Changes between Version 6 and Version 7 of publications
- Timestamp:
- 08/22/14 10:22:16 (10 years ago)
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publications
v6 v7 2 2 3 3 The following publication should be cited when using MUSCLE 2: 4 J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. Ben Belgacem, B. Chopard, et al., Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment, Journal of Computational Science. 5 (2014) 719–731. doi:10.1016/j.jocs.2014.04.004.4 J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. Ben Belgacem, B. Chopard, D. Groen, P. V. Coveney, and A. G. Hoekstra, "Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment", Journal of Computational Science. 5 (2014) 719–731. doi:[[http://dx.doi.org/10.1016/j.jocs.2014.04.004|10.1016/j.jocs.2014.04.004]]. 5 5 6 6 A previous conference article is: 7 J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, et al., Multiscale Computing with the Multiscale Modeling Library and Runtime Environment, Procedia Computer Science. 18 (2013) 1097–1105. doi:10.1016/j.procs.2013.05.275.7 J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, et al., "Multiscale Computing with the Multiscale Modeling Library and Runtime Environment", Procedia Computer Science. 18 (2013) 1097–1105. doi:[[http://dx.doi.org/10.1016/j.procs.2013.05.275|10.1016/j.procs.2013.05.275]]. 8 8 9 9 It is based on MUSCLE 1 (previously called DSCL): 10 J. Hegewald, M. Krafczyk, J. Tölke, A.G. Hoekstra, An agent-based coupling platform for complex automata, in: Iccs 2008, Lncs 5102, 2008: pp. 227–233. doi: 10.1007/978-3-540-69387-1_25.10 J. Hegewald, M. Krafczyk, J. Tölke, A.G. Hoekstra, An agent-based coupling platform for complex automata, in: Iccs 2008, Lncs 5102, 2008: pp. 227–233. doi:[[http://dx.doi.org/10.1007/978-3-540-69387-1_25|10.1007/978-3-540-69387-1_25]]. 11 11 12 12 Its use in a larger infrastructure context is described here: 13 S. J. Zasada, M. Mamonski, D. Groen, J. Borgdorff, I. Saverchenko, T. Piontek, et al., Distributed Infrastructure for Multiscale Computing, in: 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications (DS-RT), IEEE, 2012: pp. 65–74. doi: 10.1109/DS-RT.2012.17.13 S. J. Zasada, M. Mamonski, D. Groen, J. Borgdorff, I. Saverchenko, T. Piontek, et al., Distributed Infrastructure for Multiscale Computing, in: 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications (DS-RT), IEEE, 2012: pp. 65–74. doi:[[http://dx.doi.org/10.1109/DS-RT.2012.17|10.1109/DS-RT.2012.17]]. 14 14 15 15 ---- … … 17 17 The theory and formalization that lies at the basis of MUSCLE is formed by the Multiscale Modelling and Simulation Framework. It is explained here: 18 18 19 J. Borgdorff, J.-L. Falcone, E. Lorenz, C. Bona-Casas, B. Chopard, A.G. Hoekstra, Foundations of distributed multiscale computing: Formalization, specification, and analysis, Journal of Parallel and Distributed Computing. 73 (2013) 465–483. doi: 10.1016/j.jpdc.2012.12.011.19 J. Borgdorff, J.-L. Falcone, E. Lorenz, C. Bona-Casas, B. Chopard, A.G. Hoekstra, Foundations of distributed multiscale computing: Formalization, specification, and analysis, Journal of Parallel and Distributed Computing. 73 (2013) 465–483. doi:[[http://dx.doi.org/10.1016/j.jpdc.2012.12.011|10.1016/j.jpdc.2012.12.011]]. 20 20 21 B. Chopard, J. Borgdorff, A.G. Hoekstra, A framework for multi-scale modelling, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372 (2014). doi: 10.1098/rsta.2013.0378.21 B. Chopard, J. Borgdorff, A.G. Hoekstra, A framework for multi-scale modelling, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372 (2014). doi:[[http://dx.doi.org/10.1098/rsta.2013.0378|10.1098/rsta.2013.0378]]. 22 22 23 M. Ben Belgacem, B. Chopard, J. Borgdorff, M. Mamonski, K. Rycerz, D. Harezlak, Distributed Multiscale Computations Using the MAPPER Framework, Procedia Computer Science. 18 (2013) 1106–1115. doi: 10.1016/j.procs.2013.05.276.23 M. Ben Belgacem, B. Chopard, J. Borgdorff, M. Mamonski, K. Rycerz, D. Harezlak, Distributed Multiscale Computations Using the MAPPER Framework, Procedia Computer Science. 18 (2013) 1106–1115. doi:[[http://dx.doi.org/10.1016/j.procs.2013.05.276|10.1016/j.procs.2013.05.276]]. 24 24 25 25 ---- … … 28 28 29 29 An overview of applications using distributed multiscale computing: 30 J. Borgdorff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, et al., Performance of distributed multiscale simulations, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372 (2014). doi: 10.1098/rsta.2013.0407.30 J. Borgdorff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, et al., Performance of distributed multiscale simulations, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372 (2014). doi:[[http://dx.doi.org/10.1098/rsta.2013.0407|10.1098/rsta.2013.0407]]. 31 31 32 32 In-stent restenosis (ISR2D/ISR3D): 33 J. Borgdorff, C. Bona-Casas, M. Mamonski, K. Kurowski, T. Piontek, B. Bosak, et al., A Distributed Multiscale Computation of a Tightly Coupled Model Using the Multiscale Modeling Language, Procedia Computer Science. 9 (2012) 596–605. doi: 10.1016/j.procs.2012.04.064.33 J. Borgdorff, C. Bona-Casas, M. Mamonski, K. Kurowski, T. Piontek, B. Bosak, et al., A Distributed Multiscale Computation of a Tightly Coupled Model Using the Multiscale Modeling Language, Procedia Computer Science. 9 (2012) 596–605. doi:[[http://dx.doi.org/10.1016/j.procs.2012.04.064|dx.doi.org/10.1016/j.procs.2012.04.064]]. 34 34 35 D. Groen, J. Borgdorff, C. Bona-Casas, J. Hetherington, R.W. Nash, S.J. Zasada, et al., Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations, Interface Focus. 3 (2013) 20120087. doi: 10.1098/rsfs.2012.0087.35 D. Groen, J. Borgdorff, C. Bona-Casas, J. Hetherington, R.W. Nash, S.J. Zasada, et al., Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations, Interface Focus. 3 (2013) 20120087. doi:[[http://dx.doi.org/10.1098/rsfs.2012.0087|10.1098/rsfs.2012.0087]]. 36 36 37 H. Tahir, C. Bona-Casas, A.J. Narracott, J. Iqbal, J. Gunn, P.V. Lawford, et al., Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: comparing histology with in silico modelling, Journal of the Royal Society Interface. 11 (2014) 20140022–20140022. doi: 10.1161/CIRCULATIONAHA.107.720730.37 H. Tahir, C. Bona-Casas, A.J. Narracott, J. Iqbal, J. Gunn, P.V. Lawford, et al., Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: comparing histology with in silico modelling, Journal of the Royal Society Interface. 11 (2014) 20140022–20140022. doi:[[http://dx.doi.org/10.1161/CIRCULATIONAHA.107.720730|10.1161/CIRCULATIONAHA.107.720730]]. 38 38 39 39 Canal system simulation: 40 M. Ben Belgacem, B. Chopard, A. Parmigiani, Coupling Method for Building a Network of Irrigation Canals on a Distributed Computing Environment, in: G.C. Sirakoulis, S. Bandini (Eds.), 7495 ed., Springer-Verlag Berlin Heidelberg, 2012: pp. 309–318. doi: 10.1007/978-3-642-33350-7_32.40 M. Ben Belgacem, B. Chopard, A. Parmigiani, Coupling Method for Building a Network of Irrigation Canals on a Distributed Computing Environment, in: G.C. Sirakoulis, S. Bandini (Eds.), 7495 ed., Springer-Verlag Berlin Heidelberg, 2012: pp. 309–318. doi:[[http://dx.doi.org/10.1007/978-3-642-33350-7_32|10.1007/978-3-642-33350-7_32]]. 41 41 42 42 Tokamak reactor turbulence transport: … … 44 44 45 45 Reverse-engineering of gene-regulatory networks: 46 A. Mizeranschi, N. Kennedy, P. Thompson, H. Zheng, W. Dubitzky, The Influence of Network Topology on Reverse-engineering of Gene-regulatory Networks, Procedia Computer Science. 29 (2014) 410–421. doi: 10.1016/j.procs.2014.05.037.46 A. Mizeranschi, N. Kennedy, P. Thompson, H. Zheng, W. Dubitzky, The Influence of Network Topology on Reverse-engineering of Gene-regulatory Networks, Procedia Computer Science. 29 (2014) 410–421. doi:[[http://dx.doi.org/10.1016/j.procs.2014.05.037|10.1016/j.procs.2014.05.037]]. 47 47 48 48 ----
