TY - JOUR T1 - Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography JF - Ophthalmic Surg Lasers Imaging Retina Y1 - 2014 A1 - Croft, D.E. A1 - van Hemert, J. A1 - Wykoff, C.C. A1 - Clifton, D. A1 - Verhoek, M. A1 - Fleming, A. A1 - Brown, D.M. KW - medical KW - retinal imaging AB - BACKGROUND AND OBJECTIVE: Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. PATIENTS AND METHODS: Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. RESULTS: Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. CONCLUSION: By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. [Ophthalmic Surg Lasers Imaging Retina. 2014;45:312-317.]. VL - 45 ER - TY - JOUR T1 - Quantification of Ultra-Widefield Retinal Images JF - Retina Today Y1 - 2014 A1 - D.E. Croft A1 - C.C. Wykoff A1 - D.M. Brown A1 - van Hemert, J. A1 - M. Verhoek KW - medical KW - retinal imaging AB - Advances in imaging periodically lead to dramatic changes in the diagnosis, management, and study of retinal disease. For example, the innovation and wide-spread application of fluorescein angiography and optical coherence tomography (OCT) have had tremendous impact on the management of retinal disorders.1,2 Recently, ultra-widefield (UWF) imaging has opened a new window into the retina, allowing the capture of greater than 80% of the fundus with a single shot.3 With montaging, much of the remaining retinal surface area can be captured.4,5 However, to maximize the potential of these new modalities, accurate quantification of the pathology they capture is critical. UR - http://www.bmctoday.net/retinatoday/pdfs/0514RT_imaging_Croft.pdf ER - TY - JOUR T1 - Lesion Area Detection Using Source Image Correlation Coefficient for CT Perfusion Imaging JF - IEEE Journal of Biomedical and Health Informatics Y1 - 2013 A1 - Fan Zhu A1 - Rodríguez, David A1 - Carpenter, Trevor K. A1 - Atkinson, Malcolm P. A1 - Wardlaw, Joanna M. KW - CT , Pattern Recognition , Perfusion Source Images , Segmentation AB - Computer tomography (CT) perfusion imaging is widely used to calculate brain hemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that aid the diagnosis of acute stroke. Since perfusion source images contain more information than hemodynamic maps, good utilisation of the source images can lead to better understanding than the hemodynamic maps alone. Correlation-coefficient tests are used in our approach to measure the similarity between healthy tissue time-concentration curves and unknown curves. This information is then used to differentiate penumbra and dead tissues from healthy tissues. The goal of the segmentation is to fully utilize information in the perfusion source images. Our method directly identifies suspected abnormal areas from perfusion source images and then delivers a suggested segmentation of healthy, penumbra and dead tissue. This approach is designed to handle CT perfusion images, but it can also be used to detect lesion areas in MR perfusion images. VL - 17 IS - 5 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 - JOUR T1 - Computed Tomography Perfusion Imaging Denoising Using Gaussian Process Regression JF - Physics in Medicine and Biology Y1 - 2012 A1 - Fan Zhu A1 - Carpenter, Trevor A1 - Rodríguez, David A1 - Malcolm Atkinson A1 - Wardlaw, Joanna AB - Objective: Brain perfusion weighted images acquired using dynamic contrast studies have an important clinical role in acute stroke diagnosis and treatment decisions. However, Computed Tomography (CT) images suffer from low contrast-to-noise ratios (CNR) as a consequence of the limitation of the exposure to radiation of the patient. As a consequence, the developments of methods for improving the CNR are valuable. Methods: The majority of existing approaches for denoising CT images are optimized for 3D (spatial) information, including spatial decimation (spatially weighted mean filters) and techniques based on wavelet and curvelet transforms. However, perfusion imaging data is 4D as it also contains temporal information. Our approach using Gaussian process regression (GPR), which takes advantage of the temporal information, to reduce the noise level. Results: Over the entire image, GPR gains a 99% CNR improvement over the raw images and also improves the quality of haemodynamic maps allowing a better identification of edges and detailed information. At the level of individual voxel, GPR provides a stable baseline, helps us to identify key parameters from tissue time- concentration curves and reduces the oscillations in the curve. Conclusion: GPR is superior to the comparable techniques used in this study. ER - TY - CONF T1 - A databank, rather than statistical, model of normal ageing brain structure to indicate pathology T2 - OHBM 2012 Y1 - 2012 A1 - Dickie, David Alexander A1 - Dominic Job A1 - Rodríguez, David A1 - Shenkin, Susan A1 - Wardlaw, Joanna JF - OHBM 2012 UR - http://ww4.aievolution.com/hbm1201/index.cfm?do=abs.viewAbs&abs=5102 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 - Parallel perfusion imaging processing using GPGPU JF - Computer Methods and Programs in Biomedicine Y1 - 2012 A1 - Fan Zhu A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Malcolm Atkinson A1 - Wardlaw, Joanna KW - Deconvolution KW - GPGPU KW - Local AIF KW - Parallelization KW - Perfusion Imaging AB - Background and purpose The objective of brain perfusion quantification is to generate parametric maps of relevant hemodynamic quantities such as cerebral blood flow (CBF), cerebral blood volume (CBV) and mean transit time (MTT) that can be used in diagnosis of acute stroke. These calculations involve deconvolution operations that can be very computationally expensive when using local Arterial Input Functions (AIF). As time is vitally important in the case of acute stroke, reducing the analysis time will reduce the number of brain cells damaged and increase the potential for recovery. Methods GPUs originated as graphics generation dedicated co-processors, but modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its large number of computing cores and constitutes an affordable high performance computing method. In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. We present the serial and parallel implementations of such algorithms and the evaluation of the performance gains using GPUs. Results Our method has gained a 5.56 and 3.75 speedup for CT and MR images respectively. Conclusions It seems that using GPGPU is a desirable approach in perfusion imaging analysis, which does not harm the quality of cerebral hemodynamic maps but delivers results faster than the traditional computation. UR - http://www.sciencedirect.com/science/article/pii/S0169260712001587 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 - 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 - 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 - CONF T1 - A Parallel Deconvolution Algorithm in Perfusion Imaging T2 - Healthcare Informatics, Imaging, and Systems Biology (HISB) Y1 - 2011 A1 - Zhu, Fan. A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Malcolm Atkinson A1 - Wardlaw, Joanna KW - Deconvolution KW - GPGPU KW - Parallelization KW - Perfusion Imaging AB - In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. GPUs originated as graphics generation dedicated co-processors, but the modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its huge number of computing cores and constitutes an affordable high performance computing method. The objective of brain perfusion quantification is to generate parametric maps of relevant haemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that can be used in diagnosis of conditions such as stroke or brain tumors. These calculations involve deconvolution operations that in the case of using local Arterial Input Functions (AIF) can be very expensive computationally. We present the serial and parallel implementations of such algorithm and the evaluation of the performance gains using GPUs. JF - Healthcare Informatics, Imaging, and Systems Biology (HISB) CY - San Jose, California SN - 978-1-4577-0325-6 UR - http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6061411&tag=1 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 - 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 - 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 - An open source toolkit for medical imaging de-identification JF - European Radiology Y1 - 2010 A1 - Rodríguez, David A1 - Carpenter, Trevor K. A1 - van Hemert, Jano I. A1 - Wardlaw, Joanna M. KW - Anonymisation KW - Data Protection Act (DPA) KW - De-identification KW - Digital Imaging and Communications in Medicine (DICOM) KW - Privacy policies KW - Pseudonymisation KW - Toolkit AB - Objective Medical imaging acquired for clinical purposes can have several legitimate secondary uses in research projects and teaching libraries. No commonly accepted solution for anonymising these images exists because the amount of personal data that should be preserved varies case by case. Our objective is to provide a flexible mechanism for anonymising Digital Imaging and Communications in Medicine (DICOM) data that meets the requirements for deployment in multicentre trials. Methods We reviewed our current de-identification practices and defined the relevant use cases to extract the requirements for the de-identification process. We then used these requirements in the design and implementation of the toolkit. Finally, we tested the toolkit taking as a reference those requirements, including a multicentre deployment. Results The toolkit successfully anonymised DICOM data from various sources. Furthermore, it was shown that it could forward anonymous data to remote destinations, remove burned-in annotations, and add tracking information to the header. The toolkit also implements the DICOM standard confidentiality mechanism. Conclusion A DICOM de-identification toolkit that facilitates the enforcement of privacy policies was developed. It is highly extensible, provides the necessary flexibility to account for different de-identification requirements and has a low adoption barrier for new users. VL - 20 UR - http://www.springerlink.com/content/j20844338623m167/ IS - 8 ER - TY - CONF T1 - Resource management of enterprise cloud systems using layered queuing and historical performance models T2 - IEEE International Symposium on Parallel Distributed Processing Y1 - 2010 A1 - Bacigalupo, D. A. A1 - van Hemert, J. A1 - Usmani, A. A1 - Dillenberger, D. N. A1 - Wills, G. B. A1 - Jarvis, S. A. 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. It is important to quantitatively compare the effectiveness of different prediction techniques for use in cloud infrastructures. To help make the comparison of relevance to a wide range of possible cloud environments it is useful to consider the following. 1.) urgent cloud customers such as the emergency services that can demand cloud resources at short notice (e.g. for our FireGrid emergency response software). 2.) dynamic enterprise systems, that must rapidly adapt to frequent changes in workload, system configuration and/or available cloud servers. 3.) The use of the predictions in a coordinated manner by both the cloud infrastructure and cloud customer management systems. 4.) A broad range of criteria for evaluating each technique. However, there have been no previous comparisons meeting these requirements. This paper, meeting the above requirements, quantitatively compares the layered queuing and (\^A¿HYDRA\^A¿) historical techniques - including our initial thoughts on how they could be combined. Supporting results and experiments include the following: i.) defining, investigating and hence providing guidelines on the use of a historical and layered queuing model; ii.) using these guidelines showing that both techniques can make low overhead and typically over 70% accurate predictions, for new server architectures for which only a small number of benchmarks have been run; and iii.) defining and investigating tuning a prediction-based cloud workload and resource management algorithm. JF - IEEE International Symposium on Parallel Distributed Processing ER - TY - RPRT T1 - ADMIRE D1.5 – Report defining an iteration of the model and language: PM3 and DL3 Y1 - 2009 A1 - Peter Brezany A1 - Ivan Janciak A1 - Alexander Woehrer A1 - Carlos Buil Aranda A1 - Malcolm Atkinson A1 - van Hemert, Jano AB - This document is the third deliverable to report on the progress of the model, language and ontology research conducted within Workpackage 1 of the ADMIRE project. Significant progress has been made on each of the above areas. The new results that we achieved are recorded against the targets defined for project month 18 and are reported in four sections of this document PB - ADMIRE project UR - http://www.admire-project.eu/docs/ADMIRE-D1.5-model-language-ontology.pdf 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 - The Circulate Architecture: Avoiding Workflow Bottlenecks Caused By Centralised Orchestration JF - Cluster Computing Y1 - 2009 A1 - Barker, A. A1 - Weissman, J. A1 - van Hemert, J. I. KW - grid computing KW - workflow VL - 12 UR - http://www.springerlink.com/content/080q5857711w2054/?p=824749739c6a432ea95a0c3b59f4025f&pi=1 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 - CONF T1 - An Architecture for an Integrated Fire Emergency Response System for the Built Environment T2 - 9th Symposium of the International Association for Fire Safety Science (IAFSS) Y1 - 2008 A1 - Rochan Upadhyay A1 - Galvin Pringle A1 - George Beckett A1 - Stephen Potter A1 - Liangxiu Han A1 - Stephen Welch A1 - Asif Usmani A1 - Jose Torero KW - emergency response system KW - FireGrid KW - system architecture KW - technology integration AB - FireGrid is a modern concept that aims to leverage a number of modern technologies to aid fire emergency response. In this paper we provide a brief introduction to the FireGrid project. A number of different technologies such as wireless sensor networks, grid-enabled High Performance Computing (HPC) implementation of fire models, and artificial intelligence tools need to be integrated to build up a modern fire emergency response system. We propose a system architecture that provides the framework for integration of the various technologies. We describe the components of the generic FireGrid system architecture in detail. Finally we present a small-scale demonstration experiment which has been completed to highlight the concept and application of the FireGrid system to an actual fire. Although our proposed system architecture provides a versatile framework for integration, a number of new and interesting research problems need to be solved before actual deployment of the system. We outline some of the challenges involved which require significant interdisciplinary collaborations. JF - 9th Symposium of the International Association for Fire Safety Science (IAFSS) PB - IAFSS CY - Karlsruhe, GERMANY ER - TY - CONF T1 - Eliminating the Middle Man: Peer-to-Peer Dataflow T2 - HPDC '08: Proceedings of the 17th International Symposium on High Performance Distributed Computing Y1 - 2008 A1 - Barker, Adam A1 - Weissman, Jon B. A1 - van Hemert, Jano KW - grid computing KW - workflow JF - HPDC '08: Proceedings of the 17th International Symposium on High Performance Distributed Computing PB - ACM ER - TY - CONF T1 - Orchestrating Data-Centric Workflows T2 - The 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid) Y1 - 2008 A1 - Barker, Adam A1 - Weissman, Jon B. A1 - van Hemert, Jano KW - grid computing KW - workflow JF - The 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid) PB - IEEE Computer Society 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 - 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 - Generic T1 - Special Issue: Selected Papers from the 2004 U.K. e-Science All Hands Meeting T2 - All Hands Meeting 2004 Y1 - 2007 A1 - Walker, D. W. A1 - Atkinson, M. P. A1 - Sommerville, I. ED - Walker, D. W. ED - Atkinson, M. P. ED - Sommerville, I. JF - All Hands Meeting 2004 T3 - Concurrency and Computation: Practice and Experience PB - John Wiley & Sons Ltd CY - Nottingham, UK VL - 19 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 - 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 - 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 - Web Service Grids: an evolutionary approach JF - Concurrency - Practice and Experience Y1 - 2005 A1 - Atkinson, Malcolm P. A1 - Roure, David De A1 - Dunlop, Alistair N. A1 - Fox, Geoffrey A1 - Henderson, Peter A1 - Hey, Anthony J. G. A1 - Paton, Norman W. A1 - Newhouse, Steven A1 - Parastatidis, Savas A1 - Trefethen, Anne E. A1 - Watson, Paul A1 - Webber, Jim VL - 17 ER - TY - Generic T1 - Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data T2 - All Hands Meeting 2004 Y1 - 2004 A1 - Richard Sinnott A1 - Malcolm Atkinson A1 - Micha Bayer A1 - Dave Berry A1 - Anna Dominiczak A1 - Magnus Ferrier A1 - David Gilbert A1 - Neil Hanlon A1 - Derek Houghton A1 - Hunt, Ela A1 - David White AB - The BRIDGES project is a UK e-Science project that provides grid based support for biomedical research into the genetics of hypertension – the Cardiovascular Functional Genomics Project (CFG). Its main goal is to provide an effective environment for CFG, and biomedical research in general, including access to integrated data, analysis and visualization, with appropriate authorisation and privacy, as well as grid based computational tools and resources. It also aims to provide an improved understanding of the requirements of academic biomedical research virtual organizations and to evaluate the utility of existing data federation tools. JF - All Hands Meeting 2004 CY - Nottingham, UK UR - http://www.allhands.org.uk/2004/proceedings/papers/87.pdf ER - TY - CONF T1 - 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 - RPRT T1 - Web Service Grids: An Evolutionary Approach Y1 - 2004 A1 - Malcolm Atkinson A1 - Roure, David De A1 - Alistair Dunlop A1 - Fox, Geoffrey A1 - Henderson, Peter A1 - Tony Hey A1 - Norman Paton A1 - Newhouse, Steven A1 - Parastatidis, Savas A1 - Anne Trefethen A1 - Watson, Paul A1 - Webber, Jim AB - The UK e-Science Programme is a £250M, 5 year initiative which has funded over 100 projects. These application-led projects are under-pinned by an emerging set of core middleware services that allow the coordinated, collaborative use of distributed resources. This set of middleware services runs on top of the research network and beneath the applications we call the ‘Grid’. Grid middleware is currently in transition from pre-Web Service versions to a new version based on Web Services. Unfortunately, only a very basic set of Web Services embodied in the Web Services Interoperability proposal, WS-I, are agreed by most IT companies. IBM and others have submitted proposals for Web Services for Grids - the Web Services ResourceFramework and Web Services Notification specifications - to the OASIS organisation for standardisation. This process could take up to 12 months from March 2004 and the specifications are subject to debate and potentially significant changes. Since several significant UK e-Science projects come to an end before the end of this process, the UK therefore needs to develop a strategy that will protect the UK’s investment in Grid middleware by informing the Open Middleware Infrastructure Institute’s (OMII) roadmap and UK middleware repository in Southampton. This paper sets out an evolutionary roadmap that will allow us to capture generic middleware components from projects in a form that will facilitate migration or interoperability with the emerging Grid Web Services standards and with on-going OGSA developments. In this paper we therefore define a set of Web Services specifications - that we call ‘WS-I+’ to reflect the fact that this is a larger set than currently accepted by WS-I – that we believe will enable us to achieve the twin goals of capturing these components and facilitating migration to future standards. We believe that the extra Web Services specifications we have included in WS-I+ are both helpful in building e-Science Grids and likely to be widely accepted. JF - UK e-Science Technical Report Series 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 - 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 - RPRT T1 - Grid Database Access and Integration: Requirements and Functionalities Y1 - 2003 A1 - Atkinson, M. P. A1 - Dialani, V. A1 - Guy, L. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Storey, T. A1 - Watson, P. AB - This document is intended to provide the context for developing Grid data service standard recommendations within the Global Grid Forum. It defines the generic requirements for accessing and integrating persistent structured and semi-structured data. In addition, it defines the generic functionalities which a Grid data service needs to provide in supporting discovery of and controlled access to data, in performing data manipulation operations, and in virtualising data resources. The document also defines the scope of Grid data service standard recommendations which are presented in a separate document. JF - Global Grid Forum ER - TY - CONF T1 - Use of Evolutionary Algorithms for Telescope Scheduling T2 - Integrated Modeling of Telescopes Y1 - 2002 A1 - Grim, R. A1 - Jansen, M. L. M. A1 - Baan, A. A1 - van Hemert, J. I. A1 - de Wolf, H. ED - Torben Anderson KW - constraint satisfaction KW - scheduling AB - LOFAR, a new radio telescope, will be designed to observe with up to 8 independent beams, thus allowing several simultaneous observations. Scheduling of multiple observations parallel in time, each having their own constraints, requires a more intelligent and flexible scheduling function then operated before. In support of the LOFAR radio telescope project, and in co-operation with Leiden University, Fokker Space has started a study to investigate the suitability of the use of evolutionary algorithms applied to complex scheduling problems. After a positive familiarisation phase, we now examine the potential use of evolutionary algorithms via a demonstration project. Results of the familiarisation phase, and the first results of the demonstration project are presented in this paper. JF - Integrated Modeling of Telescopes PB - The International Society for Optical Engineering ({SPIE}) VL - 4757 ER - TY - CONF T1 - An Engineering Approach to Evolutionary Art T2 - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) Y1 - 2001 A1 - van Hemert, J. I. A1 - Jansen, M. L. M. ED - Lee Spector ED - Erik D. Goodman ED - Annie Wu ED - W. B. Langdon ED - Hans-Michael Voigt ED - Mitsuo Gen ED - Sandip Sen ED - Marco Dorigo ED - Shahram Pezeshk ED - Max H. Garzon ED - Edmund Burke KW - evolutionary art AB - We present a general system that evolves art on the Internet. The system runs on a server which enables it to collect information about its usage world wide; its core uses operators and representations from genetic program-ming. We show two types of art that can be evolved using this general system. JF - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) PB - Morgan Kaufmann Publishers, San Francisco ER - TY - CONF T1 - Constraint Satisfaction Problems and Evolutionary Algorithms: A Reality Check T2 - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) Y1 - 2000 A1 - van Hemert, J. I. ED - van den Bosch, A. ED - H. Weigand KW - constraint satisfaction AB - Constraint satisfaction has been the subject of many studies. Different areas of research have tried to solve all kind of constraint problems. Here we will look at a general model for constraint satisfaction problems in the form of binary constraint satisfaction. The problems generated from this model are studied in the research area of constraint programming and in the research area of evolutionary computation. This paper provides an empirical comparison of two techniques from each area. Basically, this is a check on how well both areas are doing. It turns out that, although evolutionary algorithms are doing well, classic approaches are still more successful. JF - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) PB - BNVKI, Dutch and the Belgian AI Association ER - TY - CONF T1 - Stepwise Adaptation of Weights for Symbolic Regression with Genetic Programming T2 - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) Y1 - 2000 A1 - Eggermont, J. A1 - van Hemert, J. I. ED - van den Bosch, A. ED - H. Weigand KW - data mining KW - genetic programming AB - In this paper we continue study on the Stepwise Adaptation of Weights (SAW) technique. Previous studies on constraint satisfaction and data clas-sification have indicated that SAW is a promising technique to boost the performance of evolutionary algorithms. Here we use SAW to boost per-formance 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 problems. JF - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) PB - BNVKI, Dutch and the Belgian AI Association ER - TY - JOUR T1 - On Zero-symmetric BZ-algebras JF - Journal of East China University of Science and Technology Y1 - 1997 A1 - Wang, Y. A1 - Liangxiu Han PB - East China University of Science and Technology VL - 23 IS - 6 ER -