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 - 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 - JOUR T1 - Managing dynamic enterprise and urgent workloads on clouds using layered queuing and historical performance models JF - Simulation Modelling Practice and Theory Y1 - 2011 A1 - David A. Bacigalupo A1 - van Hemert, Jano I. A1 - Xiaoyu Chen A1 - Asif Usmani A1 - Adam P. Chester A1 - Ligang He A1 - Donna N. Dillenberger A1 - Gary B. Wills A1 - Lester Gilbert A1 - Stephen A. Jarvis KW - e-Science AB - The automatic allocation of enterprise workload to resources can be enhanced by being able to make what–if response time predictions whilst different allocations are being considered. We experimentally investigate an historical and a layered queuing performance model and show how they can provide a good level of support for a dynamic-urgent cloud environment. Using this we define, implement and experimentally investigate the effectiveness of a prediction-based cloud workload and resource management algorithm. Based on these experimental analyses we: (i) comparatively evaluate the layered queuing and historical techniques; (ii) evaluate the effectiveness of the management algorithm in different operating scenarios; and (iii) provide guidance on using prediction-based workload and resource management. VL - 19 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 - Generic T1 - A Methodology for Mobile Network Security Risk Management T2 - Sixth International Conference on Information Technology: New Generations (ITNG '09) Y1 - 2009 A1 - Mahdi Seify A1 - Shahriar Bijani JF - Sixth International Conference on Information Technology: New Generations (ITNG '09) PB - IEEE Computer Society ER - TY - CONF T1 - A model of social collaboration in Molecular Biology knowledge bases T2 - Proceedings of the 6th Conference of the European Social Simulation Association (ESSA'09) Y1 - 2009 A1 - De Ferrari, Luna A1 - Stuart Aitken A1 - van Hemert, Jano A1 - Goryanin, Igor AB - Manual annotation of biological data cannot keep up with data production. Open annotation models using wikis have been proposed to address this problem. In this empirical study we analyse 36 years of knowledge collection by 738 authors in two Molecular Biology wikis (EcoliWiki and WikiPathways) and two knowledge bases (OMIM and Reactome). We first investigate authorship metrics (authors per entry and edits per author) which are power-law distributed in Wikipedia and we find they are heavy-tailed in these four systems too. We also find surprising similarities between the open (editing open to everyone) and the closed systems (expert curators only). Secondly, to discriminate between driving forces in the measured distributions, we simulate the curation process and find that knowledge overlap among authors can drive the number of authors per entry, while the time the users spend on the knowledge base can drive the number of contributions per author. JF - Proceedings of the 6th Conference of the European Social Simulation Association (ESSA'09) PB - European Social Simulation Association ER - TY - CONF T1 - Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns T2 - Communications in Computer and Information Science Y1 - 2008 A1 - van Hemert, J. I. A1 - Baldock, R. A. ED - M. Elloumi ED - \emph ED - et al KW - biomedical KW - data mining KW - DGEMap KW - e-Science AB - The Edinburgh Mouse Atlas aims to capture in-situ gene expression patterns in a common spatial framework. In this study, we construct a grammar to define spatial regions by combinations of these patterns. Combinations are formed by applying operators to curated gene expression patterns from the atlas, thereby resembling gene interactions in a spatial context. The space of combinations is searched using an evolutionary algorithm with the objective of finding the best match to a given target pattern. We evaluate the method by testing its robustness and the statistical significance of the results it finds. JF - Communications in Computer and Information Science PB - Springer Verlag ER - TY - JOUR T1 - Mobile Multimodality: A Theoretical Approach to Facilitate Virtual Device Environments JF - Mobile Networks and Applications Y1 - 2008 A1 - Srihathai Prammanee A1 - Klaus Moessner VL - 13 UR - http://dx.doi.org/10.1007/s11036-008-0091-z IS - 6 ER - TY - CONF T1 - Managing the transition from OBO to OWL: The COBrA-CT Bio-Ontology Tools T2 - UK e-Science Al l Hands Meeting 2007 Y1 - 2007 A1 - S. Aitken A1 - Y. Chen KW - Bio-ontology, Grid, OBO, OWL AB - This paper presents the COBrA-CT ontology tools, which include an ontology server database and version manager client tool for collaborative ontology development, and an editor for bio-ontologies that are represented in the Web Ontology Language (OWL) format. The ontology server uses OGSA-DAI Grid technology to provide access to the ontology server database. These tools implement the agreed standard for representing Open Biomedical Ontologies (OBO) in OWL and interoperate with other tools developed for this standard. Such tools are essential for the uptake of OWL in the biomedical ontology community. JF - UK e-Science Al l Hands Meeting 2007 CY - Nottingham, UK 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 - JOUR T1 - Mining co-regulated gene profiles for the detection of functional associations in gene expression data JF - Bioinformatics Y1 - 2007 A1 - Gyenesei, Attila A1 - Wagner, Ulrich A1 - Barkow-Oesterreicher, Simon A1 - Stolte, Etzard A1 - Schlapbach, Ralph VL - 23 ER - TY - CONF T1 - Mining spatial gene expression data for association rules T2 - Lecture Notes in Bioinformatics Y1 - 2007 A1 - van Hemert, J. I. A1 - Baldock, R. A. ED - S. Hochreiter ED - R. Wagner KW - biomedical KW - data mining KW - DGEMap KW - e-Science AB - We analyse data from the Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) which is a high quality data source for spatio-temporal gene expression patterns. Using a novel process whereby generated patterns are used to probe spatially-mapped gene expression domains, we are able to get unbiased results as opposed to using annotations based predefined anatomy regions. We describe two processes to form association rules based on spatial configurations, one that associates spatial regions, the other associates genes. JF - Lecture Notes in Bioinformatics PB - Springer Verlag UR - http://dx.doi.org/10.1007/978-3-540-71233-6_6 ER - TY - CONF T1 - Measuring the Searched Space to Guide Efficiency: The Principle and Evidence on Constraint Satisfaction T2 - Springer Lecture Notes on Computer Science Y1 - 2002 A1 - van Hemert, J. I. A1 - Bäck, T. ED - J. J. Merelo ED - A. Panagiotis ED - H.-G. Beyer ED - Jos{\'e}-Luis Fern{\'a}ndez-Villaca{\~n}as ED - Hans-Paul Schwefel KW - constraint satisfaction KW - resampling ratio AB - In this paper we present a new tool to measure the efficiency of evolutionary algorithms by storing the whole searched space of a run, a process whereby we gain insight into the number of distinct points in the state space an algorithm has visited as opposed to the number of function evaluations done within the run. This investigation demonstrates a certain inefficiency of the classical mutation operator with mutation-rate 1/l, where l is the dimension of the state space. Furthermore we present a model for predicting this inefficiency and verify it empirically using the new tool on binary constraint satisfaction problems. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-44139-5 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 - 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 - 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 - Measurement and analysis of IP network traffic T2 - In Proceedings of the 3th International Asia-Pacific Web Conference Y1 - 2000 A1 - cen, Z A1 - Gao, C A1 - Cong S A1 - Han, L JF - In Proceedings of the 3th International Asia-Pacific Web Conference CY - xi'an China ER - TY - CONF T1 - Mondriaan Art by Evolution T2 - Proceedings of the Eleventh Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'99) Y1 - 1999 A1 - van Hemert, J. I. A1 - Eiben, A. E. ED - E. Postma ED - M. Gyssens KW - evolutionary art AB - Here we show an application that generates images resembling art as it was produced by Mondriaan, a Dutch artist, well known for his minimalistic and pure abstract pieces of art. The current version generates images using a linear chromosome and a recursive function as a decoder. JF - Proceedings of the Eleventh Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'99) PB - BNVKI, Dutch and the Belgian AI Association ER -