Publications of the CSL group2011
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Article. A hybrid approach to extract protein-protein interactions. Bioinformatics 27(2), pp. 259-265.
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Proceedings. A framework for multiscale and multiscience modeling and numerical simulations. In: Unconventional Computation. ISBN 9783642213410. pp. 2-8.
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Article. A data model for analyzing user collaborations in workflow-driven e-Science. The International Journal of Computers and Their Applications (IJCA) 18(3), pp. 160-179.
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Article. A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering. Developmental Biology 351(1), pp. 217-228.
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Proceedings. A Particle-Based Model for Aggregate Formation in Biomineralization. In: Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application. ISBN 9788890580505. p. 23.
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Article. A Data Model for Analyzing User Collaborations in Workflow-Driven eScience. The International Journal of Computers and Their Applications (IJCA) 18(3), pp. 160-179.
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Article. A Complex Automata approach for in-stent restenosis: two-dimensional multiscale modelling and simulations. Journal of Computational Science 2(1), pp. 9-17.
2010
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Article. Visualization in computational science. Procedia Computer Science 1(1), pp. 1689-1690.
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Proceedings. Validating the ACGT Oncosimulator with a Grid-Supported Visualisation Environment. In: 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation.
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Proceedings. Understanding collaborative studies through interoperable workflow provenance. In: Provenance and Annotation of Data and Processes. ISBN 9783642178191. pp. 42-58.
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Proceedings. Towards distributed multiscale computing for the VPH. In: Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference. pp. 198-200.
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Proceedings. Towards an actor-driven workflow management system for Grids. In: The 2010 International Symposium on Collaborative Technologies and Systems : CTS 2010. ISBN 9781424466191. pp. 611-616.
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Article. The living application: A self-organizing system for complex grid tasks. International Journal of High Performance Computing Applications 24(2), pp. 185-193.
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Article. The influence of mitoses rate on growth dynamics of a cellular automata model of tumour growth. Procedia Computer Science 1(1), pp. 971-978.
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Article. The cross-disciplinary road to true computational science. Journal of Computational Science 1(3), p. 131.
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Proceedings. The ACGT Oncosimulator: from conceptualization to development via multiscale cancer modeling. In: 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The ContraCancrum Workshop. pp. 54-57.
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Article. Simulation of Multiphysics Multiscale Systems, 7th International Workshop. Procedia Computer Science 1(1), pp. 603-605.
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Article. Simulating the universe on an intercontinental grid. Computer 43(8), pp. 63-70.
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Book. Simulating complex systems by cellular automata. ISBN 9783642122033.
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Chapter. Simulating Calcineurin-Centered Calcium Signaling Network in Cardiac Myocytes. In: Congestive heart failure: symptoms, causes and treatment. ISBN 9781608766772. pp. 111-127.
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Article. Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system. Molecular Phylogenetics and Evolution 57(3), pp. 1072-1090.
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Article. Quantitatively evaluating interventions in the influenza A (H1N1) epidemic on China campus grounded on individual-based simulations. Procedia Computer Science 1(1), pp. 1675-1682.
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Article. Quantification of the fraction poorly deformable red blood cells using ektacytometry. Optics Express 18(13), pp. 14173-14182.
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Proceedings. Preparing, exploring and comparing cancer simulation results within a large parameter space. In: 14th International Conference Information Visualisation. ISBN 9780769541655. pp. 258-264.
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Article. Preface. Procedia Computer Science 1(1), pp. 1-2.
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Proceedings. Preface. In: Simulating Complex Systems by Cellular Automata. ISBN 9783642122033. pp. xi-xiii.
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Article. Perspectives on grid computing. Future Generation Computer Systems 26(8), pp. 1104-1115.
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Article. Optical and non-optical methods for detection and characterization of microparticles and exosomes. Journal of Thrombosis and Haemostasis 8(12), pp. 2596-2607.
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Proceedings. Multiscale modelling in real-time flood forecasting systems: From sand grain to dike failure and inundation. In: ICCS 2010. Procedia Computer Science 1(1), pp. 809 - 809.
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Article. Multiscale modelling in real-time flood forecasting systems: From sand grain to dike failure and inundation. Procedia Computer Science 1(1), p. 809.
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Proceedings. Multiscale coupling of a Lattice Boltzmann simulation of blood flow to cell- and tissue-level processes: the case of in-stent restenosis. In: Proceedings of the V European Conference on Computational Fluid Dynamics (ECCOMAS CFD 2010), Lisbon, Portugal.
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Proceedings. Multiphysics multi-model simulation of large-area plasma chemical reactors. In: Proceedings of the ASME 2009 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference. ISBN 9780791848999. pp. 1195-1196 (DETC2009-87039).
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PhD Thesis. Multi-scale simulations with complex automata: in-stent restenosis and suspension flow. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Multi-scale modelling in computational biomedicine. Briefings in Bioinformatics 11(1), pp. 142-152.
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Proceedings. Modelling and simulating in-stent restenosis with complex automata. In: Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference. pp. 222-224.
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Article. Modeling options markets by focusing on active tradersr. Procedia Computer Science 1(1), pp. 2457-2462.
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Article. Modeling HIV-1 intracellular replication: two simulation approaches. Procedia Computer Science 1(1), pp. 555-564.
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Article. Mesoscopic methods in engineering and science. Computers & Mathematics with Applications 59(7), pp. 2139-2140.
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Article. MML: towards a Multiscale Modeling Language. Procedia Computer Science 1(1), pp. 819-826.
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Chapter. Laser dynamics modelling and simulation: An application of dynamic load balancing of parallel cellular automata. In: Parallel and Distributed Computational Intelligence. ISBN 9783642106750. pp. 321-347.
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Chapter. Introduction to modeling of complex systems using cellular automata. In: Simulating complex systems by cellular automata. ISBN 9783642122033. pp. 1-16.
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Book. International Conference on Computational Science, ICCS 2010.
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Article. Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PLoS ONE 5(10), p. e13139.
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Article. Individual-based simulation of sexual selection: A quantitative genetic approach. Procedia Computer Science 1(1), pp. 2003-2011.
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Article. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Systems Biology 4, p. 96.
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PhD Thesis. High performance reconfigurable computing with cellular automata. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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PhD Thesis. High performance N-body simulation on computational grids. Supervised by S. F. Portegies Zwart, P. M. A. Sloot, and E. P. J. van den Heuvel.
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PhD Thesis. Genetic regulatory networks inference : modeling, parameters estimation & model validation. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. Extracting causal relations on HIV drug resistance from literature. BMC Bioinformatics 11, p. 101.
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Article. Exploring individual user differences in the 2D/3D interaction with medical image data. Virtual Reality 14(2), pp. 105-118.
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Article. Exploring cancer stem cell niche directed tumor growth. Cell Cycle 9(8), pp. 1472-1479.
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Article. Evaluation of 2D and 3D glove input applied to medical image analysis. International Journal of Human-Computer Studies 68(6), pp. 355-369.
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Book. Euro ISRS symposium 2010: reefs in a changing environment: book of abstracts.
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Article. Data transport between visualization web services for medical image analysis. Procedia Computer Science 1(1), pp. 1721-1730.
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Proceedings. Computer simulation of laser annealing of a nanostructured surface. In: Proceedings of the ASME 2009 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference. ISBN 9780791848999. pp. 1197-1198 (DETC2009-87087).
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Article. Computational science: A kaleidoscopic view into science. Journal of Computational Science 1(4), p. 189.
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Article. Complex agent networks explaining the HIV epidemic among homosexual men in Amsterdam. Mathematics and Computers in Simulation 80(5), pp. 1018-1030.
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Chapter. Complex Automata: Multi-scale Modeling with Coupled Cellular Automata. In: Simulating complex systems by cellular automata. ISBN 9783642122026. pp. 29-57.
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Article. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time. PLoS ONE 5(7), p. e11505.
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Article. Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity. Cancer Research 70(1), pp. 46-56.
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MSc Thesis. Applications of GPUs in Computational Finance. Supervised by R. G. Belleman and B. D. Kandhai.
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Article. Application of the discrete dipole approximation to very large refractive indices: Filtered coupled dipoles revived. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82(3), p. 036703.
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Article. Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models. PLoS ONE 5(10), p. e13753.
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Book. Advances in Grid and Pervasive Computing: 5th International Conference, GPC 2010, Hualien, Taiwan, May 10-13, 2010: Proceedings. ISBN 9783642130663.
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Article. Accuracy of the discrete dipole approximation for simulation of optical properties of gold nanoparticles. Journal of Nanophotonics 4(1), p. 041585.
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Article. A platform independent communication library for distributed computing. Procedia Computer Science 1(1), pp. 2693-2700.
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Proceedings. A history-tracing XML-based provenance framework for workflows. In: 2010 5th Workshop on Workflows in Support of Large-Scale Science (WORKS). ISBN 9781424489909.
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Article. A comparison between coral colonies of the genus Madracis and simulated forms. Proceedings of the Royal Society B-Biological Sciences 277(1700), pp. 3555-3561.
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MSc Thesis. A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis. Supervised by R. M. H. Merks and J. A. Kaandorp.
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PhD Thesis. A Semantic Model for Complex Computer Networks: The Network Description Language. ISBN 978-90-814160-2-3. Supervised by P. M. A. Sloot and C. T. A. M. de Laat.
2009
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Article. ‘In silico' oncology for clinical decision making in the context of nephroblastoma. Klinische Pädiatrie 221(3), pp. 141-149.
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Chapter. Virtual Laboratory for Collaborative Applications. In: Handbook of research on computational grid technologies for life sciences, biomedicine, and healthcare. ISBN 9781605663746. pp. 531-551.
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Article. Using the minimum spanning tree to trace mass segregation. Monthly Notices of the Royal Astronomical Society 395(3), pp. 1449-1454.
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Book. Trends in interactive visualization: State-of-the-art survey. ISBN 9781848002685.
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Proceedings. Towards a Complex Automata multiscale model of in-stent restenosis. In: Computational Science – ICCS 2009. ISBN 9783642019708. I, pp. 705-714.
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Proceedings. Time Evolution of the Stellar Mass Function of Galactic Clusters. In: American Astronomical Society Meeting #213, #442.06 Abstracts. American Astronomical Society Meeting Abstracts 41, p. 320.
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Article. Time Evolution of the Stellar Mass Function of Galactic Clusters. Bulletin - American Astronomical Society 41, p. 320.
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Proceedings. Threat model for MOCCA component environment. In: Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings. ISBN 9788361433002. pp. 94-102.
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Proceedings. Third Workshop on Teaching Computational Science (WTCS 2009). In: Computational Science – ICCS 2009. ISBN 9783642019739. II, pp. 3-4.
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Article. The user-level scheduling of divisible load parallel applications with resource selection and adaptive workload balancing on the Grid. IEEE Systems Journal 3(1), pp. 121-130.
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Article. The lost siblings of the Sun. Astrophysical Journal Letters 696(1), pp. L13-L16.
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Article. The formation of the black hole in the X-ray binary system V404 Cyg. Monthly Notices of the Royal Astronomical Society 394(3), pp. 1440-1448.
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Article. The evolution of runaway stellar collision products. Astronomy & Astrophysics 497(1), pp. 255-264.
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Report. The Cook Report on Internet Protocol on WiVR: a Window into Virtual Reality.
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Report. The Cook Report on Internet Protocol on Interactive Networks (A User Interface for Appliction Owned Lightpath Networks).
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Article. Systems biology: parameter estimation for biochemical models. The FEBS Journal 276(4), pp. 886-902.
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Proceedings. Structure and status of National Grid Initiative in Poland. In: Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings. ISBN 978-83-61433-00-2. pp. 39-51.
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PhD Thesis. Stochasticity in signal transduction pathways. ISBN 9789090247397. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. Special section: Simulation of Multiphysics Multiscale Systems: Going Nano. Preface. International Journal for Multiscale Computational Engineering 7(1), pp. vii-viii.
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Article. Special section: OptIPlanet - The OptIPuter global collaboratory. Future Generation Computer Systems 25(2), pp. 109-113.
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Article. Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods. BioMedical Engineering OnLine 8, p. 23.
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Proceedings. Simulation of plasma chemical processes on heterogeneous Grid resourses with adaptive load balancing for parallel solvers (Моделирование плазмохимических процессов на гетерогенных ресурсах Grid с адаптивной балансировкой нагрузки для параллельных солверов). In: Proceedings of the all-Russian supercomputer conference 'Scientific services on the Internet: Scalability, parallelism, efficiency'. ISBN 9785211056978. pp. 351-352.
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Other: misc. Simulation of Multiphysics Multiscale Systems: Going Nano. International Journal for Multiscale Computational Engineering 7(1).
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Other: misc. Simulation of Multiphysics Multiscale Systems: Going Nano. International Journal for Multiscale Computational Engineering, Special Section 7(1), pp. vii-viii.
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Proceedings. Simulation of Multiphysics Multiscale Systems, 6th International Workshop. In: Computational Science – ICCS 2009. ISBN 9783642019708. I, pp. 653-654.
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Proceedings. Simulating individual-based models of epidemics in hierarchical networks. In: Computational Science – ICCS 2009. ISBN 9783642019708. I, pp. 725-734.
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Article. Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 45(2), pp. 123-132.
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Chapter. Semantic Integration for Research Environments. In: Handbook of research on computational grid technologies for life sciences, biomedicine, and healthcare. ISBN 9781605663746. pp. 514-530.
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Article. SAPPORO: A way to turn your graphics cards into a GRAPE-6. New Astronomy 14(7), pp. 630-637.
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Proceedings. Running parallel applications with topology-aware grid middleware. In: Proceedings of the 2009 Fifth IEEE International Conference on e-Science. ISBN 9780769538778. pp. 292-299.