohlbacher, Oliver KW - DCIs KW - Science gateway KW - security KW - Single sign-on KW - Structural bioinformatics VL - 10 UR - http://dx.doi.org/10.1007/s10723-012-9247-y ER - TY - CONF T1 - Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway T2 - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences Y1 - 2012 A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Jäkel, René A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Dos Santos Vieira, Ines JF - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences PB - IOS Press 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 - 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 - RapidBrain: Developing a Portal for Brain Research Imaging T2 - All Hands Meeting 2011, York Y1 - 2011 A1 - Kenton D'Mellow A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Jos Koetsier A1 - Dominic Job A1 - van Hemert, Jano A1 - Wardlaw, Joanna A1 - Fan Zhu AB - Brain imaging researchers execute complex multistep workflows in their computational analysis. Those workflows often include applications that have very different user interfaces and sometimes use different data formats. A good example is the brain perfusion quantification workflow used at the BRIC (Brain Research Imaging Centre) in Edinburgh. Rapid provides an easy method for creating portlets for computational jobs, and at the same it is extensible. We have exploited this extensibility with additions that stretch the functionality beyond the original limits. These changes can be used by other projects to create their own portals, but it should be noted that the development of such portals involve a greater effort than the required in the regular use of Rapid for creating portlets. In our case it has been used to provide a user-friendly interface for perfusion analysis that covers from volume JF - All Hands Meeting 2011, York CY - York ER - TY - CONF T1 - A Science Gateway for Molecular Simulations T2 - EGI User Forum 2011 Y1 - 2011 A1 - Gesing, Sandra A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Krüger, Jens A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Warzecha, Klaus A1 - Wewior, Martin A1 - Kohlbacher, Oliver JF - EGI User Forum 2011 SN - 978 90 816927 1 7 ER - TY - JOUR T1 - Special Issue: Portals for life sciences---Providing intuitive access to bioinformatic tools JF - Concurrency and Computation: Practice and Experience Y1 - 2011 A1 - Gesing, Sandra A1 - van Hemert, J. A1 - Kacsuk, P. A1 - Kohlbacher, O. AB - The topic ‘Portals for life sciences’ includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user’s interaction with computational resources that are concerted to a supported application domain. PB - Wiley VL - 23 IS - 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 - JOUR T1 - Validation and mismatch repair of workflows through typed data streams JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Y1 - 2011 A1 - Yaikhom, Gagarine A1 - Malcolm Atkinson A1 - van Hemert, Jano A1 - Oscar Corcho A1 - Krause, Amy AB - The type system of a language guarantees that all of the operations on a set of data comply with the rules and conditions set by the language. While language typing is a fundamental requirement for any programming language, the typing of data that flow between processing elements within a workflow is currently being treated as optional. In this paper, we introduce a three-level type system for typing workflow data streams. These types are parts of the Data Intensive System Process Engineering Language programming language, which empowers users with the ability to validate the connections inside a workflow composition, and apply appropriate data type conversions when necessary. Furthermore, this system enables the enactment engine in carrying out type-directed workflow optimizations. VL - 369 IS - 1949 ER - TY - JOUR T1 - Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles JF - BMC Genomics Y1 - 2010 A1 - R. R. Kitchen A1 - V. S. Sabine A1 - A. H. Sims A1 - E. J. Macaskill A1 - L. Renshaw A1 - J. S. Thomas A1 - van Hemert, J. I. A1 - J. M. Dixon A1 - J. M. S. Bartlett AB - Background Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. Results A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. Conclusion In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data. VL - 11 UR - http://www.biomedcentral.com/1471-2164/11/134 IS - 134 ER - TY - Generic T1 - Federated Enactment of Workflow Patterns T2 - Lecture Notes in Computer Science Y1 - 2010 A1 - Yaikhom, Gagarine A1 - Liew, Chee A1 - Liangxiu Han A1 - van Hemert, Jano A1 - Malcolm Atkinson A1 - Krause, Amy ED - D’Ambra, Pasqua ED - Guarracino, Mario ED - Talia, Domenico AB - In this paper we address two research questions concerning workflows: 1) how do we abstract and catalogue recurring workflow patterns?; and 2) how do we facilitate optimisation of the mapping from workflow patterns to actual resources at runtime? Our aim here is to explore techniques that are applicable to large-scale workflow compositions, where the resources could change dynamically during the lifetime of an application. We achieve this by introducing a registry-based mechanism where pattern abstractions are catalogued and stored. In conjunction with an enactment engine, which communicates with this registry, concrete computational implementations and resources are assigned to these patterns, conditional to the execution parameters. Using a data mining application from the life sciences, we demonstrate this new approach. JF - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 6271 UR - http://dx.doi.org/10.1007/978-3-642-15277-1_31 N1 - 10.1007/978-3-642-15277-1_31 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 - Integrating distributed data sources with OGSA--DAI DQP and Views JF - Philosophical Transactions A Y1 - 2010 A1 - Dobrzelecki, B. A1 - Krause, A. A1 - Hume, A. C. A1 - Grant, A. A1 - Antonioletti, M. A1 - Alemu, T. Y. A1 - Atkinson, M. A1 - Jackson, M. A1 - Theocharopoulos, E. AB - OGSA-DAI (Open Grid Services Architecture Data Access and Integration) is a framework for building distributed data access and integration systems. Until recently, it lacked the built-in functionality that would allow easy creation of federations of distributed data sources. The latest release of the OGSA-DAI framework introduced the OGSA-DAI DQP (Distributed Query Processing) resource. The new resource encapsulates a distributed query processor, that is able to orchestrate distributed data sources when answering declarative user queries. The query processor has many extensibility points, making it easy to customize. We have also introduced a new OGSA-DAI Views resource that provides a flexible method for defining views over relational data. The interoperability of the two new resources, together with the flexibility of the OGSA-DAI framework, allows the building of highly customized data integration solutions. VL - 368 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 - CONF T1 - The MoSGrid Gaussian Portlet – Technologies for the Implementation of Portlets for Molecular Simulations T2 - Proceedings of the International Workshop on Science Gateways (IWSG10) Y1 - 2010 A1 - Wewior, Martin A1 - Packschies, Lars A1 - Blunk, Dirk A1 - Wickeroth, D. A1 - Warzecha, Klaus A1 - Herres-Pawlis, Sonja A1 - Gesing, Sandra A1 - Breuers, Sebastian A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Lang, Ulrich ED - Barbera, Roberto ED - Andronico, Giuseppe ED - La Rocca, Giuseppe JF - Proceedings of the International Workshop on Science Gateways (IWSG10) PB - Consorzio COMETA ER - TY - JOUR T1 - Quality control for quantitative PCR based on amplification compatibility test JF - Methods Y1 - 2010 A1 - Tichopad, Ales A1 - Tzachi Bar A1 - Ladislav Pecen A1 - Robert R. Kitchen A1 - Kubista, Mikael A1 - Michael W. Pfaffl AB - Quantitative qPCR is a routinely used method for the accurate quantification of nucleic acids. Yet it may generate erroneous results if the amplification process is obscured by inhibition or generation of aberrant side-products such as primer dimers. Several methods have been established to control for pre-processing performance that rely on the introduction of a co-amplified reference sequence, however there is currently no method to allow for reliable control of the amplification process without directly modifying the sample mix. Herein we present a statistical approach based on multivariate analysis of the amplification response data generated in real-time. The amplification trajectory in its most resolved and dynamic phase is fitted with a suitable model. Two parameters of this model, related to amplification efficiency, are then used for calculation of the Z-score statistics. Each studied sample is compared to a predefined reference set of reactions, typically calibration reactions. A probabilistic decision for each individual Z-score is then used to identify the majority of inhibited reactions in our experiments. We compare this approach to univariate methods using only the sample specific amplification efficiency as reporter of the compatibility. We demonstrate improved identification performance using the multivariate approach compared to the univariate approach. Finally we stress that the performance of the amplification compatibility test as a quality control procedure depends on the quality of the reference set. PB - Elsevier VL - 50 UR - http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4Y88DBN-3&_user=10&_coverDate=04%2F30%2F2010&_alid=1247745718&_rdoc=1&_fmt=high&_orig=search&_cdi=6953&_sort=r&_docanchor=&view=c&_ct=2&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5 IS - 4 ER - TY - JOUR T1 - Statistical aspects of quantitative real-time PCR experiment design JF - Methods Y1 - 2010 A1 - Robert R. Kitchen A1 - Kubista, Mikael A1 - Tichopad, Ales KW - Error propagation KW - Experiment design KW - Gene expression KW - Nested analysis of variance KW - powerNest KW - Prospective power analysis KW - qPCR KW - Real-time PCR KW - Sampling plan KW - Statistical power AB - Experiments using quantitative real-time PCR to test hypotheses are limited by technical and biological variability; we seek to minimise sources of confounding variability through optimum use of biological and technical replicates. The quality of an experiment design is commonly assessed by calculating its prospective power. Such calculations rely on knowledge of the expected variances of the measurements of each group of samples and the magnitude of the treatment effect; the estimation of which is often uninformed and unreliable. Here we introduce a method that exploits a small pilot study to estimate the biological and technical variances in order to improve the design of a subsequent large experiment. We measure the variance contributions at several ‘levels’ of the experiment design and provide a means of using this information to predict both the total variance and the prospective power of the assay. A validation of the method is provided through a variance analysis of representative genes in several bovine tissue-types. We also discuss the effect of normalisation to a reference gene in terms of the measured variance components of the gene of interest. Finally, we describe a software implementation of these methods, powerNest, that gives the user the opportunity to input data from a pilot study and interactively modify the design of the assay. The software automatically calculates expected variances, statistical power, and optimal design of the larger experiment. powerNest enables the researcher to minimise the total confounding variance and maximise prospective power for a specified maximum cost for the large study. PB - Elsevier VL - 50 UR - http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&_uoikey=B6WN5-4Y88DBN-1&_origin=SDEMFRHTML&_version=1&md5=7bb0b5b797d6e1f7c5c2df478fc88e5a IS - 4 ER - TY - CONF T1 - TOPP goes Rapid T2 - Cluster Computing and the Grid, IEEE International Symposium on Y1 - 2010 A1 - Gesing, Sandra A1 - van Hemert, Jano A1 - Jos Koetsier A1 - Bertsch, Andreas A1 - Kohlbacher, Oliver AB - 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 portlets 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. JF - Cluster Computing and the Grid, IEEE International Symposium on PB - IEEE Computer Society CY - Los Alamitos, CA, USA SN - 978-0-7695-4039-9 ER - TY - CONF T1 - Workflow Interoperability in a Grid Portal for Molecular Simulations T2 - Proceedings of the International Workshop on Science Gateways (IWSG10) Y1 - 2010 A1 - Gesing, Sandra A1 - Marton, Istvan A1 - Birkenheuer, Georg A1 - Schuller, Bernd A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Breuers, Sebastian A1 - Blunk, Dirk A1 - Fels, Gregor A1 - Packschies, Lars A1 - Brinkmann, André A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos JF - Proceedings of the International Workshop on Science Gateways (IWSG10) PB - Consorzio COMETA ER - TY - CONF T1 - Advanced Data Mining and Integration Research for Europe T2 - All Hands Meeting 2009 Y1 - 2009 A1 - Atkinson, M. A1 - Brezany, P. A1 - Corcho, O. A1 - Han, L A1 - van Hemert, J. A1 - Hluchy, L. A1 - Hume, A. A1 - Janciak, I. A1 - Krause, A. A1 - Snelling, D. A1 - Wöhrer, A. AB - There is a rapidly growing wealth of data [1]. The number of sources of data is increasing, while, at the same time, the diversity, complexity and scale of these data resources are also increasing dramatically. This cornucopia of data o ers much potential; a combinatorial explosion of opportunities for knowledge discovery, improved decisions and better policies. Today, most of these opportunities are not realised because composing data from multiple sources and extracting information is too dicult. Every business, organisation and government faces problems that can only be addressed successfully if we improve our techniques for exploiting the data we gather. JF - All Hands Meeting 2009 CY - Oxford ER - TY - JOUR T1 - Design and Optimization of Reverse-Transcription Quantitative PCR Experiments JF - Clin Chem Y1 - 2009 A1 - Tichopad, Ales A1 - Kitchen, Rob A1 - Riedmaier, Irmgard A1 - Becker, Christiane A1 - Stahlberg, Anders A1 - Kubista, Mikael AB - BACKGROUND: Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression. Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. METHOD: We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations. We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. RESULTS: A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design. We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue. In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. CONCLUSIONS: We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood. We show how an optimal sampling plan can be calculated for a limited budget. UR - http://www.clinchem.org/cgi/content/abstract/clinchem.2009.126201v1 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 - An Open Grid Services Architecture Primer JF - Computer Y1 - 2009 A1 - Grimshaw, Andrew A1 - Morgan, Mark A1 - Merrill, Duane A1 - Kishimoto, Hiro A1 - Savva, Andreas A1 - Snelling, David A1 - Smith, Chris A1 - Dave Berry PB - IEEE Computer Society Press CY - Los Alamitos, CA, USA VL - 42 ER - TY - CONF T1 - Portals for Life Sciences—a Brief Introduction T2 - Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences Y1 - 2009 A1 - Gesing, Sandra A1 - Kohlbacher, O. A1 - van Hemert, J. I. AB - The topic ”‘Portals for Life Sciences”’ includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user’s interaction with computational resources which are concer- ted to a supported application domain. JF - Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences T3 - CEUR Workshop Proceedings UR - http://ceur-ws.org/Vol-513/paper01.pdf 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 - TY - JOUR T1 - Simultaneous alignment of short reads against multiple genomes JF - Genome Biol Y1 - 2009 A1 - Schneeberger, Korbinian A1 - Hagmann, Jörg A1 - Ossowski, Stephan A1 - Warthmann, Norman A1 - Gesing, Sandra A1 - Kohlbacher, Oliver A1 - Weigel, Detlef VL - 10 UR - http://www.biomedsearch.com/nih/Simultaneous-alignment-short-reads-against/19761611.html 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 - Generic T1 - HIDGM: A Hybrid Intrusion Detection System for Mobile networks T2 - International Conference on Computer and Electrical Engineering (ICEEE) Y1 - 2008 A1 - Shahriar Bijani A1 - Maryam Kazemitabar JF - International Conference on Computer and Electrical Engineering (ICEEE) PB - IEEE Computer Society ER - TY - CONF T1 - OGSA-DAI: Middleware for Data Integration: Selected Applications T2 - ESCIENCE '08: Proceedings of the 2008 Fourth IEEE International Conference on eScience Y1 - 2008 A1 - Grant, Alistair A1 - Antonioletti, Mario A1 - Hume, Alastair C. A1 - Krause, Amy A1 - Dobrzelecki, Bartosz A1 - Jackson, Michael J. A1 - Parsons, Mark A1 - Atkinson, Malcolm P. A1 - Theocharopoulos, Elias JF - ESCIENCE '08: Proceedings of the 2008 Fourth IEEE International Conference on eScience PB - IEEE Computer Society CY - Washington, DC, USA SN - 978-0-7695-3535-7 ER - TY - CONF T1 - Accessing Data in Grids Using OGSA-DAI T2 - Knowledge and Data Management in Grids Y1 - 2007 A1 - Chue Hong, N. P. A1 - Antonioletti, M. A1 - Karasavvas, K. A. A1 - Atkinson, M. ED - Talia, D. ED - Bilas, A. ED - Dikaiakos, M. AB - The grid provides a vision in which resources, including storage and data, can be shared across organisational boundaries. The original emphasis of grid computing lay in the sharing of computational resources but technological and scientific advances have led to an ongoing data explosion in many fields. However, data is stored in many different storage systems and data formats, with different schema, access rights, metadata attributes, and ontologies all of which are obstacles to the access, integration and management of this information. In this chapter we examine some of the ways in which these differences can be addressed by grid technology to enable the meaningful sharing of data. In particular, we present an overview of the OGSA-DAI (Open Grid Service Architecture - Data Access and Integration) software, which provides a uniform, extensible framework for accessing structured and semi-structured data and provide some examples of its use in other projects. The open-source OGSA-DAI software is freely available from http://www.ogsadai.org.uk. JF - Knowledge and Data Management in Grids SN - 978-0-387-37830-5 UR - http://www.springer.com/computer/communication+networks/book/978-0-387-37830-5 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 - JOUR T1 - MAPFS-DAI, an extension of OGSA-DAI based on a parallel file system JF - Future Generation Computer Systems Y1 - 2007 A1 - Sanchez, A. A1 - Perez, M. S. A1 - Karasavvas, K. A1 - Herrero, P. A1 - Perez, A. VL - 23 ER - TY - CONF T1 - OGSA-DAI 3.0 - The What's and Whys T2 - UK e-Science All Hands Meeting Y1 - 2007 A1 - Antonioletti, M. A1 - Hong, N. P. Chue A1 - Hume, A. C. A1 - Jackson, M. A1 - Karasavvas, K. A1 - Krause, A. A1 - Schopf, J. M. A1 - Atkinson, M. P. A1 - Dobrzelecki, B. A1 - Illingworth, M. A1 - McDonnell, N. A1 - Parsons, M. A1 - Theocharopoulous, E. JF - UK e-Science All Hands Meeting ER - TY - CONF T1 - EGEE: building a pan-European grid training organisation T2 - ACSW Frontiers Y1 - 2006 A1 - Berlich, R{\"u}diger A1 - Hardt, Marcus A1 - Kunze, Marcel A1 - Atkinson, Malcolm P. A1 - Fergusson, David JF - ACSW Frontiers 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 - CHAP T1 - Knowledge and Data Management in Grids, CoreGRID T2 - Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing Y1 - 2006 A1 - Chue Hong, N. P. A1 - Antonioletti, M. A1 - Karasavvas, K. A. A1 - Atkinson, M. ED - Lehner, W. ED - Meyer, N. ED - Streit, A. ED - Stewart, C. JF - Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing T3 - Lecture Notes in Computer Science PB - Springer CY - Berlin, Germany VL - 4375 SN - 978-3-540-72226-7 UR - http://www.springer.com/computer/communication+networks/book/978-3-540-72226-7 ER - TY - CONF T1 - Neighborhood Searches for the Bounded Diameter Minimum Spanning Tree Problem Embedded in a VNS, EA, and ACO T2 - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) Y1 - 2006 A1 - Gruber, M. A1 - van Hemert, J. I. A1 - Raidl, G. R. ED - Maarten Keijzer ED - et al KW - constraint satisfaction KW - evolutionary computation KW - variable neighbourhood search AB - We consider the Bounded Diameter Minimum Spanning Tree problem and describe four neighbourhood searches for it. They are used as local improvement strategies within a variable neighbourhood search (VNS), an evolutionary algorithm (EA) utilising a new encoding of solutions, and an ant colony optimisation (ACO).We compare the performance in terms of effectiveness between these three hybrid methods on a suite f popular benchmark instances, which contains instances too large to solve by current exact methods. Our results show that the EA and the ACO outperform the VNS on almost all used benchmark instances. Furthermore, the ACO yields most of the time better solutions than the EA in long-term runs, whereas the EA dominates when the computation time is strongly restricted. JF - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) PB - ACM CY - Seattle, USA VL - 2 ER - TY - CONF T1 - Profiling OGSA-DAI Performance for Common Use Patterns T2 - UK e-Science All Hands Meeting Y1 - 2006 A1 - Dobrzelecki, B. A1 - Antonioletti, M. A1 - Schopf, J. M. A1 - Hume, A. C. A1 - Atkinson, M. A1 - Hong, N. P. Chue A1 - Jackson, M. A1 - Karasavvas, K. A1 - Krause, A. A1 - Parsons, M. A1 - Sugden, T. A1 - Theocharopoulos, E. JF - UK e-Science All Hands Meeting ER - TY - CONF T1 - A Shibboleth-Protected Privilege Management Infrastructure for e-Science Education T2 - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006 Y1 - 2006 A1 - J. Watt A1 - Oluwafemi Ajayi A1 - J. Jiang A1 - Jos Koetsier A1 - Richard O. Sinnott KW - security JF - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006 PB - IEEE Computer Society CY - Singapore ER - TY - JOUR T1 - A Criticality-Based Framework for Task Composition in Multi-Agent Bioinformatics Integration Systems JF - Bioinformatics Y1 - 2005 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. VL - 21 ER - TY - JOUR T1 - The design and implementation of Grid database services in OGSA-DAI JF - Concurrency - Practice and Experience Y1 - 2005 A1 - Antonioletti, Mario A1 - Atkinson, Malcolm P. A1 - Baxter, Robert M. A1 - Borley, Andrew A1 - Hong, Neil P. Chue A1 - Collins, Brian A1 - Hardman, Neil A1 - Hume, Alastair C. A1 - Knox, Alan A1 - Mike Jackson A1 - Krause, Amrey A1 - Laws, Simon A1 - Magowan, James A1 - Pato VL - 17 ER - TY - Generic T1 - Experience with the international testbed in the crossgrid project T2 - Advances in Grid Computing-EGC 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - A García A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Jesus A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - J Sánchez A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. A1 - K Nawrocki A1 - A Padee A1 - W Wislicki ED - Peter M. A. Sloot, Alfons G. Hoekstra, Thierry Priol, Alexander Reinefeld ED - Marian Bubak JF - Advances in Grid Computing-EGC 2005 T3 - LNCS PB - Springer Berlin/Heidelberg CY - Amsterdam VL - 3470 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 - CONF T1 - Introduction to OGSA-DAI Services T2 - Scientific Applications of Grid Computing Y1 - 2005 A1 - Karasavvas, K. A1 - Antonioletti, M. A1 - Atkinson, M. A1 - Hong, N. C. A1 - Sugden, T. A1 - Hume, A. A1 - Jackson, M. A1 - Krause, A. A1 - Palansuriya, C. JF - Scientific Applications of Grid Computing VL - 3458 SN - 978-3-540-25810-0 ER - TY - CONF T1 - A New Architecture for OGSA-DAI T2 - UK e-Science All Hands Meeting Y1 - 2005 A1 - Atkinson, M. A1 - Karasavvas, K. A1 - Antonioletti, M. A1 - Baxter, R. A1 - Borley, A. A1 - Hong, N. C. A1 - Hume, A. A1 - Jackson, M. A1 - Krause, A. A1 - Laws, S. A1 - Paton, N. A1 - Schopf, J. A1 - Sugden, T. A1 - Tourlas, K. A1 - Watson, P. JF - UK e-Science All Hands Meeting ER - TY - CONF T1 - OGSA-DAI Status and Benchmarks T2 - All Hands Meeting 2005 Y1 - 2005 A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Andrew Borle A1 - Hong, Neil P. Chue A1 - Patrick Dantressangle A1 - Hume, Alastair C. A1 - Mike Jackson A1 - Krause, Amy A1 - Laws, Simon A1 - Parsons, Mark A1 - Paton, Norman W. A1 - Jennifer M. Schopf A1 - Tom Sugden A1 - Watson, Paul AB - This paper presents a status report on some of the highlights that have taken place within the OGSADAI project since the last AHM. A description of Release 6.0 functionality and details of the forthcoming release, due in September 2005, is given. Future directions for this project are discussed. This paper also describes initial results of work being done to systematically benchmark recent OGSADAI releases. The OGSA-DAI software distribution, and more information about the project, is available from the project website at www.ogsadai.org.uk. JF - All Hands Meeting 2005 CY - Nottingham, UK ER - TY - CONF T1 - Organization of the International Testbed of the CrossGrid Project T2 - Cracow Grid Workshop 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - Garcia, A. A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - Sanchez, J. A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. JF - Cracow Grid Workshop 2005 ER - TY - JOUR T1 - Bioinformatics System Integration and Agent Technology JF - Journal of Biomedical Informatics Y1 - 2004 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. VL - 37 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 - CONF T1 - OGSA-DAI Status Report and Future Directions T2 - All Hands Meeting 2004 Y1 - 2004 A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Borley, Andrew A1 - Hong, Neil P. Chue A1 - Collins, Brian A1 - Jonathan Davies A1 - Desmond Fitzgerald A1 - Hardman, Neil A1 - Hume, Alastair C. A1 - Mike Jackson A1 - Krause, Amrey A1 - Laws, Simon A1 - Paton, Norman W. A1 - Tom Sugden A1 - Watson, Paul A1 - Mar AB - Data Access and Integration (DAI) of data resources, such as relational and XML databases, within a Grid context. Project members also participate in the development of DAI standards through the GGF DAIS WG. The standards that emerge through this effort will be adopted by OGSA-DAI once they have stabilised. The OGSA-DAI developers are also engaging with a growing user community to gather their data and functionality requirements. Several large projects are already using OGSA-DAI to provide their DAI capabilities. This paper presents a status report on OGSA-DAI activities since the last AHM and announces future directions. The OGSA-DAI software distribution and more information about the project is available from the project website at http://www.ogsadai.org.uk/. JF - All Hands Meeting 2004 CY - Nottingham, UK ER - TY - CONF T1 - OGSA-DAI: Two Years On T2 - GGF10 Y1 - 2004 A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Borley, Andrew A1 - Neil Chue Hong A1 - Collins, Brian A1 - Jonathan Davies A1 - Hardman, Neil A1 - George Hicken A1 - Ally Hume A1 - Mike Jackson A1 - Krause, Amrey A1 - Laws, Simon A1 - Magowan, James A1 - Jeremy Nowell A1 - Paton, Norman W. A1 - Dave Pearson A1 - To AB - The OGSA-DAI project has been producing Grid-enabled middleware for almost two years now, providing data access and integration capabilities to data resources, such as databases, within an OGSA context. In these two years, OGSA-DAI has been tracking rapidly evolving standards, managing changes in software dependencies, contributing to the standardisation process and liasing with a growing user community together with their associated data requirements. This process has imparted important lessons and raised a number of issues that need to be addressed if a middleware product is to be widely adopted. This paper examines the experiences of OGSA-DAI in implementing proposed standards, the likely impact that the still-evolving standards landscape will have on future implementations and how these affect uptake of the software. The paper also examines the gathering of requirements from and engagement with the Grid community, the difficulties of defining a process for the management and publishing of metadata, and whether relevant standards can be implemented in an efficient manner. The OGSA-DAI software distribution and more details about the project are available from the project Web site at http://www.ogsadai.org.uk/. JF - GGF10 CY - Berlin, Germany ER - TY - CHAP T1 - Data Access, Integration, and Management T2 - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition), Y1 - 2003 A1 - Atkinson. M. A1 - Chervenak, A. L. A1 - Kunszt, P. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Shoshani, A. A1 - Watson, P. ED - Foster, I. ED - Kesselman, C JF - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition), PB - Morgan Kaufmann SN - 1-55860-933-4 ER - TY - CONF T1 - The Design and Implementation of Grid Database Services in OGSA-DAI T2 - All Hands Meeting 2003 Y1 - 2003 A1 - Ali Anjomshoaa A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Borley, Andrew A1 - Hong, Neil P. Chue A1 - Collins, Brian A1 - Hardman, Neil A1 - George Hicken A1 - Ally Hume A1 - Knox, Alan A1 - Mike Jackson A1 - Krause, Amrey A1 - Laws, Simon A1 - Magowan, James A1 - Charaka Palansuriya A1 - Paton, Norman W. AB - This paper presents a high-level overview of the design and implementation of the core components of the OGSA-DAI project. It describes the design decisions made, the project’s interaction with the Data Access and Integration Working Group of the Global Grid Forum and provides an overview of implementation characteristics. Further details of the implementation are provided in the extensive documentation available from the project web site. JF - All Hands Meeting 2003 CY - Nottingham, UK ER - TY - CONF T1 - Experiences of Designing and Implementing Grid Database Services in the OGSA-DAI project T2 - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9 Y1 - 2003 A1 - Antonioletti, Mario A1 - Neil Chue Hong A1 - Ally Hume A1 - Mike Jackson A1 - Krause, Amy A1 - Jeremy Nowell A1 - Charaka Palansuriya A1 - Tom Sugden A1 - Martin Westhead AB - This paper describes the experiences of the OGSA-DAI team in designing and building a database access layer using the OGSI and the emerging DAIS GGF recommendations. This middleware is designed for enabling other UK e-Science projects that require database access and providing the basic primitives for higher-level services such as Distributed Query Processing. OGSA-DAI also intends to produce one of the required reference implementations of the DAIS specification once this becomes a proposed recommendation and, until then, scope out their ideas, provide feedback as well as directly contributing to the GGF working group. This paper enumerates the issues that have arisen in tracking the DAIS and OGSI specifications whilst developing a software distribution using the Grid services model; trying to serve the needs of the various target communities; and using the Globus Toolkit OGSI core distribution. The OGSA-DAI software distribution and more details are available from the project web site at http://www.ogsadai.org.uk/. JF - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9 CY - Chicago, USA ER - TY - CONF T1 - Criticality-Based Task Composition in Distributed Bioinformatics Systems T2 - Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology Y1 - 2002 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. JF - Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology ER - TY - CONF T1 - A Multi-Agent Bioinformatics Integration System with Adjustable Autonomy: An Overview T2 - Proceedings of the First International Conference on Autonomous Agents and Multi-Agent Systems Y1 - 2002 A1 - Karasavvas, K. A1 - Burger, A. A1 - Baldock, R. JF - Proceedings of the First International Conference on Autonomous Agents and Multi-Agent Systems PB - ACM ER - TY - CONF T1 - A Multi-Agent Bioinformatics Integration System with Adjustable Autonomy T2 - Lecture Notes in Computer Science Y1 - 2002 A1 - Karasavvas, K. A1 - Burger, A. A1 - Baldock, R. JF - Lecture Notes in Computer Science VL - 2417 ER - TY - CHAP T1 - Scalable and Recoverable Implementation of Object Evolution for the PJama1 Platform T2 - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers Y1 - 2001 A1 - Atkinson, M. P. A1 - Dmitriev, M. A. A1 - Hamilton, C. A1 - Printezis, T. ED - Graham N. C. ED - Kirby, Alan Dearle ED - Dag I. K. Sjøberg AB - PJama1 is the latest version of an orthogonally persistent platform for Java. It depends on a new persistent object store, Sphere, and provides facilities for class evolution. This evolution technology supports an arbitrary set of changes to the classes, which may have arbitrarily large populations of persistent objects. We verify that the changes are safe. When there are format changes, we also convert all of the instances, while leaving their identities unchanged. We aspire to both very large persistent object stores and freedom for developers to specify arbitrary conversion methods in Java to convey information from old to new formats. Evolution operations must be safe and the evolution cost should be approximately linear in the number of objects that must be reformatted. In order that these conversion methods can be written easily, we continue to present the pre-evolution state consistently to Java executions throughout an evolution. At the completion of applying all of these transformations, we must switch the store state to present only the post-evolution state, with object identity preserved. We present an algorithm that meets these requirements for eager, total conversion. This paper focuses on the mechanisms built into Sphere to support safe, atomic and scalable evolution. We report our experiences in using this technology and include a preliminary set of performance measurements. JF - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers T3 - Lecture Notes in Computer Science PB - Springer VL - 2135 UR - http://www.springerlink.com/content/09hx07h9lw0p1h82/?p=2bc20319905146bab8ba93b2fcc8cc01&pi=23 ER - TY - CONF T1 - Managing Transparency in Distributed Bioinformatics Systems T2 - European Media Lab Workshop on Management and Integration of Biochemical Data Y1 - 2000 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. JF - European Media Lab Workshop on Management and Integration of Biochemical Data ER - TY - CONF T1 - A comparison of genetic programming variants for data classification T2 - Springer Lecture Notes on Computer Science Y1 - 1999 A1 - Eggermont, J. A1 - Eiben, A. E. A1 - van Hemert, J. I. ED - D. J. Hand ED - J. N. Kok ED - M. R. Berthold KW - classification KW - data mining KW - genetic programming AB - In this paper we report the results of a comparative study on different variations of genetic programming applied on binary data classification problems. The first genetic programming variant is weighting data records for calculating the classification error and modifying the weights during the run. Hereby the algorithm is defining its own fitness function in an on-line fashion giving higher weights to `hard' records. Another novel feature we study is the atomic representation, where `Booleanization' of data is not performed at the root, but at the leafs of the trees and only Boolean functions are used in the trees' body. As a third aspect we look at generational and steady-state models in combination of both features. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-66332-0 ER -