SESSL: A domain-specific language for simulation experiments

ACM Transactions on Modeling and Computer Simulation

Volumn 24, Issue 2, 2014, Pages

  Ewald, Roland ^a   Uhrmacher, Adelinde M ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

Author keywords

Domain specific language; Experiments; Scala; Simulation

Indexed keywords

EXPERIMENTS; PROBLEM ORIENTED LANGUAGES;

DOMAIN SPECIFIC LANGUAGES; EMBEDDED DOMAIN-SPECIFIC LANGUAGES; PERFORMANCE ANALYSIS; REPRODUCIBILITIES; SCALA; SIMULATION; SIMULATION SYSTEMS; SIMULATION-BASED OPTIMIZATIONS;

COMPUTER SOFTWARE;

EID: 84897473124     PISSN: 10493301     EISSN: 15581195     Source Type: Journal    
DOI: 10.1145/2567895     Document Type: Article

References (102)

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22. P. Hudak. 1996. Building domain-specific embedded languages. ACM Computing Surveys 28, 4, 196.
23. L. N. Joppa, G. McInerny, R. Harper, L. Salido, K. Takeda, K. O'Hara, D. Gavaghan, and S. Emmott. 2013. Troubling trends in scientific software use. Science 340, 6134, 814-815.
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27. F. Leisch. 2002. Sweave: Dynamic generation of statistical reports using literate data analysis. In Compstat 2002 - Proceedings in Computational Statistics. Physica Verlag, Heidelberg, 575-580.
28. C. Li, M. Donizelli, N. Rodriguez, H. Dharuri, L. Endler, V. Chelliah, L. Li, E. He, A. Henry, M. I. Stefan, J. L. Snoep, M. Hucka, N. Le Novère, and C. Laibe. 2010. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4, 92.
29. C. F. Lopez, J. L. Muhlich, J. A. Bachman, and P. K. Sorger. 2013. Programming biological models in Python using PySB. Molecular systems biology 9, 1.
30. M. Lukasiewycz, M. Glass, F. Reimann, and J. Teich. 2011. Opt4J: a modular framework for meta-heuristic optimization. In Proceedings of the 13th Annual Conference on Genetic and Evolutionary Computation. GECCO '11. ACM, 1723-1730.
31. Z. Merali. 2010. Computational science: .error. Nature 467, 775-777.
32. J. A. Miller, G. T. Baramidze, A. P. Sheth, and P. A. Fishwick. 2004. Investigating ontologies for simulation modeling. In Proceedings of the 37th Annual Simulation Symposium. IEEE CS.
33. J. A. Miller, J. Han, and M. Hybinette. 2010. Using domain specific language for modeling and simulation: ScalaTion as a case study. In Proceedings of the 2010 Winter Simulation Conference, B. Johansson, S. Jain, J. Montoya-Torres, J. Hugan, and E. Yücesan, Eds. IEEE.
34. M. Odersky, L. Spoon, and B. Venners. 2011. Programming in Scala, 2nd ed. Artima.
35. M. Odersky and M. Zenger. 2005. Scalable component abstractions. In Proceedings of the 20th ACMSIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA'05). ACM, 41-57.
36. E. H. Page, L. Litwin, M. T. McMahon, B. Wickham, M. Shadid, and E. Chang. 2012. Goal-directed gridenabled computing for legacy simulations. In IEEE International Symposium on Cluster Computing and the Grid. IEEE, 873-879.
37. K. Pawlikowski, H. D. J. Jeong, and J. S. R. Lee. 2002. On credibility of simulation studies of telecommunication networks. IEEE Communications Magazine 40, 1, 132-139.
38. L. F. Perrone, C. Cicconetti, G. Stea, and B. C. Ward. 2009. On the automation of computer network simulators. In Proceedings of the 2nd International Conference on Simulation Tools and Techniques (SIMTUTools' 09). ICST.
39. L. F. Perrone, C. S. Main, and B. C. Ward. 2012. SAFE: simulation automation framework for experiments. In Proceedings of the 2012 Winter Simulation Conference, C. Laroque, J. Himmelspach, R. Pasupathy, O. Rose, and A. M. Uhrmacher, Eds. IEEE.
40. J. Ribault. 2011. Reuse and Scalability in Modeling and Simulation Software Engineering. Ph.D. thesis, Université de Nice Sophia-Antipolis.
41. H. M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano. 2003. Next generation simulation tools: The systems biology workbench and BioSPICE integration. OMICS: A Journal of Integrative Biology 7, 4, 355-372.
42. A. M. Sloane. 2008. Experiences with domain-specific language embedding in scala. In Proceedings of the 2nd InternationalWorkshop on Domain-Specific Program Development, J. Lawall and L. Reveillere, Eds.
43. S. Sobernig, P. Gaubatz, M. Strembeck, and U. Zdun. 2011. Comparing complexity of API designs: an exploratory experiment on DSL-based framework integration. In Proceedings of the 10th ACM International Conference on Generative Programming and Component Engineering. ACM, 157-166.
44. M. Strembeck and U. Zdun. 2009. An approach for the systematic development of domain-specific languages. Software: Practice and Experience 39, 15, 1253-1292.
45. A. Sujeeth, H. Lee, K. J. Brown, T. Rompf, H. Chafi, M. Wu, A. Atreya, M. Odersky, and K. Olukotun. 2011. OptiML: An implicitly parallel domain-specific language for machine learning. In Proceedings of the 28th International Conference on Machine Learning (ICML'11). 609-616.
46. A. van Deursen, P. Klint, and J. Visser. 2000. Domain-specific languages: an annotated bibliography. SIGPLAN Notices 35, 6, 26-36.
47. A. Varga. 2001. The OMNeT++ Discrete Event Simulation System. In Proceedings of the European Simulation Multiconference (ESM'2001). SCS Europe.
48. A. Varga. 2011. OMNeT++ User Manual Version 4.4. OpenSim Ltd. Retrieved from http://www.omnetpp.org/doc/omnetpp/Manual.pdf.
49. D. Waltemath, R. Adams, F. Bergmann, M. Hucka, F. Kolpakov, A. Miller, I. Moraru, D. Nickerson, S. Sahle, J. Snoep, and N. Le Novere. 2011. Reproducible computational biology experiments with SED-ML-The simulation experiment description markup language. BMC Systems Biology 5, 198.
50. M.Weber and E. Kindler. 2003. The petri net markup language. In Petri Net Technology for Communication- Based Systems, H. Ehrig, W. Reisig, G. Rozenberg, and H. Weber, Eds. Lecture Notes in Computer Science Series, vol. 2472. Springer, 124-144.
51. U. Zdun andM. Strembeck. 2009. Reusable architectural decisions for DSL design: Foundational decisions in DSL development. In Proceedings of the 14th European Conference on Pattern Languages of Programs.
52. F. T. Bergmann, J. Cooper, N. Le Novère, D. Nickerson, and D. Waltemath. 2013. Simulation experiment description markup language (SED-ML): Level 1 version 2. Retrieved from http://sed-ml.org/documents/sed-ml-L1V2.pdf.
53. D. Bruce. 1997. What makes a good domain-specific language? APOSTLE, and its approach to parallel discrete event simulation. In Proceedings of the ACM SIGPLAN Workshop on Domain Specific Languages. ACM, 17-35.
54. Y. Cao, D. T. Gillespie, and L. R. Petzold. 2006. Efficient step size selection for the tau-leaping simulation method. Journal of Chemical Physics 124, 4.
55. M. Courtot, N. Juty, C. Knupfer, D. Waltemath, A. Zhukova, A. Drager, M. Dumontier, A. Finney, M. Golebiewski, J. Hastings, S. Hoops, S. Keating, D. B. Kell, S. Kerrien, J. Lawson, A. Lister, J. Lu, R. Machne, P. Mendes, M. Pocock, N. Rodriguez, A. Villeger, D. J. Wilkinson, S. Wimalaratne, C. Laibe, M. Hucka, and N. Le Novere. 2011. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology 7, 1.
56. T. Despeyroux. 2008. Evolution of ontologies and types. In Proceedings of the IADIS International Conference WWW/Internet 2008, P. Isaías, M. B. Nunes, and D. Ifenthaler, Eds. 419-422.
57. Z. DeVito, N. Joubert, F. Palacios, S. Oakley, M. Medina, M. Barrientos, E. Elsen, F. Ham, A. Aiken, K. Duraisamy, E. Darve, J. Alonso, and P. Hanrahan. 2011. Liszt: aA domain specific language for building portable mesh-based PDE solvers. In Proceedings of the 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC'11). ACM.
58. A. Dráger, R. Keller, A. Dörr, S. Tscherneck, U. Hofmann, C. Wrzodek, A. Funahashi, A. Tabira, B. Kandel, M. Klein, M. Thomas, N. Rodriguez, N. Le Novère, U. M. Zanger, and A. Zell. 2012. SBMLsimulator: An efficient Java solver implementation for SBML. Retrieved from http://www.ra.cs.unituebingen.de/software/SBMLsimulator.
59. I. Dragos, M. Odersky, L. Bourlier, M. Dotta, M. Farwell, H. Miller, E. Molitor, H. Plociniczak, M. Russell, and M. Stocker. 2013. ScalaIDE for Eclipse. Retrieved from http://scala-ide.org.
60. R. Ewald. 2011. Automatic Algorithm Selection for Complex Simulation Problems. Vieweg + Teubner.
61. R. Ewald, J. Himmelspach, M. Jeschke, S. Leye, and A. M. Uhrmacher. 2010. Flexible experimentation in the modeling and simulation framework JAMES II-implications for computational systems biology. Briefings in Bioinformatics 11, 3, 290-300.
62. M. Fowler. 2010. Domain-Specific Languages, 1st ed. Addison-Wesley Professional.
63. M. Garcia, A. Izmaylova, and S. Schupp. 2010. Extending scala with database query capability. Journal of Object Technology 9, 45-68.
64. M. A. Gibson and J. Bruck. 2000. Efficient exact stochastic simulation of chemical systems withmany species and many channels. Journal of Chemical Physics 104, 1876-1889.
65. A. W. Hallagan. 2011. The design of XML-based model and experiment description languages for network simulation. Bachelor's thesis, Department of Computer Science, Bucknell University.
66. T. Helms, J. Himmelspach, C. Maus, O. Röwer, J. Schützel, and A. M. Uhrmacher. 2012. Toward a language for the flexible observation of simulations. In Proceedings of the 2012 Winter Simulation Conference, C. Laroque, J. Himmelspach, R. Pasupathy, O. Rose, and A. M. Uhrmacher, Eds. IEEE.
67. I. Hepburn, W. Chen, S. Wils, and E. De Schutter. 2012. STEPS: Efficient simulation of stochastic reactiondiffusion models in realistic morphologies. BMC Systems Biology 6, 36.
68. J. Himmelspach, R. Ewald, S. Leye, and A. M. Uhrmacher. 2010. Enhancing the scalability of simulations by embracing multiple levels of parallelization. In Proceedings of the 2nd International Workshop on High Performance Computational Systems Biology (HiBi'10). IEEE, 57-66.
69. J. Himmelspach, R. Ewald, and A. M. Uhrmacher. 2008. A flexible and scalable experimentation layer. In Proceedings of the 2008 Winter Simulation Conference, S. Mason, R. Hill, L. Moench, and O. Rose, Eds.
70. J. Himmelspach and A. M. Uhrmacher. 2007. Plug'n simulate. In Proceedings of the 40th Annual Simulation Symposium. IEEE CS, 137-143.
71. K. Hinsen. 2013. A glimpse of the future of scientific programming. Computing in Science & Engineering 15, 1, 84-88.
72. M. Hucka, et al. 2003. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 4, 524-531.
73. P. Hudak. 1996. Building domain-specific embedded languages. ACM Computing Surveys 28, 4, 196.
74. L. N. Joppa, G. McInerny, R. Harper, L. Salido, K. Takeda, K. O'Hara, D. Gavaghan, and S. Emmott. 2013. Troubling trends in scientific software use. Science 340, 6134, 814-815.
75. S. Kite, C. Wood, S. J. E. Taylor, and N. Mustafee. 2011. SakerGrid: Simulation experimentation using grid enabled simulation software. In Proceedings of the 2011 Winter Simulation Conference, S. Jain, R. R. Creasey, J. Himmelspach, K. P. White, and M. Fu, Eds.
76. A. Law. 2006. Simulation Modeling and Analysis, 4th ed. McGraw-Hill.
77. P. L'Ecuyer, L. Meliani, and J. Vaucher. 2002. SSJ: A framework for stochastic simulation in Java. In Proceedings of the 2002 Winter Simulation Conference, E. Yücesan and C. H. Chen, Eds. IEEE.
78. F. Leisch. 2002. Sweave: Dynamic generation of statistical reports using literate data analysis. In Compstat 2002 - Proceedings in Computational Statistics. Physica Verlag, Heidelberg, 575-580.
79. C. Li, M. Donizelli, N. Rodriguez, H. Dharuri, L. Endler, V. Chelliah, L. Li, E. He, A. Henry, M. I. Stefan, J. L. Snoep, M. Hucka, N. Le Novère, and C. Laibe. 2010. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4, 92.
80. C. F. Lopez, J. L. Muhlich, J. A. Bachman, and P. K. Sorger. 2013. Programming biological models in Python using PySB. Molecular systems biology 9, 1.
81. M. Lukasiewycz, M. Glass, F. Reimann, and J. Teich. 2011. Opt4J: a modular framework for meta-heuristic optimization. In Proceedings of the 13th Annual Conference on Genetic and Evolutionary Computation. GECCO '11. ACM, 1723-1730.
82. Z. Merali. 2010. Computational science: .error. Nature 467, 775-777.
83. J. A. Miller, G. T. Baramidze, A. P. Sheth, and P. A. Fishwick. 2004. Investigating ontologies for simulation modeling. In Proceedings of the 37th Annual Simulation Symposium. IEEE CS.
84. J. A. Miller, J. Han, and M. Hybinette. 2010. Using domain specific language for modeling and simulation: ScalaTion as a case study. In Proceedings of the 2010 Winter Simulation Conference, B. Johansson, S. Jain, J. Montoya-Torres, J. Hugan, and E. Yücesan, Eds. IEEE.
85. M. Odersky, L. Spoon, and B. Venners. 2011. Programming in Scala, 2nd ed. Artima.
86. M. Odersky and M. Zenger. 2005. Scalable component abstractions. In Proceedings of the 20th ACMSIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA'05). ACM, 41-57.
87. E. H. Page, L. Litwin, M. T. McMahon, B. Wickham, M. Shadid, and E. Chang. 2012. Goal-directed gridenabled computing for legacy simulations. In IEEE International Symposium on Cluster Computing and the Grid. IEEE, 873-879.
88. K. Pawlikowski, H. D. J. Jeong, and J. S. R. Lee. 2002. On credibility of simulation studies of telecommunication networks. IEEE Communications Magazine 40, 1, 132-139.
89. L. F. Perrone, C. Cicconetti, G. Stea, and B. C. Ward. 2009. On the automation of computer network simulators. In Proceedings of the 2nd International Conference on Simulation Tools and Techniques (SIMTUTools' 09). ICST.
90. L. F. Perrone, C. S. Main, and B. C. Ward. 2012. SAFE: simulation automation framework for experiments. In Proceedings of the 2012 Winter Simulation Conference, C. Laroque, J. Himmelspach, R. Pasupathy, O. Rose, and A. M. Uhrmacher, Eds. IEEE.
91. J. Ribault. 2011. Reuse and Scalability in Modeling and Simulation Software Engineering. Ph.D. thesis, Université de Nice Sophia-Antipolis.
92. H. M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano. 2003. Next generation simulation tools: The systems biology workbench and BioSPICE integration. OMICS: A Journal of Integrative Biology 7, 4, 355-372.
93. A. M. Sloane. 2008. Experiences with domain-specific language embedding in scala. In Proceedings of the 2nd InternationalWorkshop on Domain-Specific Program Development, J. Lawall and L. Reveillere, Eds.
94. S. Sobernig, P. Gaubatz, M. Strembeck, and U. Zdun. 2011. Comparing complexity of API designs: an exploratory experiment on DSL-based framework integration. In Proceedings of the 10th ACM International Conference on Generative Programming and Component Engineering. ACM, 157-166.
95. M. Strembeck and U. Zdun. 2009. An approach for the systematic development of domain-specific languages. Software: Practice and Experience 39, 15, 1253-1292.
96. A. Sujeeth, H. Lee, K. J. Brown, T. Rompf, H. Chafi, M. Wu, A. Atreya, M. Odersky, and K. Olukotun. 2011. OptiML: An implicitly parallel domain-specific language for machine learning. In Proceedings of the 28th International Conference on Machine Learning (ICML'11). 609-616.
97. A. van Deursen, P. Klint, and J. Visser. 2000. Domain-specific languages: an annotated bibliography. SIGPLAN Notices 35, 6, 26-36.
98. A. Varga. 2001. The OMNeT++ Discrete Event Simulation System. In Proceedings of the European Simulation Multiconference (ESM'2001). SCS Europe.
99. A. Varga. 2011. OMNeT++ User Manual Version 4.4. OpenSim Ltd. Retrieved from http://www.omnetpp.org/doc/omnetpp/Manual.pdf.
100. D. Waltemath, R. Adams, F. Bergmann, M. Hucka, F. Kolpakov, A. Miller, I. Moraru, D. Nickerson, S. Sahle, J. Snoep, and N. Le Novere. 2011. Reproducible computational biology experiments with SED-ML-The simulation experiment description markup language. BMC Systems Biology 5, 198.
101. M. Weber and E. Kindler. 2003. The petri net markup language. In Petri Net Technology for Communication- Based Systems, H. Ehrig, W. Reisig, G. Rozenberg, and H. Weber, Eds. Lecture Notes in Computer Science Series, vol. 2472. Springer, 124-144.
102. U. Zdun andM. Strembeck. 2009. Reusable architectural decisions for DSL design: Foundational decisions in DSL development. In Proceedings of the 14th European Conference on Pattern Languages of Programs.