TY  - CONF
T1  - Ad hoc Cloud Computing
T2  - IEEE Cloud
Y1  - 2015
A1  - Gary McGilvary
A1  - Barker, Adam
A1  - Malcolm Atkinson
KW  - ad hoc
KW  - cloud computing
KW  - reliability
KW  - virtualization
KW  - volunteer computing
AB  - This paper presents the first complete, integrated and end-to-end solution for ad hoc cloud computing environments. Ad hoc clouds harvest resources from existing sporadically available, non-exclusive (i.e. primarily used for some other purpose) and unreliable infrastructures. In this paper we discuss the problems ad hoc cloud computing solves and outline our architecture which is based on BOINC.
JF  - IEEE Cloud
UR  - http://arxiv.org/abs/1505.08097
ER  - 

TY  - BOOK
T1  - Ad hoc Cloud Computing (PhD Thesis)
Y1  - 2014
A1  - Gary McGilvary
AB  - Commercial and private cloud providers offer virtualized resources via a set of co-located and dedicated hosts that are exclusively reserved for the purpose of offering a cloud service. While both cloud models appeal to the mass market, there are many cases where outsourcing to a remote platform or procuring an in-house infrastructure may not be ideal or even possible.    To offer an attractive alternative, we introduce and develop an <i>ad hoc</i> cloud computing platform to transform spare resource capacity from an infrastructure owner's locally available, but non-exclusive and unreliable infrastructure, into an overlay cloud platform. The foundation of the <i>ad hoc</i> cloud relies on transferring and instantiating lightweight virtual machines on-demand upon near-optimal hosts while virtual machine checkpoints are distributed in a P2P fashion to other members of the <i>ad hoc</i> cloud. Virtual machines found to be non-operational are restored elsewhere ensuring the continuity of cloud jobs.     In this thesis <i>we investigate the feasibility, reliability and performance of ad hoc cloud computing infrastructures</i>. We firstly show that the combination of both volunteer computing and virtualization is the backbone of the <i>ad hoc</i> cloud. We outline the process of virtualizing the volunteer system BOINC to create V-BOINC. V-BOINC distributes virtual machines to volunteer hosts allowing volunteer applications to be executed in the sandbox environment to solve many of the downfalls of BOINC; this however also provides the basis for an <i>ad hoc</i> cloud computing platform to be developed.    We detail the challenges of transforming V-BOINC into an <i>ad hoc</i> cloud and outline the transformational process and integrated extensions. These include a BOINC job submission system, cloud job and virtual machine restoration schedulers and a periodic P2P checkpoint distribution component. Furthermore, as current monitoring tools are unable to cope with the dynamic nature of <i>ad hoc</i> clouds, a dynamic infrastructure monitoring and management tool called the Cloudlet Control Monitoring System is developed and presented.    We evaluate each of our individual contributions as well as the reliability, performance and overheads associated with an <i>ad hoc</i> cloud deployed on a realistically simulated unreliable infrastructure. We conclude that the <i>ad hoc</i> cloud is not only a feasible concept but also a viable computational alternative that offers high levels of reliability and can at least offer reasonable performance, which at times may exceed the performance of a commercial cloud infrastructure.
PB  - The University of Edinburgh
CY  - Edinburgh
ER  - 

TY  - CONF
T1  - C2MS: Dynamic Monitoring and Management of Cloud Infrastructures
T2  - IEEE CloudCom
Y1  - 2013
A1  - Gary McGilvary
A1  - Josep Rius
A1  - Íñigo Goiri
A1  - Francesc Solsona
A1  - Barker, Adam
A1  - Atkinson, Malcolm P.
AB  - Server clustering is a common design principle employed by many organisations who require high availability, scalability and easier management of their infrastructure. Servers are typically clustered according to the service they provide whether it be the application(s) installed, the role of the server or server accessibility for example. In order to optimize performance, manage load and maintain availability, servers may migrate from one cluster group to another making it difficult for server monitoring tools to continuously monitor these dynamically changing groups. Server monitoring tools are usually statically configured and with any change of group membership requires manual reconfiguration; an unreasonable task to undertake on large-scale cloud infrastructures.   In this paper we present the Cloudlet Control and Management System (C2MS); a system for monitoring and controlling dynamic groups of physical or virtual servers within cloud infrastructures. The C2MS extends Ganglia - an open source scalable system performance monitoring tool - by allowing system administrators to define, monitor and modify server groups without the need for server reconfiguration. In turn administrators can easily monitor group and individual server metrics on large-scale dynamic cloud infrastructures where roles of servers may change frequently. Furthermore, we complement group monitoring with a control element allowing administrator-specified actions to be performed over servers within service groups as well as introduce further customized monitoring metrics. This paper outlines the design, implementation and evaluation of the C2MS.
JF  - IEEE CloudCom
CY  - Bristol, UK
ER  - 

TY  - CHAP
T1  - Definition of the DISPEL Language
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Paul Martin
A1  - Yaikhom, Gagarine
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 Computing
KW  - Dispel
AB  - Chapter 10: "Definition of the DISPEL language", describes the novel aspects of the DISPEL language: its constructs, capabilities, and anticipated programming style.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
T3  - {Parallel and Distributed Computing, series editor Albert Y. Zomaya}
PB  - John Wiley & Sons Inc.
ER  - 

TY  - CHAP
T1  - DISPEL Development
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Adrian Mouat
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  - Diagnostics
KW  - Dispel
KW  - IDE
KW  - Libraries
KW  - Processing Elements
AB  - Chapter 11: "DISPEL development", describes the tools and libraries that a DISPEL developer might expect to use. The tools include those needed during process definition, those required to organize enactment, and diagnostic aids for developers of applications and platforms.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Inc.
ER  - 

TY  - JOUR
T1  - Embedded systems for global e-Social Science: Moving computation rather than data
JF  - Future Generation Computer Systems
Y1  - 2013
A1  - Ashley D. Lloyd
A1  - Terence M. Sloan
A1  - Antonioletti, Mario
A1  - Gary McGilvary
AB  - There is a wealth of digital data currently being gathered by commercial and private concerns that could supplement academic research. To unlock this data it is important to gain the trust of the companies that hold the data as well as showing them how they may benefit from this research. Part of this trust is gained through established reputation and the other through the technology used to safeguard the data. This paper discusses how different technology frameworks have been applied to safeguard the data and facilitate collaborative work between commercial concerns and academic institutions. The paper focuses on the distinctive requirements of e-Social Science: access to large-scale data on behaviour in society in environments that impose confidentiality constraints on access. These constraints arise from both privacy concerns and the commercial sensitivities of that data. In particular, the paper draws on the experiences of building an intercontinental Grid–INWA–from its first operation connecting Australia and Scotland to its subsequent extension to China across the Trans-Eurasia Information Network–the first large-scale research and education network for the Asia-Pacific region. This allowed commercial data to be analysed by experts that were geographically distributed across the globe. It also provided an entry point for a major Chinese commercial organization to approve use of a Grid solution in a new collaboration provided the centre of gravity of the data is retained within the jurisdiction of the data owner. We describe why, despite this approval, an embedded solution was eventually adopted. We find that ‘data sovereignty’ dominates any decision on whether and how to participate in e-Social Science collaborations and how this might impact on a Cloud based solution to this type of collaboration.
VL  - 29
UR  - http://www.sciencedirect.com/science/article/pii/S0167739X12002336
IS  - 5
ER  - 

TY  - JOUR
T1  - Exploiting Parallel R in the Cloud with SPRINT
JF  - Methods of Information in Medicine
Y1  - 2013
A1  - Piotrowski, Michal
A1  - Gary McGilvary
A1  - Sloan, Terence
A1  - Mewissen, Muriel
A1  - Ashley Lloyd
A1  - Forster, Thorsten
A1  - Mitchell, Lawrence
A1  - Ghazal, Peter
A1  - Hill, Jon
AB  - Background: Advances in DNA Microarray devices and next-generation massively parallel DNA sequencing platforms have led to an exponential growth in data availability but the arising opportunities require adequate computing resources. High Performance Computing (HPC) in the Cloud offers an affordable way of meeting this need.    Objectives: Bioconductor, a popular tool for high-throughput genomic data analysis, is distributed as add-on modules for the R statistical programming language but R has no native capabilities for exploiting multi-processor architectures. SPRINT is an R package that enables easy access to HPC for genomics researchers. This paper investigates: setting up and running SPRINT-enabled genomic analyses on Amazon’s Elastic Compute Cloud (EC2), the advantages of submitting applications to EC2 from different parts of the world and, if resource underutilization can improve application performance.    Methods: The SPRINT parallel implementations of correlation, permutation testing, partitioning around medoids and the multi-purpose papply have been benchmarked on data sets of various size on Amazon EC2. Jobs have been submitted from both the UK and Thailand to investigate monetary differences.    Results: It is possible to obtain good, scalable performance but the level of improvement is dependent upon the nature of algorithm. Resource underutilization can further improve the time to result. End-user’s location impacts on costs due to factors such as local taxation.     Conclusions: Although not designed to satisfy HPC requirements, Amazon EC2 and cloud computing in general provides an interesting alternative and provides new possibilities for smaller organisations with limited funds.
VL  - 52
IS  - 1
ER  - 

TY  - RPRT
T1  - The Implementation of OpenStack Cinder and Integration with NetApp and Ceph
Y1  - 2013
A1  - Gary McGilvary
A1  - Thomas Oulevey
AB  - With the ever increasing amount of data produced from Large Hadron Collider (LHC) experiments, new ways are sought to help analyze and store this data as well as help researchers perform their own experiments. To help offer solutions to such problems, CERN has employed the use of cloud computing and in particular OpenStack; an open source and scalable platform for building public and private clouds.     The OpenStack project contains many components such as Cinder used to create block storage that can be attached to virtual machines and in turn help increase performance. However instead of creating volumes locally with OpenStack, others remote storage clusters exist offering block based storage with features not present in the current OpenStack implementation; two popular solutions are NetApp and Ceph.     Two features Ceph offers is the ability to stripe data stored within volumes over the distributed cluster as well as locally cache this data, both with the aim of improving performance. When in use with OpenStack, Ceph performs default data striping where the number and size of stripes is fixed and cannot be changed dependent on the volume to be created. Similarly, Ceph does not perform data caching when integrated with OpenStack.    In this project we outline and document the integration of NetApp and Ceph with OpenStack as well as benchmark the performance of the NetApp and Ceph clusters already present at CERN. To allow Ceph data striping, we modify OpenStack to take the number and size of stripes input via the user to create volumes whose data is then striped according to the values they specify. Similarly, we also modify OpenStack to enable Ceph caching and allow users to select the caching policy they require per-volume. In this report, we describe how these features are implemented.
JF  - CERN Openlab
PB  - CERN
ER  - 

TY  - CONF
T1  - SANComSim: A Scalable, Adaptive and Non-intrusive Framework to Optimize Performance in Computational Science Applications
T2  - ICCS
Y1  - 2013
A1  - Alberto Nuñez
A1  - Rosa Filgueira
A1  - Mercedes G. Merayo
JF  - ICCS
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  - V-BOINC: The Virtualization of BOINC
T2  - In Proceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2013).
Y1  - 2013
A1  - Gary McGilvary
A1  - Barker, Adam
A1  - Ashley Lloyd
A1  - Malcolm Atkinson
AB  - The Berkeley Open Infrastructure for Network Computing (BOINC) is an open source client-server middleware system created to allow projects with large computational requirements, usually set in the scientific domain, to utilize a technically unlimited number of volunteer machines distributed over large physical distances. However various problems exist deploying applications over these heterogeneous machines using BOINC: applications must be ported to each machine architecture type, the project server must be trusted to supply authentic applications,  applications that do not regularly checkpoint may lose execution progress upon volunteer machine termination and applications that have dependencies may find it difficult to run under BOINC.    To solve such problems we introduce virtual BOINC, or V-BOINC, where virtual machines are used to run computations on volunteer machines. Application developers can then compile their applications on a single architecture, checkpointing issues are solved through virtualization API's and many security concerns are addressed via the virtual machine's sandbox environment. In this paper we focus on outlining a unique approach on how virtualization can be introduced into BOINC and demonstrate that V-BOINC offers acceptable computational performance when compared to regular BOINC. Finally we show that applications with dependencies can easily run under V-BOINC in turn increasing the computational potential volunteer computing offers to the general public and project developers.    V-BOINC can be downloaded at http://garymcgilvary.co.uk/vboinc.html
JF  - In Proceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2013).
CY  - Delft, The Netherlands
ER  - 

TY  - CONF
T1  - The W3C PROV family of specifications for modelling provenance metadata
T2  - EDBT
Y1  - 2013
A1  - Paolo Missier
A1  - Khalid Belhajjame
A1  - James Cheney
JF  - EDBT
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  - RPRT
T1  - Dispel Tutorial
Y1  - 2012
A1  - Paul Martin
KW  - Dispel
AB  - Dispel is a strongly-typed imperative language for generating executable workflows for data-intensive distributed applications, particularly (but not exclusively) for use in computational sciences such as bioinformatics, astronomy and seismology — it has been designed to be a portable lingua franca by which researchers can interact with complex distributed research infrastructures without detailed knowledge of the underlying computational middleware, all in order to more easily conduct experiments in data integration, simulation and data-intensive modelling.    This document is a tutorial for Dispel.
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  - JOUR
T1  - OMERO: flexible, model-driven data management for experimental biology
JF  - NATURE METHODS
Y1  - 2012
A1  - Chris Allan
A1  - Jean-Marie Burel
A1  - Josh Moore
A1  - Colin Blackburn
A1  - Melissa Linkert
A1  - Scott Loynton
A1  - Donald MacDonald
A1  - et al.
AB  - Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.
PB  - Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
VL  - 9
SN  - 1548-7091
UR  - http://dx.doi.org/10.1038/nmeth.1896
IS  - 3
ER  - 

TY  - JOUR
T1  - Requirements for Provenance on the Web
JF  - IJDC
Y1  - 2012
A1  - Paul T. Groth
A1  - Yolanda Gil
A1  - James Cheney
A1  - Simon Miles
VL  - 7
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  - 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  - Automatic Agent Protocol Generation from Argumentation
T2  - 13th European Agent Systems Summer Schoo
Y1  - 2011
A1  - Ashwag Omar Maghraby
JF  - 13th European Agent Systems Summer Schoo
ER  - 

TY  - CHAP
T1  - DISPEL Reference Manual
T2  - Advanced Data Mining and Integration Research for Europe (ADMIRE)
Y1  - 2011
A1  - Paul Martin
A1  - Yaikhom, Gagarine
KW  - DISPEL, ADMIRE
AB  - Reference manual for the Data Intensive Systems Process Engineering Language (DISPEL).
JF  - Advanced Data Mining and Integration Research for Europe (ADMIRE)
UR  - www.admire-project.eu
ER  - 

TY  - RPRT
T1  - EDIM1 Progress Report
Y1  - 2011
A1  - Paul Martin
A1  - Malcolm Atkinson
A1  - Parsons, Mark
A1  - Adam Carter
A1  - Gareth Francis
AB  - The Edinburgh Data-Intensive Machine (EDIM1) is the product of a joint collaboration between the data-intensive group at the School of Informatics and EPCC. EDIM1 is an experimental system, offering an alternative architecture for data-intensive computation and providing a platform for evaluating tools for data-intensive research; a 120 node cluster of ‘data-bricks’ with high storage yet modest computational capacity. This document gives some background into the context in which EDIM1 was designed and constructed, as well as providing an overview of its use so far and future plans.
ER  - 

TY  - JOUR
T1  - An evaluation of ontology matching in geo-service applications
JF  - Geoinformatica
Y1  - 2011
A1  - Lorenzino Vaccari
A1  - Pavel Shvaiko
A1  - Juan Pane
A1  - Paolo Besana
A1  - Maurizio Marchese
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  - Optimum Platform Selection and Configuration for Computational Jobs
T2  - All Hands Meeting 2011
Y1  - 2011
A1  - Gary McGilvary
A1  - Malcolm Atkinson
A1  - Barker, Adam
A1  - Ashley Lloyd
AB  - The performance and cost of many scientific applications which execute on a variety of High Performance Computing (HPC), local cluster environments and cloud services could be enhanced, and costs reduced if the platform was carefully selected on a per-application basis and the application itself was optimally configured for a given platform.    With a wide-variety of computing platforms on offer, each possessing different properties, all too frequently platform decisions are made on an ad-hoc basis with limited ‘black-box’ information. The limitless number of possible application configurations also make it difficult for an individual who wants to achieve cost-effective results with the maximum performance available. Such individuals may include biomedical researchers analysing microarray data, software developers running aviation simulations or bankers performing risk assessments. However in either case, it is likely that many may not have the required knowledge to select the optimum platform and setup for their application; to do so, would require extensive knowledge of their applications and various platforms.    In this paper we describe a framework that aims to resolve such issues by (i) reducing the detail required in the decision making process by placing this information within a selection framework, thereby (ii) maximising an application’s performance gain and/or reducing costs. We present a set of preliminary results where we compare the performance of running the Simple Parallel R INTerface (SPRINT) over a variety of platforms. SPRINT is a framework providing parallel functions of the statistical package R, allowing post genomic data to be easily analysed on HPC resources [1]. We run SPRINT on Amazon’s Elastic Compute Cloud (EC2) to compare the performance with the results obtained from HECToR, the UK’s National Supercomputing Service, and the Edinburgh Compute and Data Facilities (ECDF) cluster.
JF  - All Hands Meeting 2011
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  - 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  - RPRT
T1  - Data-Intensive Research Workshop (15-19 March 2010) Report
Y1  - 2010
A1  - Malcolm Atkinson
A1  - Roure, David De
A1  - van Hemert, Jano
A1  - Shantenu Jha
A1  - Ruth McNally
A1  - Robert Mann
A1  - Stratis Viglas
A1  - Chris Williams
KW  - Data-intensive Computing
KW  - Data-Intensive Machines
KW  - Machine Learning
KW  - Scientific Databases
AB  - We met at the National e-Science Institute in Edinburgh on 15-19 March 2010 to develop our understanding of DIR. Approximately 100 participants (see Appendix A) worked together to develop their own understanding, and we are offering this report as the first step in communicating that to a wider community.  We present this in turns of our developing/emerging understanding of "What is DIR?" and "Why it is important?'". We then review the status of the field, report what the workshop achieved and what remains as open questions.
JF  - National e-Science Centre
PB  - Data-Intensive Research Group, School of Informatics, University of Edinburgh
CY  - Edinburgh
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  - 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  - 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  - JOUR
T1  - Strategies and Policies to Support and Advance Education in e-Science
JF  - Computing Now
Y1  - 2009
A1  - Malcolm Atkinson
A1  - Elizabeth Vander Meer
A1  - Fergusson, David
A1  - Clive Davenhall
A1  - Hamza Mehammed
AB  - In previous installments of this series, we’ve presented tools and resources that university undergraduate and graduate environments must provide to allow for the continued development and success of e-Science education. We’ve introduced related summer (http://doi.ieeecomputersociety.org/ 10.1109/MDSO.2008.20) and winter (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.26) schools and important issues such as t-Infrastructure provision (http://doi.ieeecomputersociety.org/ 10.1109/MDSO.2008.28), intellectual property rights in the context of digital repositories (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.34), and curriculum content (http://www2. computer.org/portal/web/computingnow/0309/education). We conclude now with an overview of areas in which we must focus effort and strategies and policies that could provide much-needed support in these areas.    We direct these strategy and policy recommendations toward key stakeholders in e-Science education, such as ministries of education, councils in professional societies, and professional teachers and educational strategists. Ministries of education can influence funding councils, thus financially supporting our proposals. Professional societies can assist in curricula revision, and teachers and strategists shape curricula in institutions, which makes them valuable in improving and developing education in e-Science and (perhaps) e-Science in education.    We envision incremental change in curricula, so our proposals aim to evolve existing courses, rather than suggesting drastic upheavals and isolated additions. The long-term goal is to ensure that every graduate obtains the appropriate level of e-Science competency for their field, but we don’t presume to define that level for any given discipline or institution. We set out issues and ideas but don’t offer rigid prescriptions, which would take control away from important stakeholders.
UR  - http://www.computer.org/portal/web/computingnow/education
ER  - 

TY  - JOUR
T1  - Distributed Computing Education, Part 3: The Winter School Online Experience
JF  - Distributed Systems Online
Y1  - 2008
A1  - Low, B.
A1  - Cassidy, K.
A1  - Fergusson, D.
A1  - Atkinson, M.
A1  - Vander Meer, E.
A1  - McGeever, M.
AB  - The International Summer Schools in Grid Computing (ISSGC) have provided numerous international students with the opportunity to learn grid systems, as detailed in part 2 of this series (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.20). The International Winter School on Grid Computing 2008 (IWSGC 08) followed the successful summer schools, opening up the ISSGC experience to a wider range of students because of its online format. The previous summer schools made it clear that many students found the registration and travel costs and the time requirements prohibitive. The EU FP6 ICEAGE project held the first winter school from 6 February to 12 March 2008. The winter school repurposed summer school materials and added resources such as the ICEAGE digital library and summer-school-tested t-Infrastructures such as GILDA (Grid INFN Laboratory for Dissemination Activities).    The winter schools shared the goals of the summer school, which emphasized disseminating grid knowledge. The students act as multipliers, spreading the skills and knowledge they acquired at the winter school to their colleagues to build strong and enthusiastic local grid communities.
PB  - IEEE Computer Society
VL  - 9
UR  - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4659260
IS  - 9
ER  - 

TY  - JOUR
T1  - Distributed Computing Education, Part 5: Coming to Terms with Intellectual Property Rights
JF  - Distributed Systems Online
Y1  - 2008
A1  - Boon Low
A1  - Kathryn Cassidy
A1  - Fergusson, David
A1  - Malcolm Atkinson
A1  - Elizabeth Vander Meer
A1  - Mags McGeever
AB  - In part 1 of this series on distributed computing education, we introduced a list of components important for teaching environments. We outlined the first three components, which included development of materials for education, education for educators and teaching infrastructures, identifying current practice, challenges, and opportunities for provision. The final component, a supportive policy framework that encourages cooperation and sharing, includes the need to manage intellectual property rights (IPR).
PB  - IEEE Computer Society
VL  - 9
UR  - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4755177
IS  - 12
ER  - 

TY  - CONF
T1  - Fostering e-Infrastructures: from user-designer relations to community engagement
T2  - Symposium on Project Management in e-Science
Y1  - 2008
A1  - Voss, A.
A1  - Asgari-Targhi, M.
A1  - Halfpenny, P.
A1  - Procter, R.
A1  - Anderson, S.
A1  - Dunn, S.
A1  - Fragkouli, E.
A1  - Hughes, L.
A1  - Atkinson, M.
A1  - Fergusson, D.
A1  - Mineter, M.
A1  - Rodden, T.
AB  - In this paper we discuss how e-Science can draw on the findings, approaches and methods developed in other disciplines to foster e-Infrastructures for research. We also discuss the issue of making user involvement in IT development scale across an open ommunity of researchers and from single systems to distributed e-Infrastructures supporting collaborative research.
JF  - Symposium on Project Management in e-Science
CY  - Oxford
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  - JOUR
T1  - The interactive European Grid: Project objectives and achievements
JF  - Computing and Informatics
Y1  - 2008
A1  - J Marco
A1  - Campos, I.
A1  - Coterillo, I.
A1  - Diaz, I.
A1  - Lopez, A.
A1  - Marco,  R.
A1  - Martinez-Rivero, C.
A1  - Orviz, P.
A1  - Rodríguez, David
A1  - Gomes, J.
A1  - Borges, G.
A1  - Montecelo, M.
A1  - David, M.
A1  - Silva, B.
A1  - Dias, N.
A1  - Martins, JP
A1  - Fernandez, C.
A1  - Garcia-Tarres, L.
VL  - 27
IS  - 2
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  - Widening Uptake of e-Infrastructure Services
T2  - 4th International Conference on e-Social Science
Y1  - 2008
A1  - Voss, A.
A1  - Asgari-Targhi, M.
A1  - Procter, R.
A1  - Halfpenny, P.
A1  - Dunn, S.
A1  - Fragkouli, E.
A1  - Anderson, S.
A1  - Hughes, L.
A1  - Mineter, M.
A1  - Fergusson, D.
A1  - Atkinson, M.
AB  - This paper presents findings from the e-Uptake project which aims to widen the uptake of e-Infrastructure Services for research. We focus specifically on the identification of barriers and enablers of uptake and the taxonomy developed to structure our findings. Based on these findings, we describe the development of a number of interventions such as training and outreach events, workshops and the deployment of a UK 'one-stop-shop' for support and event information as well as training material. Finally, we will describe how the project relates to other ongoing community engagement efforts in the UK and worldwide. Introduction Existing investments in e-Science and Grid computing technologies have helped to develop the capacity to build e-Infrastructures for research: distributed, networked, interoperable computing and data resources that are available to underpin a wide range of research activities in all research disciplines. In the UK, the Research Councils and the JISC are funding programmes to support the development of essential components of such infrastructures such as National Grid Service (www.ngs.ac.uk) or the UK Access Management Federation (www.ukfederation.org.uk) as well as discipline-specific efforts to build consistent and accessible instantiations of e-Infrastructures, for example the e- Infrastructure for the Social Sciences (Daw et al. 2007). These investments are complemented by an active programme of community engagement (Voss et al. 2007). As part of the community engagement strand of its e-Infrastructure programme, JISC has funded the e-Uptake project, a collaboration between the ESRC National Centre for e-Social Science at the University of Manchester, the Arts & Humanities e-Science Support Centre at King's College London and the National e-Science Centre at the University of Edinburgh. In this paper we present the project's activities to date to widen the uptake of e-Infrastructure services by eliciting information about the barriers to and enablers of uptake, developing adequate interventions such as training and outreach events, running workshops and the deploying a UK 'one-stop-shop' for support and event information as well as training material.
JF  - 4th International Conference on e-Social Science
CY  - Manchester
UR  - http://www.ncess.ac.uk/events/conference/programme/workshop1/?ref=/programme/thurs/1aVoss.htm
ER  - 

TY  - CONF
T1  - The Architectural Design of Multi Interface-Device Binding (MID-B) System
T2  - The 3rd Workshop on Context Awareness for Proactive Systems
Y1  - 2007
A1  - Srihathai Prammanee
A1  - Klaus Moessner
AB  - The Multi Interface-Device Binding (MID-B) System enhances a multimodal interaction in a virtual-device environment. The system promises to overcome the drawbacks of classic multimodal interaction. In the classic sense,  multimodality uses a strategy of simultaneously utilising several modalities  generally offered on a single device. In contrast, the MID-B’s mechanism gets  multimodality out of the solitary-device scenario. In MID-B, a ‘controller- device’ (UE_C) is aware of the availability of various devices in the vicinity,  each of which may host one or more user interfaces (modalities). The   capabilities of each of the co-located devices, together with the context in which the user acts, is exploited to dynamically customise the interface services available. This paper describes the MID-B architecture and its mechanisms to collect and exploit device and user context information to dynamically adapt the user interfaces.
JF  - The 3rd Workshop on Context Awareness for Proactive Systems
CY  - Guildford, UK
UR  - http://www.geocities.com/sprammanee/
ER  - 

TY  - CONF
T1  - Data Integration in eHealth: A Domain/Disease Specific Roadmap
T2  - Studies in Health Technology and Informatics
Y1  - 2007
A1  - Ure, J.
A1  - Proctor, R.
A1  - Martone, M.
A1  - Porteous, D.
A1  - Lloyd, S.
A1  - Lawrie, S.
A1  - Job, D.
A1  - Baldock, R.
A1  - Philp, A.
A1  - Liewald, D.
A1  - Rakebrand, F.
A1  - Blaikie, A.
A1  - McKay, C.
A1  - Anderson, S.
A1  - Ainsworth, J.
A1  - van Hemert, J.
A1  - Blanquer, I.
A1  - Sinno
ED  - N. Jacq
ED  - Y. Legr{\'e}
ED  - H. Muller
ED  - I. Blanquer
ED  - V. Breton
ED  - D. Hausser
ED  - V. Hern{\'a}ndez
ED  - T. Solomonides
ED  - M. Hofman-Apitius
KW  - e-Science
AB  - The paper documents a series of data integration workshops held in 2006 at the UK National e-Science Centre, summarizing a range of the problem/solution scenarios in multi-site and multi-scale data integration with six HealthGrid projects using schizophrenia as a domain-specific test case. It outlines   emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain.
JF  - Studies in Health Technology and Informatics
PB  - IOPress
VL  - 126
SN  - 978-1-58603-738-3
ER  - 

TY  - CONF
T1  - e-Research Infrastructure Development and Community Engagement
T2  - All Hands Meeting 2007
Y1  - 2007
A1  - Voss, A.
A1  - Mascord, M.
A1  - Fraser, M.
A1  - Jirotka, M.
A1  - Procter, R.
A1  - Halfpenny, P.
A1  - Fergusson, D.
A1  - Atkinson, M.
A1  - Dunn, S.
A1  - Blanke, T.
A1  - Hughes, L.
A1  - Anderson, S.
AB  - The UK and wider international e-Research initiatives are entering a critical phase in which they need to move from the development of the basic underlying technology, demonstrators, prototypes and early applications to wider adoption and the development of stable infrastructures. In this paper we will review existing work on studies of infrastructure and community development, requirements elicitation for existing services as well as work within the arts and humanities and the social sciences to establish e-Research in these communities. We then describe two projects recently funded by JISC to study barriers to adoption and responses to them as well as use cases and service usage models.
JF  - All Hands Meeting 2007
CY  - Nottingham, UK
ER  - 

TY  - CONF
T1  - Interaction as a Grounding for Peer to Peer Knowledge Sharing
T2  - Advances in Web Semantics
Y1  - 2007
A1  - Robertson, D.
A1  - Walton, C.
A1  - Barker, A.
A1  - Besana, P.
A1  - Chen-Burger, Y.
A1  - Hassan, F.
A1  - Lambert, D.
A1  - Li, G.
A1  - McGinnis, J
A1  - Osman, N.
A1  - Bundy, A.
A1  - McNeill, F.
A1  - van Harmelen, F.
A1  - Sierra, C.
A1  - Giunchiglia, F.
JF  - Advances in Web Semantics
PB  - LNCS-IFIP
VL  - 1
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  - Towards a Grid-Enabled Simulation Framework for Nano-CMOS Electronics
T2  - 3rd IEEE International Conference on eScience and Grid Computing
Y1  - 2007
A1  - Liangxiu Han
A1  - Asen Asenov
A1  - Dave Berry
A1  - Campbell Millar
A1  - Gareth Roy
A1  - Scott Roy
A1  - Richard Sinnott
A1  - Gordon Stewart
AB  - The electronics design industry is facing major challenges as transistors continue to decrease in size.  The next generation of devices will be so small that the position of individual atoms will affect their behaviour.  This will cause the transistors on a chip to have highly variable characteristics, which in turn will impact  circuit and system design tools. The EPSRC project “Meeting the Design Challenges of Nano-CMOS  Electronics” (Nano-CMOS) has been funded to explore this area. In this paper, we describe the  distributed data-management and computing framework under development within Nano-CMOS. A  key aspect of this framework is the need for robust and reliable security mechanisms that support distributed  electronics design groups who wish to collaborate by sharing designs, simulations, workflows, datasets and  computation resources. This paper presents the system design, and an early prototype of the project which hasbeen useful in helping us to understand the benefits of such a grid infrastructure. In particular, we also present two typical use cases: user authentication, and execution of large-scale device simulations.
JF  - 3rd IEEE International Conference on eScience and Grid Computing
PB  - IEEE Computer Society
CY  - Bangalore, India
ER  - 

TY  - CONF
T1  - FireGrid: Integrated emergency response and fire safety engineering for the future built environment
T2  - All Hands Meeting 2005
Y1  - 2006
A1  - D. Berry
A1  - Usmani, A.
A1  - Torero, J.
A1  - Tate, A.
A1  - McLaughlin, S.
A1  - Potter, S.
A1  - Trew, A.
A1  - Baxter, R.
A1  - Bull, M.
A1  - Atkinson, M.
AB  - Analyses of disasters such as the Piper Alpha explosion (Sylvester-Evans and Drysdale, 1998), the World Trade Centre collapse (Torero et al, 2002, Usmani et al, 2003) and the fires at Kings Cross (Drysdale et al, 1992) and the Mont Blanc tunnel (Rapport Commun, 1999) have revealed many mistaken decisions, such as that which sent 300 fire-fighters to their deaths in the World Trade Centre. Many of these mistakes have been attributed to a lack of information about the conditions within the fire and the imminent consequences of the event.    E-Science offers an opportunity to significantly improve the intervention in fire emergencies. The FireGrid Consortium is working on a mixture of research projects to make this vision a reality. This paper describes the research challenges and our plans for solving them.
JF  - All Hands Meeting 2005
CY  - Nottingham, UK
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  - Cross-Layer Peer-to-Peer Traffic Identification and Optimization Based on Active Networking
T2  - 7th International Working Conference on Active and Programmable Networks
Y1  - 2005
A1  - Dedinski, I.
A1  - De Meer, H.
A1  - Liangxiu Han
A1  - Mathy, L.
A1  - Pezaros, D.
A1  - P. , Sventek, J. S.
A1  - Xiaoying, Z.
JF  - 7th International Working Conference on Active and Programmable Networks
CY  - Sophia Antipolis, French Riviera, La Cote d'Azur, France, November 21-23, 2005.
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  - 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  - CONF
T1  - Dynamic Routing Problems with Fruitful Regions: Models and Evolutionary Computation
T2  - LNCS
Y1  - 2004
A1  - van Hemert, J. I.
A1  - la Poutré, J. A.
ED  - Xin Yao
ED  - Edmund Burke
ED  - Jose A. Lozano
ED  - Jim Smith
ED  - Juan J. Merelo-Guerv\'os
ED  - John A. Bullinaria
ED  - Jonathan Rowe
ED  - Peter Ti\v{n}o Ata Kab\'an
ED  - Hans-Paul Schwefel
KW  - dynamic problems
KW  - evolutionary computation
KW  - vehicle routing
AB  - We introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the problem is being solved, which makes it a real-time routing problem. The solver is a self-adaptive evolutionary algorithm that ensures feasible solutions at all times. We investigate under what conditions the exploration of fruitful regions improves the effectiveness of the evolutionary algorithm.
JF  - LNCS
PB  - Springer-Verlag
CY  - Birmingham, UK
VL  - 3242
SN  - 3-540-23092-0
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  - CONF
T1  - Phase transition properties of clustered travelling salesman problem instances generated with evolutionary computation
T2  - LNCS
Y1  - 2004
A1  - van Hemert, J. I.
A1  - Urquhart, N. B.
ED  - Xin Yao
ED  - Edmund Burke
ED  - Jose A. Lozano
ED  - Jim Smith
ED  - Juan J. Merelo-Guerv\'os
ED  - John A. Bullinaria
ED  - Jonathan Rowe
ED  - Peter Ti\v{n}o Ata Kab\'an
ED  - Hans-Paul Schwefel
KW  - evolutionary computation
KW  - problem evolving
KW  - travelling salesman
AB  - This paper introduces a generator that creates problem instances for the Euclidean symmetric travelling salesman problem. To fit real world problems, we look at maps consisting of clustered nodes. Uniform random sampling methods do not result in maps where the nodes are spread out to form identifiable clusters. To improve upon this, we propose an evolutionary algorithm that uses the layout of nodes on a map as its genotype. By optimising the spread until a set of constraints is satisfied, we are able to produce better clustered maps, in a more robust way. When varying the number of clusters in these maps and, when solving the Euclidean symmetric travelling salesman person using Chained Lin-Kernighan, we observe a phase transition in the form of an easy-hard-easy pattern.
JF  - LNCS
PB  - Springer-Verlag
CY  - Birmingham, UK
VL  - 3242
SN  - 3-540-23092-0
UR  - http://www.vanhemert.co.uk/files/clustered-phase-transition-tsp.tar.gz
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  - Comparing Classical Methods for Solving Binary Constraint Satisfaction Problems with State of the Art Evolutionary Computation
T2  - Springer Lecture Notes on Computer Science
Y1  - 2002
A1  - van Hemert, J. I.
ED  - S. Cagnoni
ED  - J. Gottlieb
ED  - E. Hart
ED  - M. Middendorf
ED  - G. Raidl
KW  - constraint satisfaction
AB  - Constraint Satisfaction Problems form a class of problems that are generally computationally difficult and have been addressed with many complete and heuristic algorithms. We present two complete algorithms, as well as two evolutionary algorithms, and compare them on randomly generated instances of binary constraint satisfaction prob-lems. We find that the evolutionary algorithms are less effective than the classical techniques.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
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  - Adaptive Genetic Programming Applied to New and Existing Simple Regression Problems
T2  - Springer Lecture Notes on Computer Science
Y1  - 2001
A1  - Eggermont, J.
A1  - van Hemert, J. I.
ED  - J. Miller
ED  - Tomassini, M.
ED  - P. L. Lanzi
ED  - C. Ryan
ED  - A. G. B. Tettamanzi
ED  - W. B. Langdon
KW  - data mining
AB  - In this paper we continue our study on adaptive genetic pro-gramming. We use Stepwise Adaptation of Weights to boost performance of a genetic programming algorithm on simple symbolic regression problems. We measure the performance of a standard GP and two variants of SAW extensions on two different symbolic regression prob-lems from literature. Also, we propose a model for randomly generating polynomials which we then use to further test all three GP variants.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
SN  - 9-783540-418993
ER  - 

TY  - CONF
T1  - Evolutionary Computation in Constraint Satisfaction and Machine Learning --- An abstract of my PhD.
T2  - Proceedings of the Brussels Evolutionary Algorithms Day (BEAD-2001)
Y1  - 2001
A1  - van Hemert, J. I.
ED  - Anne Defaweux
ED  - Bernard Manderick
ED  - Tom Lenearts
ED  - Johan Parent
ED  - Piet van Remortel
KW  - constraint satisfaction
KW  - data mining
JF  - Proceedings of the Brussels Evolutionary Algorithms Day (BEAD-2001)
PB  - Vrije Universiteit Brussel (VUB)
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  - CHAP
T1  - Persistence and Java — A Balancing Act
T2  - Objects and Databases
Y1  - 2001
A1  - Atkinson, M.
ED  - Klaus Dittrich
ED  - Giovanna Guerrini
ED  - Isabella Merlo
ED  - Marta Oliva
ED  - M. Elena Rodriguez
AB  - Large scale and long-lived application systems, enterprise applications, require persistence, that is provision of storage for many of their data structures. The JavaTM programming language is a typical example of a strongly-typed, object-oriented programming language that is becoming popular for building enterprise applications. It therefore needs persistence. The present options for obtaining this persistence are reviewed. We conclude that the Orthogonal Persistence Hypothesis, OPH, is still persuasive. It states that the universal and automated provision of longevity or brevity for all data will significantly enhance developer productivity and improve applications. This position paper reports on the PJama project with particular reference to its test of the OPH. We review why orthogonal persistence has not been taken up widely, and why the OPH is still incompletely tested. This leads to a more general challenge of how to conduct experiments which reveal large-scale and long-term effects and some thoughts on how that challenge might be addressed by the software research community.
JF  - Objects and Databases
T3  - Lecture Notes in Computer Science
PB  - Springer
VL  - 1944
UR  - http://www.springerlink.com/content/8t7x3m1ehtdqk4bm/?p=7ece1338fff3480b83520df395784cc6&pi=0
ER  - 

TY  - CONF
T1  - Extended abstract: Solving Binary Constraint Satisfaction Problems using Evolutionary Algorithms with an Adaptive Fitness Function
T2  - Proceedings of the Xth Netherlands/Belgium Conference on Artificial Intelligence (NAIC'98)
Y1  - 1998
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
A1  - Marchiori, E.
A1  - Steenbeek, A. G.
ED  - la Poutré, J. A.
ED  - van den Herik, J.
KW  - constraint satisfaction
JF  - Proceedings of the Xth Netherlands/Belgium Conference on Artificial Intelligence (NAIC'98)
PB  - BNVKI, Dutch and the Belgian AI Association
N1  - Abstract of \cite{EHMS98}
ER  - 

TY  - CONF
T1  - Solving Binary Constraint Satisfaction Problems using Evolutionary Algorithms with an Adaptive Fitness Function
T2  - Springer Lecture Notes on Computer Science
Y1  - 1998
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
A1  - Marchiori, E.
A1  - Steenbeek, A. G.
ED  - Eiben, A. E.
ED  - Th. B{\"a}ck
ED  - M. Schoenauer
ED  - H.-P. Schwefel
KW  - constraint satisfaction
AB  - This paper presents a comparative study of Evolutionary Algorithms (EAs) for Constraint Satisfaction Problems (CSPs). We focus on EAs where fitness is based on penalization of constraint violations and the penalties are adapted during the execution. Three different EAs based on this approach are implemented. For highly connected constraint networks, the results provide further empirical support to the theoretical prediction of the phase transition in binary CSPs.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
ER  -