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Proceedings
A. Tirado-Ramos and Q. Luo.
Second Workshop on Teaching Computational Science WTCS 2008.
In: Computational Science – ICCS 2008.
pp. 657-658.
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Proceedings
A. Caiazzo, J. L. Falcone, B. Chopard, and A. G. Hoekstra.
Scale-splitting error in complex automata models for reaction-diffusion systems.
In:
Computational Science – ICCS 2008.
pp. 291-300.
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Article
M. Wiens, S. I. Belikov, O. V. Kaluzhnaya, T. Adell, H. C. Schröder, S. Perovic-Ottstadt, J. A. Kaandorp, and W. E. G. Müller.
Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis.
Micron
pp. 447-460.
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Proceedings
S. F. Portegies Zwart and H.-C. Chen.
Reconstructing the initial relaxation time of young star clusters in the Large Magellanic Cloud.
In: Mass Loss from Stars and the Evolution of Stellar Clusters.
pp. 329-336.
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Proceedings
B. Baliś, M. Bubak, and J. Wach.
Provenance tracking in the ViroLab Virtual Laboratory.
In: Parallel Processing and Applied Mathematics.
pp. 381-390.
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Proceedings
B. Balis, M. Bubak, M. Pelczar, and J. Wach.
Provenance tracking and querying in the ViroLab Virtual Laboratory.
In: CCGRID 2008.
pp. 675-680.
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Proceedings
B. Balis, M. Bubak, M. Pelczar, and J. Wach.
Provenance tracking and querying in ViroLab.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 71-76.
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Proceedings
B. Baliś, M. Bubak, M. Pelczar, and J. Wach.
Provenance querying for end-users: A drug resistance case study.
In: Computational Science – ICCS 2008.
pp. 80-89.
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Proceedings
K. Rycerz, M. Bubak, P. Sloot, and V. Getov.
Problem solving environment for distributed interactive applications.
In:
Achievements in European research on grid systems: CoreGRID Integration Workshop 2006 (selected papers), October 19-20, Krakow, Poland.
pp. 55-66.
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Proceedings
R. M. Badia, R. Sirvent, M. T. Bubak, W. Funika, and P. Machner.
Performance monitoring of Grid superscalar: visualization modes.
In: CoreGRID integration workshop 2008 -- Integrated Research in Grid Computing: April 24, Hersonissos, Crete, Greece.
ISBN 978-960-524-260-2.
pp. 266-274.
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Proceedings
R. M. Badia, R. Sirvent, M. Bubak, W. Funika, and P. Machner.
Performance monitoring of Grid superscalar with OCM-G/G-PM: visualization modes.
In: Integrated research in grid computing.
pp. 265-274.
-
Proceedings
R. M. Badia, R. Sirvent, M. Bubak, W. Funika, and P. Machner.
Performance monitoring of GRID superscalar with OCM-G/G-PM: Integration issues.
In: Achievements in European reseach on Grid systems: CoreGRID Integration Workshop 2006 (selected papers): October 19-20, Krakow, Poland.
pp. 193-205.
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Article
L. Axner, J. Bernsdorf, T. Zeiser, P. Lammers, J. Linxweiler, and A. G. Hoekstra.
Performance evaluation of a parallel sparse lattice Boltzmann solver.
Journal of computational Physics
pp. 4895-4911.
-
Proceedings
V. V. Krzhizhanovskaya, V. V. Korkhov, M. A. Zatevakhin, and Y. E. Gorbachev.
Parallel distributed computing in modeling of the nanomaterials production technologies.
In:
Proceedings of the International Conference on Parallel Computing Technologies (PaVT'2008), St. Petersburg, Russia.
pp. 585-590.
-
Proceedings
J. L. Guisado, F. Fernández de Vega, F. Jiménez Morales, K. A. Iskra, and P. M. A. Sloot.
Parallel Cellular Automata-based simulation of laser dynamics using dynamic load balancing.
In:
First International Workshop on Parallel Architectures and Bioinspired Algorithms.
pp. 49-55.
-
Article
M. B. N. Kouwenhoven, A. G. A. Brown, S. P. Goodwin, S. F. Portegies Zwart, and L. Kaper.
Pairing mechanisms for binary stars.
Astronomische Nachrichten
pp. 984-987.
-
Proceedings
M. Malawski, J. Kocot, E. Ciepiela, and M. Bubak.
Optimization of application execution in the ViroLab Virtual Laboratory.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 65-70.
-
Report
M. Malawski, J. Kocot, I. Ryszka, M. Bubak, M. Wieczorek, and T. Fahringer.
Optimization of application execution in the GridSpace environment.
-
Proceedings
M. Malawski, J. Kocot, I. Ryszka, M. Bubak, and M. Wieczorek.
Optimization of application execution in the GridSpace environment.
In: Integrated research in grid computing.
pp. 395-405.
-
Article
N. T. Faber, C. M. Boily, and S. F. Portegies Zwart.
On time-dependent orbital complexity in gravitational N-body simulations.
Monthly Notices of the Royal Astronomical Society
pp. 425-439.
-
Article
E. Gaburov, A. Gualandris, and S. Portegies Zwart.
On the onset of runaway stellar collisions in dense star clusters: I. Dynamics of the first collision.
Monthly Notices of the Royal Astronomical Society
pp. 376-385.
-
Article
L. R. Yungelson, E. P. J. van den Heuvel, J. S. Vink, S. F. Portegies Zwart, and A. de Koter.
On the evolution and fate of super-massive stars.
Astronomy & Astrophysics
pp. 223-237.
-
Proceedings
B. Chopard, J.-L. Falcone, R. Razakanirina, A. Hoekstra, and A. Caiazzo.
On the collision-propagation and gather-update formulations of a cellular automata rule.
In:
Cellular Automata.
pp. 144-151.
-
Proceedings
B. Chopard, J.-L. Falcone, R. Razakarinina, A. G. Hoekstra, and A. Caiazzo.
On the collision-propagation and gather-update formulations of a Cellular Automata rule.
In:
Cellular Automata, 8th International Conference on Cellular Automata for Reseach and Industry, ACRI 2008.
ISBN
978-3-540-79991-7.
Lecture Notes in Computer Science
5191, pp. 144-151.
-
Proceedings
W. Funika, M. Zientarski, R. M. Badia, J. Labarta, and M. Bubak.
OCM2PRV: performance visualization of Grid applications based on OCM-G and Paraver.
In: Integrated research in grid computing.
pp. 87-98.
-
Proceedings
D. J. W. Evans, A. G. Hoekstra, J. Gunn, D. Walker, D. R. Hose, R. H. Smallwood, B. Chopard, M. Krafczyk, J. M. Bernsdorf, and P. V. Lawford.
Multiscale Modelling: Application of the Complex Automata Simulation Technique (COAST).
In:
Proceedings of the European Biomechanics Society conference 2008.
-
MSc Thesis
L. Y. L. Muller.
Multi-touch displays: design, applications and performance evaluation.
Supervised by
R. G. Belleman.
-
Article
P. Sloot, P. Coveney, M. T. Bubak, A.-M. Vandamme, B. Ó Nualláin, D. van de Vijver, and C. Boucher.
Multi-science decision support for HIV drug resistance treatment.
Studies in Health Technology and Informatics
pp. 188-198.
-
Proceedings
A. G. Hoekstra, J.-L. Falcone, A. Caiazzo, and B. Chopard.
Multi-scale modeling with cellular automata: The complex automata approach.
In:
Cellular Automata.
pp. 192-199.
-
Article
B. Balis, M. Bubak, and B. Łabno.
Monitoring of Grid scientific workflows.
Scientific Programming
pp. 205-216.
-
Article
J. A. Kaandorp, J. G. Blom, J. Verhoef, M. Filatov, M. Postma, and W. E. G. Müller.
Modelling genetic regulation of growth and form in a branching sponge.
Proceedings of the Royal Society B-Biological Sciences
pp. 2569-2575.
-
MSc Thesis
R. Quax.
Modeling and Simulating the Propagation of Infectious Diseases Using Complex Networks.
Supervised by
David Bader.
-
Article
E. Gaburov, J. C. jr. Lombardi, and S. Portegies Zwart.
Mixing in massive stellar mergers.
Monthly Notices of the Royal Astronomical Society. Letters
pp. L5-L9.
-
MSc Thesis
A. Sottoriva.
Mathematical Modeling of Tumour Growth and Invasion Using a Hybrid Cellular Automaton.
Supervised by
P. M. A. Sloot and L. Vermeulen.
-
Article
D. Y. Orlova, M. A. Yurkin, A. G. Hoekstra, and V. P. Maltsev.
Light scattering by neutrophils: Model, simulation, and experiment.
Journal of Biomedical Optics
p. 054057.
-
Article
B. Baliś, M. Bubak, and M. Wegiel.
LGF: A flexible framework for exposing legacy codes as services.
Future Generation Computer Systems
pp. 711-719.
-
Proceedings
T. Bartyński, M. Malawski, and M. Bubak.
Invocation of Grid operations in the ViroLab Virtual Laboratory.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 59-64.
-
Proceedings
T. Szepieniec and M. Bubak.
Investigation of the DAG eligible jobs maximization algorithm in a grid.
In: Grid 2008: proceedings of the 2008 9th IEEE/ACM International Conference on Grid Computing: September 29th-October 1st, 2008, Tsukuba, Japan.
pp. 340-345.
-
Proceedings
A. Belloum, Z. Zhao, and M. Bubak.
International Workshop on Applications of Workflows in Computational Science (AWCS 08).
In: Computational Science – ICCS 2008.
pp. 459-462.
-
Proceedings
M. Assel, P. Nowakowski, and M. Bubak.
Integrating and accessing medical data resources within the ViroLab Virtual Laboratory.
In: Computational Science – ICCS 2008.
pp. 90-99.
-
Article
V. V. Gvaramadze, A. Gualandris, and S. Portegies Zwart.
Hyperfast pulsars as the remnants of massive stars ejected from young star clusters.
Monthly Notices of the Royal Astronomical Society
pp. 929-938.
-
Proceedings
M. Malawski, T. Gubała, M. Kasztelnik, T. Bartynski, and M. Bubak.
High-level scripting approach for building component-based applications on the Grid.
In: Making grids work: Proceedings of the CoreGRID Workshop on Programming Models, Grid and P2P System Architecture, Grid Systems, Tools and Environments, 12-13 June 2007, Heraklion, Crete, Greece.
pp. 309-321.
-
Article
R. G. Belleman, J. Bédorf, and S. F. Portegies Zwart.
High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA.
New Astronomy
pp. 103-112.
-
Article
J. A. van Meel, A. Arnold, D. Frenkel, S. F. Portegies Zwart, and R. G. Belleman.
Harvesting graphics power for MD simulations.
Molecular Simulation
pp. 259-266.
-
Proceedings
K. Rycerz, M. Bubak, and P. M. A. Sloot.
HLA component model on the example of multiscale simulation.
In:
Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 272-275.
-
Report
K. Rycerz, M. Bubak, P. M. A. Sloot, and V. Getov.
HLA component based environment for distributed multiscale simulations.
-
Proceedings
K. Rycerz, M. Bubak, and P. M. A. Sloot.
HLA component based environment for distributed multiscale simulations.
In:
From grids to service and pervasive computing.
pp. 229-239.
-
Article
H.-C. Huang, A. Konagaya, V. Lanza, and P. M. A. Sloot.
Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid.
IEEE Transactions on Information Technology in Biomedicine
pp. 133-137.
-
Chapter
A. Tirado-Ramos, P. M. A. Sloot, and M. Bubak.
Gridbased interactive decision support in biomedicine.
In:
Grid computing for bioinformatics and computational biology.
pp. 225-246.
-
Proceedings
E. Ciepiela, J. Kocot, T. Gubala, M. Malawski, M. Kasztelnik, and M. Bubak.
GridSpace Engine of the ViroLab Virtual Laboratory.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 53-58.
-
Proceedings
J. K. Rath, A. D. Verkerk, M. Brinza, R. E. I. Schropp, W. J. Goedheer, V. V. Krzhizhanovskaya, Y. E. Gorbachev, K. E. Orlov, E. M. Khilkevitch, and A. S. Smirnov.
Gas phase considerations for the deposition of thin film silicon solar cells by VHF-PECVD at low substrate temperatures.
In:
Proceedings of the 33rd IEEE Photovoltaic Specialists Conference, San Diego, California.
-
Proceedings
J. K. Rath, A. Verkerk, M. Brinza, R. E. I. Schropp, W. J. Goedheer, V. V. Krzhizhanovskaya, Y. E. Gorbachev, K. E. Orlov, E. M. Khilkevitch, and A. S. Smirnov.
Gas phase considerations for the deposition of thin film silicon cells by VHF-PECVD at low substrate temperatures.
In:
Proceedings of 33rd IEEE Photovoltaic Specialists Conference.
-
Proceedings
S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot.
Floating point based Cellular Automata simulations using a dual FPGA-enabled system.
In:
2008 Second International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA): proceedings: held in conjunction with SC 08, Austin, TX, November 17, 2008.
-
Other: misc
J. A. Kaandorp.
Exploring Theoretical Morphospaces, Book review: The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. George R. McGhee.
BioScience
58, pp. 271-273.
-
Article
A. Gualandris, S. Harfst, D. Merritt, and S. Mikkola.
Evolution of stellar orbits in the galactic centre.
Astronomische Nachrichten
pp. 1008-1011.
-
Proceedings
T. Szepieniec and M. Bubak.
Evaluation of eligible jobs maximization algorithm for DAG scheduling in grids.
In: Computational Science – ICCS 2008.
pp. 254-263.
-
Article
A. V. Chernyshev, P. A. Tarasov, K. A. Semianov, V. M. Nekrasov, A. G. Hoekstra, and V. P. Maltsev.
Erythrocyte lysis in isotonic solution of ammonium chloride: Theoretical modelling and experimental verification.
Journal of Theoretical Biology
pp. 93-107.
-
Proceedings
A. Caiazzo, J. L. Falcone, B. Chopard, and A. G. Hoekstra.
Error investigations in complex automata models for reaction-diffusion systems.
In:
Cellular Automata.
pp. 260-267.
-
Proceedings
W. Funika, D. Harężlak, D. Król, and M. Bubak.
Environment for collaborative development and execution of Virtual Laboratory applications.
In: Computational Science – ICCS 2008.
pp. 446-455.
-
MSc Thesis
J. B. W. Geerdink.
Entropic and multiple relaxation time lattice Boltzmann methods compared for time harmonic flows.
Supervised by
A. G. Hoekstra.
-
Proceedings
B. Ó Nualláin, D. A. M. C. van de Vijver, C. A. B. Boucher, A. Tirado Ramos, and P. M. A. Sloot.
Enhanced Decision Support for HIV Drug Resistance Interpretation.
In:
Proceedings of the 6th European HIV Drug Resistance Workshop.
-
Article
S. L. Moll, R. de Grijs, P. Anders, P. A. Crowther, S. S. Larsen, L. J. Smith, and S. F. Portegies Zwart.
Dynamical mass of a star cluster in M 83: A test of fibre-fed multi-object spectroscopy.
Astronomy & Astrophysics
pp. 125-133.
-
Article
Y. Demchenko, O. Mulmo, L. Gommans, C. de Laat, and A. Wan.
Dynamic security context management in Grid-based applications.
Future Generation Computer Systems
pp. 434-441.
-
Proceedings
K. Rycerz, M. Bubak, and P. M. A. Sloot.
Dynamic interactions in HLA component model for multiscale simulations.
In:
Computational Science – ICCS 2008.
pp. 217-226.
-
Proceedings
K. J. Rycerz, P. M. A. Sloot, and M. T. Bubak.
Dynamic Interactions in HLA Component Model for Multiscale Simulations.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II.
ISBN
978-3-540-69386-4.
Lecture Notes in Computer Science
5102, pp. 217-226.
-
Article
D. Groen, S. Portegies Zwart, S. McMillan, and J. Makino.
Distributed N-body simulation on the grid using dedicated hardware.
New Astronomy
pp. 348-358.
-
Proceedings
M. Kasztelnik, T. Gubała, M. Malawski, and M. Bubak.
Development and execution of collaborative application on the ViroLab virtual laboratory.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 41-46.
-
Article
C. H. Liu, A. K. Satoh, M. Postma, J. Huang, D. F. Ready, and R. C. Hardie.
Ca2+-dependent metarhodopsin inactivation mediated by calmodulin and NINAC myosin III.
Neuron
pp. 778-789.
-
Other: misc
J. A. Kaandorp.
Book review: P. Pelce, New visions on growth and form: fingering growth, dendrites, and flames.
Mathematical Biosciences
in press.
-
Other: misc
A. G. Hoekstra.
Book review: Optical Polarization in Biomedical Applications, V.V. Tuchin, L.V. Wang, D.A. Zimnyakov.
Journal of Quantitative Spectroscopy \& Radiative Transfer
109, pp. 531-531.
-
Article
X. Wang, A. Boreiko, U. Schloßmacher, D. Brandt, H. C. Schröder, J. Li, J. A. Kaandorp, H. Götz, H. Duschner, and W. E. G. Müller.
Axial growth of hexactinellid spicules: Formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis.
Journal of Structural Biology
pp. 270-280.
-
Proceedings
M. A. Yurkin, M. Min, and A. G. Hoekstra.
Application of the discrete dipole approximation to extreme refractive indices: Filtered coupled dipoles revived.
In:
11th Electromagnetic & Light Scattering Conference: Extended abstracts: 7-12 September 2008, de Havilland Campus, University of Hertfordshire.
pp. 109-112.
-
Proceedings
M. Bubak, D. Harezlak, P. Nowakowski, T. Gubala, and M. Malawski.
Appea: a framework for the design and development of business applications on the Grid.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
pp. 220-225.
-
Proceedings
B. Baliś and M. Bubak.
An ontology model for execution records of Grid scientific applications.
In: Proceedings of the Fourth International Conference on Semantics, Knowledge and Grid: December 3-5, 2008, Beijing, China.
pp. 34-41.
-
Proceedings
B. Kowalewski, M. Bubak, and B. Baliś.
An event-based approach to reducing coupling in large-scale applications.
In: Computational Science – ICCS 2008.
pp. 358-367.
-
Proceedings
J. Hegewald, M. Krafczyk, J. Tölke, A. Hoekstra, and B. Chopard.
An agent-based coupling platform for complex automata.
In:
Computational Science – ICCS 2008.
pp. 227-233.
-
PhD Thesis
-
Proceedings
M. Malawski, T. Bartyński, and M. Bubak.
A tool for building collaborative applications by invocation of Grid Operations.
In: Computational Science – ICCS 2008.
pp. 243-252.
-
MSc Thesis
D. M. Chu.
A survey of classical simulation methods for quantum computation.
Supervised by H. Buhrman and R. de Wolf.
-
Article
S. Portegies Zwart, S. McMillan, D. Groen, A. Gualandris, M. Sipior, and W. Vermin.
A parallel gravitational N-body kernel.
New Astronomy
pp. 285-295.
-
Proceedings
S. Portegies Zwart, S. McMillan, B. Ó Nualláin, D. Heggie, J. Lombardi, P. Hut, S. Banerjee, H. Belkus, T. Fragos, J. Fregeau, M. Fuji, E. Gaburov, E. Glebbeek, D. Groen, S. Harfst, R. Izzard, M. Jurić, S. Justham, P. Teuben, J. van Bever, O. Yaron, and M. Zemp.
A multiphysics and multiscale software environment for modeling astrophysical systems.
In: Computational Science – ICCS 2008.
pp. 207-216.
-
Article
Z. Guo, P. M. A. Sloot, and J. C. Tay.
A hybrid agent-based approach for modeling microbiological systems.
Journal of Theoretical Biology
pp. 163-175.
-
Article
S. Harfst, A. Gualandris, D. Merritt, and S. Mikkola.
A hybrid N-body code incorporating algorithmic regularization and post-Newtonian forces.
Monthly Notices of the Royal Astronomical Society
pp. 2-12.
-
Article
V. V. Korkhov, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
A grid-based virtual reactor: Parallel performance and adaptive load balancing.
Journal of Parallel and Distributed Computing
pp. 596-608.
-
Proceedings
A. Wibisono, Z. Zhao, A. Belloum, and M. Bubak.
A framework for interactive parameter sweep applications.
In: Computational Science – ICCS 2008.
pp. 481-490.
-
MSc Thesis
M. V. Filatov.
A compression-based group similarity measure with applications in phylogeny. Automatic detection of viral RNA recombination..
Supervised by B. Ó Nualláin.
-
Proceedings
G. Ertaylan and P. M. A. Sloot.
A complex automata model of HIV-1 co-receptor tropism: Mutation rate prediction.
In:
Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
p. 85.
-
Proceedings
B. Łabno, M. Bubak, and B. Baliś.
A P2P approach to resource discovery in on-line monitoring of Grid workflows.
In: Euro-Par 2008 – Parallel Processing.
pp. 37-46.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I.
ISBN
978-3-540-69383-3.
Lecture Notes in Computer Science
5101.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II.
ISBN
978-3-540-69386-4.
Lecture Notes in Computer Science
5102.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III.
ISBN
978-3-540-69388-8.
Lecture Notes in Computer Science
5103.